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Entry version 109 (13 Feb 2019)
Sequence version 2 (29 Apr 2008)
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Protein

Structural maintenance of chromosomes flexible hinge domain-containing protein 1

Gene

SMCHD1

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score:

Annotation score:5 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the ‘protein existence’ evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

Non-canonical member of the structural maintenance of chromosomes (SMC) protein family that plays a key role in epigenetic silencing by regulating chromatin architecture (By similarity). Promotes heterochromatin formation in both autosomes and chromosome X, probably by mediating the merge of chromatin compartments (By similarity). Plays a key role in chromosome X inactivation in females by promoting the spreading of heterochromatin (PubMed:23542155). Recruited to inactivated chromosome X by Xist RNA and acts by mediating the merge of chromatin compartments: promotes random chromatin interactions that span the boundaries of existing structures, leading to create a compartment-less architecture typical of inactivated chromosome X (By similarity). Required to facilitate Xist RNA spreading (By similarity). Also required for silencing of a subset of clustered autosomal loci in somatic cells, such as the DUX4 locus (PubMed:23143600). Has ATPase activity; may participate in structural manipulation of chromatin in an ATP-dependent manner as part of its role in gene expression regulation (PubMed:29748383). Also plays a role in DNA repair: localizes to sites of DNA double-strand breaks in response to DNA damage to promote the repair of DNA double-strand breaks (PubMed:25294876, PubMed:24790221). Acts by promoting non-homologous end joining (NHEJ) and inhibiting homologous recombination (HR) repair (PubMed:25294876).By similarity5 Publications

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

GO - Biological processi

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionChromatin regulator, DNA-binding, Hydrolase
Biological processDNA damage, DNA repair

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
Structural maintenance of chromosomes flexible hinge domain-containing protein 1By similarity (EC:3.6.1.-1 Publication)
Short name:
SMC hinge domain-containing protein 1By similarity
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: ‘Name’, ‘Synonyms’, ‘Ordered locus names’ and ‘ORF names’.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:SMCHD1Imported
Synonyms:KIAA06501 Publication
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiHomo sapiens (Human)
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the ‘taxonomic identifier’ or ‘taxid’.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri9606 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000005640 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">proteome</a> can consist of several components. <br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome 18

Organism-specific databases

Eukaryotic Pathogen Database Resources

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EuPathDBi
HostDB:ENSG00000101596.14

Human Gene Nomenclature Database

More...
HGNCi
HGNC:29090 SMCHD1

Online Mendelian Inheritance in Man (OMIM)

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MIMi
614982 gene

neXtProt; the human protein knowledge platform

More...
neXtProti
NX_A6NHR9

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Chromosome

<p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

<p>This subsection of the ‘Pathology and Biotech’ section provides information on the disease(s) associated with genetic variations in a given protein. The information is extracted from the scientific literature and diseases that are also described in the <a href="http://www.ncbi.nlm.nih.gov/sites/entrez?db=omim">OMIM</a> database are represented with a <a href="http://www.uniprot.org/diseases">controlled vocabulary</a> in the following way:<p><a href='/help/involvement_in_disease' target='_top'>More...</a></p>Involvement in diseasei

Facioscapulohumeral muscular dystrophy 2 (FSHD2)8 Publications
The disease is caused by mutations affecting the gene represented in this entry. SMCHD1 mutations lead to DUX4 expression in somatic tissues, including muscle cells, when an haplotype on chromosome 4 is permissive for DUX4 expression (PubMed:23143600). Ectopic expression of DUX4 in skeletal muscle activates the expression of stem cell and germline genes, and, when overexpressed in somatic cells, DUX4 can ultimately lead to cell death (PubMed:23143600). FSHD2 and FSHD1 share a common pathophysiological pathway in which the FSHD2 gene SMCHD1 can act as a modifier for disease severity in families affected by FSHD1 (PubMed:24075187, PubMed:25370034).3 Publications
Disease descriptionA degenerative muscle disease characterized by slowly progressive weakness of the muscles of the face, upper-arm, and shoulder girdle. The onset of symptoms usually occurs in the first or second decade of life. Affected individuals usually present with impairment of upper extremity elevation. This tends to be followed by facial weakness, primarily involving the orbicularis oris and orbicularis oculi muscles.
See also OMIM:158901
Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Sequence’ section describes natural variant(s) of the protein sequence.<p><a href='/help/variant' target='_top'>More...</a></p>Natural variantiVAR_080698110A → T in FSHD2. 1 Publication1
Natural variantiVAR_078877137G → E in BAMS and FSHD2; no change in protein abundance; strongly increased ATPase activity. 3 PublicationsCorresponds to variant dbSNP:rs1057519644Ensembl.1
Natural variantiVAR_078878138 – 2005Missing in FSHD2. 1 PublicationAdd BLAST1868
Natural variantiVAR_078882194L → F in FSHD2; decreased ATPase activity. 2 Publications1
Natural variantiVAR_078883195 – 2005Missing in FSHD2. 1 PublicationAdd BLAST1811
Natural variantiVAR_078885263H → D in FSHD2; decreased ATPase activity. 2 Publications1
Natural variantiVAR_080699275Missing in FSHD2; unknown pathological significance. 1 Publication1
Natural variantiVAR_080700283Y → C in FSHD2; does not affect ATPase activity. 1 PublicationCorresponds to variant dbSNP:rs886041921EnsemblClinVar.1
Natural variantiVAR_078887344 – 2005Missing in FSHD2. 1 PublicationAdd BLAST1662
Natural variantiVAR_069067353Y → C in FSHD2; decreased protein level in fibroblasts as compared to wild-type protein; abolished ATPase activity. 4 Publications1
Natural variantiVAR_078892425G → R in FSHD2. 2 Publications1
Natural variantiVAR_078893434 – 2005Missing in FSHD2. 1 PublicationAdd BLAST1572
Natural variantiVAR_080701478G → E in FSHD2; abolished ATPase activity. 2 Publications1
Natural variantiVAR_069068479R → P in FSHD2; decreased protein level in fibroblasts as compared to wild-type protein. 2 Publications1
Natural variantiVAR_069069492C → R in FSHD2; decreased protein level in fibroblasts as compared to wild-type protein. 1 Publication1
Natural variantiVAR_078898527T → M in FSHD2; decreased ATPase activity. 3 PublicationsCorresponds to variant dbSNP:rs397518422EnsemblClinVar.1
Natural variantiVAR_080702615V → D in FSHD2. 1 Publication1
Natural variantiVAR_069070690P → S in FSHD2; decreased protein level in fibroblasts as compared to wild-type protein; decreased ATPase activity. 3 PublicationsCorresponds to variant dbSNP:rs397514623EnsemblClinVar.1
Natural variantiVAR_078900716G → S in FSHD2. 1 Publication1
Natural variantiVAR_078901731 – 2005Missing in FSHD2. 1 PublicationAdd BLAST1275
Natural variantiVAR_078902748L → P in FSHD2. 1 Publication1
Natural variantiVAR_078903780 – 2005Missing in FSHD2. 1 PublicationAdd BLAST1226
Natural variantiVAR_078904849D → N in FSHD2. 1 Publication1
Natural variantiVAR_069071868S → N in FSHD2; decreased protein level in fibroblasts as compared to wild-type protein. 2 Publications1
Natural variantiVAR_0789051176 – 1177TD → MH in FSHD2. 1 Publication2
Natural variantiVAR_0807031449R → K in FSHD2. 1 Publication1
Natural variantiVAR_0807041463Q → P in FSHD2. 1 Publication1
Natural variantiVAR_0789061468M → I in FSHD2. 1 Publication1
Natural variantiVAR_0807051485P → L in FSHD2. 1 Publication1
Natural variantiVAR_0789071487 – 1488QP → HQ in FSHD2. 1 Publication2
Natural variantiVAR_0690721554F → S in FSHD2; decreased protein level in fibroblasts as compared to wild-type protein. 2 Publications1
Natural variantiVAR_0807061663 – 2005Missing in FSHD2. 1 PublicationAdd BLAST343
Natural variantiVAR_0789081795 – 2005Missing in FSHD2. 1 PublicationAdd BLAST211
Natural variantiVAR_0789091868 – 2005Missing in FSHD2. 1 PublicationAdd BLAST138
Bosma arhinia microphthalmia syndrome (BAMS)3 Publications
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionAn autosomal dominant syndrome characterized by severe hypoplasia of the nose, palatal abnormalities, hypoplasia of the eyes, sensory abnormalities of taste and smell, hypogonadotropic hypogonadism with cryptorchidism, and normal intelligence.
See also OMIM:603457
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_078869107L → P in BAMS; no change in protein abundance. 1 PublicationCorresponds to variant dbSNP:rs1135402737Ensembl.1
Natural variantiVAR_078870129M → K in BAMS; no change in protein abundance. 1 PublicationCorresponds to variant dbSNP:rs1135402738Ensembl.1
Natural variantiVAR_078871134A → S in BAMS; has an increased ATPase activity. 1 Publication1
Natural variantiVAR_078872135S → C in BAMS; has an increased ATPase activity; no change in protein abundance. 2 PublicationsCorresponds to variant dbSNP:rs1057519645Ensembl.1
Natural variantiVAR_078873135S → I in BAMS; no change in protein abundance. 1 PublicationCorresponds to variant dbSNP:rs1057519646Ensembl.1
Natural variantiVAR_078874135S → N in BAMS; no change in protein abundance; does not affect ATPase activity. 3 PublicationsCorresponds to variant dbSNP:rs1057519646Ensembl.1
Natural variantiVAR_078875136E → D in BAMS; no change in protein abundance. 1 PublicationCorresponds to variant dbSNP:rs1057519643Ensembl.1
Natural variantiVAR_078876136E → G in BAMS; has an increased ATPase activity. 1 Publication1
Natural variantiVAR_078877137G → E in BAMS and FSHD2; no change in protein abundance; strongly increased ATPase activity. 3 PublicationsCorresponds to variant dbSNP:rs1057519644Ensembl.1
Natural variantiVAR_078879139N → H in BAMS; no change in protein abundance. 1 PublicationCorresponds to variant dbSNP:rs1135402739Ensembl.1
Natural variantiVAR_078880141L → F in BAMS; no change in protein abundance. 1 PublicationCorresponds to variant dbSNP:rs1057519641Ensembl.1
Natural variantiVAR_078881171F → V in BAMS; no change in protein abundance. 1 PublicationCorresponds to variant dbSNP:rs1135402740Ensembl.1
Natural variantiVAR_078884242A → G in BAMS; no change in protein abundance. 1 PublicationCorresponds to variant dbSNP:rs1135402741Ensembl.1
Natural variantiVAR_078886342W → S in BAMS; slightly decreased ATPase activity. 2 Publications1
Natural variantiVAR_078888345Q → R in BAMS; no change in protein abundance. 1 PublicationCorresponds to variant dbSNP:rs1057519639Ensembl.1
Natural variantiVAR_078889348H → R in BAMS; no change in protein abundance; does not affect ATPase activity. 3 PublicationsCorresponds to variant dbSNP:rs1057519640Ensembl.1
Natural variantiVAR_078890400Q → L in BAMS; no change in protein abundance. 1 PublicationCorresponds to variant dbSNP:rs1057519642Ensembl.1
Natural variantiVAR_078891420D → V in BAMS; no change in protein abundance; slightly decreased ATPase activity. 3 PublicationsCorresponds to variant dbSNP:rs1135402742Ensembl.1
Natural variantiVAR_078894473E → Q in BAMS; no change in protein abundance; slightly decreased ATPase activity. 2 PublicationsCorresponds to variant dbSNP:rs1135402743Ensembl.1
Natural variantiVAR_078895518K → E in BAMS; increased ATPase activity. 2 Publications1
Natural variantiVAR_078896523T → K in BAMS; no change in protein abundance; slightly decreased ATPase activity. 2 PublicationsCorresponds to variant dbSNP:rs1135402744Ensembl.1
Natural variantiVAR_078897524N → S in BAMS; no change in protein abundance. 1 PublicationCorresponds to variant dbSNP:rs1135402745Ensembl.1
Natural variantiVAR_078899552R → Q in BAMS; no change in protein abundance; does not affect ATPase activity. 3 PublicationsCorresponds to variant dbSNP:rs886042392EnsemblClinVar.1

Keywords - Diseasei

Disease mutation, Hypogonadotropic hypogonadism, Kallmann syndrome, Microphthalmia

Organism-specific databases

DisGeNET

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DisGeNETi
23347

GeneReviews a resource of expert-authored, peer-reviewed disease descriptions.

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GeneReviewsi
SMCHD1

MalaCards human disease database

More...
MalaCardsi
SMCHD1
MIMi158901 phenotype
603457 phenotype

Open Targets

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OpenTargetsi
ENSG00000101596

Orphanet; a database dedicated to information on rare diseases and orphan drugs

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Orphaneti
269 Facioscapulohumeral dystrophy
2250 Hyposmia-nasal and ocular hypoplasia-hypogonadotropic hypogonadism syndrome

The Pharmacogenetics and Pharmacogenomics Knowledge Base

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PharmGKBi
PA128395776

Polymorphism and mutation databases

BioMuta curated single-nucleotide variation and disease association database

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BioMutai
SMCHD1

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/ptm_processing_section">PTM / Processing</a> section indicates that the initiator methionine is cleaved from the mature protein.<p><a href='/help/init_met' target='_top'>More...</a></p>Initiator methionineiRemovedCombined sources1 Publication
<p>This subsection of the ‘PTM / Processing’ section describes the extent of a polypeptide chain in the mature protein following processing.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00003321442 – 2005Structural maintenance of chromosomes flexible hinge domain-containing protein 1Add BLAST2004

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘PTM / Processing’ section specifies the position and type of each modified residue excluding <a href="http://www.uniprot.org/manual/lipid">lipids</a>, <a href="http://www.uniprot.org/manual/carbohyd">glycans</a> and <a href="http://www.uniprot.org/manual/crosslnk">protein cross-links</a>.<p><a href='/help/mod_res' target='_top'>More...</a></p>Modified residuei2N-acetylalanineCombined sources1 Publication1
Modified residuei1349N6-acetyllysineCombined sources1
<p>This subsection of the <a href="http://www.uniprot.org/help/ptm_processing_section">PTM / Processing</a> section describes <strong>covalent linkages</strong> of various types formed <strong>between two proteins (interchain cross-links)</strong> or <strong>between two parts of the same protein (intrachain cross-links)</strong>, except the disulfide bonds that are annotated in the <a href="http://www.uniprot.org/manual/disulfid">'Disulfide bond'</a> subsection.<p><a href='/help/crosslnk' target='_top'>More...</a></p>Cross-linki1374Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Cross-linki1496Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei1499PhosphothreonineCombined sources1
Modified residuei1802N6-succinyllysineBy similarity1
Modified residuei1974PhosphoserineCombined sources1

<p>This subsection of the <a href="http://www.uniprot.org/help/ptm_processing_section">PTM/processing</a> section describes post-translational modifications (PTMs). This subsection <strong>complements</strong> the information provided at the sequence level or describes modifications for which <strong>position-specific data is not yet available</strong>.<p><a href='/help/post-translational_modification' target='_top'>More...</a></p>Post-translational modificationi

Sumoylated with SUMO1.By similarity

Keywords - PTMi

Acetylation, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

Encyclopedia of Proteome Dynamics

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EPDi
A6NHR9

jPOST - Japan Proteome Standard Repository/Database

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jPOSTi
A6NHR9

MaxQB - The MaxQuant DataBase

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MaxQBi
A6NHR9

PaxDb, a database of protein abundance averages across all three domains of life

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PaxDbi
A6NHR9

PRoteomics IDEntifications database

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PRIDEi
A6NHR9

ProteomicsDB human proteome resource

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ProteomicsDBi
1220
1221 [A6NHR9-2]
1222 [A6NHR9-3]

PTM databases

iPTMnet integrated resource for PTMs in systems biology context

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iPTMneti
A6NHR9

Comprehensive resource for the study of protein post-translational modifications (PTMs) in human, mouse and rat.

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PhosphoSitePlusi
A6NHR9

<p>This section provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of multicellular organisms.<p><a href='/help/expression_section' target='_top'>More...</a></p>Expressioni

Gene expression databases

Bgee dataBase for Gene Expression Evolution

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Bgeei
ENSG00000101596 Expressed in 223 organ(s), highest expression level in intestine

ExpressionAtlas, Differential and Baseline Expression

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ExpressionAtlasi
A6NHR9 baseline and differential

Genevisible search portal to normalized and curated expression data from Genevestigator

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Genevisiblei
A6NHR9 HS

Organism-specific databases

Human Protein Atlas

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HPAi
HPA039441

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction_section">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Homodimer; homodimerizes via its SMC hinge domain (By similarity). Interacts with LRIF1 (PubMed:23542155).By similarity1 Publication

GO - Molecular functioni

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGrid)

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BioGridi
116929, 40 interactors

Protein interaction database and analysis system

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IntActi
A6NHR9, 24 interactors

Molecular INTeraction database

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MINTi
A6NHR9

STRING: functional protein association networks

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STRINGi
9606.ENSP00000326603

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

3D structure databases

Protein Model Portal of the PSI-Nature Structural Biology Knowledgebase

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ProteinModelPortali
A6NHR9

SWISS-MODEL Repository - a database of annotated 3D protein structure models

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SMRi
A6NHR9

Database of comparative protein structure models

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ModBasei
Search...

MobiDB: a database of protein disorder and mobility annotations

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MobiDBi
Search...

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/family_and_domains_section">Family and Domains</a> section describes the position and type of a domain, which is defined as a specific combination of secondary structures organized into a characteristic three-dimensional structure or fold.<p><a href='/help/domain' target='_top'>More...</a></p>Domaini1720 – 1847SMC hingeSequence analysisAdd BLAST128

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Family and Domains’ section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>Regioni111 – 702ATPase activity domainBy similarityAdd BLAST592

<p>This subsection of the ‘Family and domains’ section provides general information on the biological role of a domain. The term ‘domain’ is intended here in its wide acceptation, it may be a structural domain, a transmembrane region or a functional domain. Several domains are described in this subsection.<p><a href='/help/domain_cc' target='_top'>More...</a></p>Domaini

Atypical member of the structural maintenance of chromosomes (SMC) protein family. Like other members of the SMC family, has ATPase activity, which is probably necessary for its engagement with chromatin, and a SMC hinge domain. However, the SMC hinge domain adopts an unconventional homodimeric arrangement augmented by an intermolecular coiled coil formed between the two monomers. This suggests that protein may assemble as a head-to-head parallel dimer without adopting a hairpin shape at the hinge domain, unlike the dimeric arrangement conventionally found in other members of the SMC protein family. The SMC hinge domain binds DNA and RNA.By similarity

<p>This subsection of the ‘Family and domains’ section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Belongs to the SMC family. Highly divergent.Curated

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

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eggNOGi
ENOG410IISP Eukaryota
ENOG410XRY2 LUCA

Ensembl GeneTree

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GeneTreei
ENSGT00390000006950

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

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HOGENOMi
HOG000007754

The HOVERGEN Database of Homologous Vertebrate Genes

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HOVERGENi
HBG108493

InParanoid: Eukaryotic Ortholog Groups

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InParanoidi
A6NHR9

Identification of Orthologs from Complete Genome Data

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OMAi
IVTDQYG

Database of Orthologous Groups

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OrthoDBi
34310at2759

Database for complete collections of gene phylogenies

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PhylomeDBi
A6NHR9

TreeFam database of animal gene trees

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TreeFami
TF329426

Family and domain databases

Conserved Domains Database

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CDDi
cd00075 HATPase_c, 1 hit

Gene3D Structural and Functional Annotation of Protein Families

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Gene3Di
3.30.565.10, 1 hit

Integrated resource of protein families, domains and functional sites

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InterProi
View protein in InterPro
IPR003594 HATPase_C
IPR036890 HATPase_C_sf
IPR010935 SMC_hinge
IPR036277 SMC_hinge_sf
IPR038892 SMCHD1

The PANTHER Classification System

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PANTHERi
PTHR22640 PTHR22640, 1 hit

Pfam protein domain database

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Pfami
View protein in Pfam
PF06470 SMC_hinge, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

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SMARTi
View protein in SMART
SM00968 SMC_hinge, 1 hit

Superfamily database of structural and functional annotation

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SUPFAMi
SSF55874 SSF55874, 1 hit
SSF75553 SSF75553, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>.<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequences (3+)i

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is in its mature form or if it represents the precursor.<p><a href='/help/sequence_processing' target='_top'>More...</a></p>Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 3 <p>This subsection of the ‘Sequence’ section lists the alternative protein sequences (isoforms) that can be generated from the same gene by a single or by the combination of up to four biological events (alternative promoter usage, alternative splicing, alternative initiation and ribosomal frameshifting). Additionally, this section gives relevant information on each alternative protein isoform.<p><a href='/help/alternative_products' target='_top'>More...</a></p> isoformsi produced by alternative splicing. AlignAdd to basket

This entry has 3 described isoforms and 6 potential isoforms that are computationally mapped.Show allAlign All

Isoform 1 (identifier: A6NHR9-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide
        10         20         30         40         50
MAAADGGGPG GASVGTEEDG GGVGHRTVYL FDRREKESEL GDRPLQVGER
60 70 80 90 100
SDYAGFRACV CQTLGISPEE KFVITTTSRK EITCDNFDET VKDGVTLYLL
110 120 130 140 150
QSVNQLLLTA TKERIDFLPH YDTLVKSGMY EYYASEGQNP LPFALAELID
160 170 180 190 200
NSLSATSRNI GVRRIQIKLL FDETQGKPAV AVIDNGRGMT SKQLNNWAVY
210 220 230 240 250
RLSKFTRQGD FESDHSGYVR PVPVPRSLNS DISYFGVGGK QAVFFVGQSA
260 270 280 290 300
RMISKPADSQ DVHELVLSKE DFEKKEKNKE AIYSGYIRNR KPSDSVHITN
310 320 330 340 350
DDERFLHHLI IEEKEKDSFT AVVITGVQPE HIQYLKNYFH LWTRQLAHIY
360 370 380 390 400
HYYIHGPKGN EIRTSKEVEP FNNIDIEISM FEKGKVPKIV NLREIQDDMQ
410 420 430 440 450
TLYVNTAADS FEFKAHVEGD GVVEGIIRYH PFLYDRETYP DDPCFPSKLK
460 470 480 490 500
DEDDEDDCFI LEKAARGKRP IFECFWNGRL IPYTSVEDFD WCTPPKKRGL
510 520 530 540 550
APIECYNRIS GALFTNDKFQ VSTNKLTFMD LELKLKDKNT LFTRILNGQE
560 570 580 590 600
QRMKIDREFA LWLKDCHEKY DKQIKFTLFK GVITRPDLPS KKQGPWATYA
610 620 630 640 650
AIEWDGKIYK AGQLVKTIKT LPLFYGSIVR FFLYGDHDGE VYATGGEVQI
660 670 680 690 700
AMEPQALYDE VRTVPIAKLD RTVAEKAVKK YVEDEMARLP DRLSVTWPEG
710 720 730 740 750
DELLPNEVRP AGTPIGALRI EILNKKGEAM QKLPGTSHGG SKKLLVELKV
760 770 780 790 800
ILHSSSGNKE IISHISQHGG KWPYWFKKME NIQKLGNYTL KLQVVLNESN
810 820 830 840 850
ADTYAGRPLP SKAIKFSVKE GKPEKFSFGL LDLPFRVGVP FNIPLEFQDE
860 870 880 890 900
FGHTSQLVTD IQPVLEASGL SLHYEEITKG PNCVIRGVTA KGPVNSCQGK
910 920 930 940 950
NYNLKVTLPG LKEDSQILKI RLLPGHPRRL KVKPDSEILV IENGTAFPFQ
960 970 980 990 1000
VEVLDESDNI TAQPKLIVHC KFSGAPNLPV YVVDCSSSGT SILTGSAIQV
1010 1020 1030 1040 1050
QNIKKDQTLK ARIEIPSCKD VAPVEKTIKL LPSSHVARLQ IFSVEGQKAI
1060 1070 1080 1090 1100
QIKHQDEVNW IAGDIMHNLI FQMYDEGERE INITSALAEK IKVNWTPEIN
1110 1120 1130 1140 1150
KEHLLQGLLP DVQVPTSVKD MRYCQVSFQD DHVSLESAFT VRPLPDEPKH
1160 1170 1180 1190 1200
LKCEMKGGKT VQMGQELQGE VVIIITDQYG NQIQAFSPSS LSSLSIAGVG
1210 1220 1230 1240 1250
LDSSNLKTTF QENTQSISVR GIKFIPGPPG NKDLCFTWRE FSDFIRVQLI
1260 1270 1280 1290 1300
SGPPAKLLLI DWPELKESIP VINGRDLQNP IIVQLCDQWD NPAPVQHVKI
1310 1320 1330 1340 1350
SLTKASNLKL MPSNQQHKTD EKGRANLGVF SVFAPRGEHT LQVKAIYNKS
1360 1370 1380 1390 1400
IIEGPIIKLM ILPDPEKPVR LNVKYDKDAS FLAGGLFTDF MISVISEDDS
1410 1420 1430 1440 1450
IIKNINPARI SMKMWKLSTS GNRPPANAET FSCNKIKDND KEDGCFYFRD
1460 1470 1480 1490 1500
KVIPNKVGTY CIQFGFMMDK TNILNSEQVI VEVLPNQPVK LVPKIKPPTP
1510 1520 1530 1540 1550
AVSNVRSVAS RTLVRDLHLS ITDDYDNHTG IDLVGTIIAT IKGSNEEDTD
1560 1570 1580 1590 1600
TPLFIGKVRT LEFPFVNGSA EIMSLVLAES SPGRDSTEYF IVFEPRLPLL
1610 1620 1630 1640 1650
SRTLEPYILP FMFYNDVKKQ QQMAALTKEK DQLSQSIVMY KSLFEASQQL
1660 1670 1680 1690 1700
LNEMKCQVEE ARLKEAQLRN ELKIHNIDIP TTQQVPHIEA LLKRKLSEQE
1710 1720 1730 1740 1750
ELKKKPRRSC TLPNYTKGSG DVLGKIAHLA QIEDDRAAMV ISWHLASDMD
1760 1770 1780 1790 1800
CVVTLTTDAA RRIYDETQGR QQVLPLDSIY KKTLPDWKRS LPHFRNGKLY
1810 1820 1830 1840 1850
FKPIGDPVFA RDLLTFPDNV EHCETVFGML LGDTIILDNL DAANHYRKEV
1860 1870 1880 1890 1900
VKITHCPTLL TRDGDRIRSN GKFGGLQNKA PPMDKLRGMV FGAPVPKQCL
1910 1920 1930 1940 1950
ILGEQIDLLQ QYRSAVCKLD SVNKDLNSQL EYLRTPDMRK KKQELDEHEK
1960 1970 1980 1990 2000
NLKLIEEKLG MTPIRKCNDS LRHSPKVETT DCPVPPKRMR REATRQNRII

TKTDV
Length:2,005
Mass (Da):226,374
Last modified:April 29, 2008 - v2
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:iB662C681424241B7
GO
Isoform 2 (identifier: A6NHR9-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1907-1917: DLLQQYRSAVC → VHACVPSYSGG
     1918-2005: Missing.

Note: No experimental confirmation available.
Show »
Length:1,917
Mass (Da):215,745
Checksum:i1E16E802BA6F7FD7
GO
Isoform 3 (identifier: A6NHR9-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-1065: Missing.
     1826-1827: VF → GC
     1828-2005: Missing.

Note: No experimental confirmation available.
Show »
Length:762
Mass (Da):85,965
Checksum:i3FD613313D84C89A
GO

<p>In eukaryotic reference proteomes, unreviewed entries that are likely to belong to the same gene are computationally mapped, based on gene identifiers from Ensembl, EnsemblGenomes and model organism databases.<p><a href='/help/gene_centric_isoform_mapping' target='_top'>More...</a></p>Computationally mapped potential isoform sequencesi

There are 6 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
J3KTL8J3KTL8_HUMAN
Structural maintenance of chromosom...
SMCHD1
1,388Annotation score:

Annotation score:1 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
A0A2R8YCU7A0A2R8YCU7_HUMAN
Structural maintenance of chromosom...
SMCHD1
308Annotation score:

Annotation score:1 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
J3KRK8J3KRK8_HUMAN
Structural maintenance of chromosom...
SMCHD1
49Annotation score:

Annotation score:1 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
J3KTK7J3KTK7_HUMAN
Structural maintenance of chromosom...
SMCHD1
48Annotation score:

Annotation score:1 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
J3QSH1J3QSH1_HUMAN
Structural maintenance of chromosom...
SMCHD1
150Annotation score:

Annotation score:1 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
A0A2R8YE92A0A2R8YE92_HUMAN
Structural maintenance of chromosom...
SMCHD1
212Annotation score:

Annotation score:1 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>

<p>This subsection of the ‘Sequence’ section reports difference(s) between the protein sequence shown in the UniProtKB entry and other available protein sequences derived from the same gene.<p><a href='/help/sequence_caution' target='_top'>More...</a></p>Sequence cautioni

The sequence BAB15202 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
The sequence BC035774 differs from that shown. Reason: Frameshift at position 1730.Curated
The sequence CAH10538 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Sequence’ section reports difference(s) between the canonical sequence (displayed by default in the entry) and the different sequence submissions merged in the entry. These various submissions may originate from different sequencing projects, different types of experiments, or different biological samples. Sequence conflicts are usually of unknown origin.<p><a href='/help/conflict' target='_top'>More...</a></p>Sequence conflicti1278Q → E in CAB45732 (PubMed:17974005).Curated1
Sequence conflicti1384G → E in CAH10538 (PubMed:17974005).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_078869107L → P in BAMS; no change in protein abundance. 1 PublicationCorresponds to variant dbSNP:rs1135402737Ensembl.1
Natural variantiVAR_080698110A → T in FSHD2. 1 Publication1
Natural variantiVAR_078870129M → K in BAMS; no change in protein abundance. 1 PublicationCorresponds to variant dbSNP:rs1135402738Ensembl.1
Natural variantiVAR_078871134A → S in BAMS; has an increased ATPase activity. 1 Publication1
Natural variantiVAR_078872135S → C in BAMS; has an increased ATPase activity; no change in protein abundance. 2 PublicationsCorresponds to variant dbSNP:rs1057519645Ensembl.1
Natural variantiVAR_078873135S → I in BAMS; no change in protein abundance. 1 PublicationCorresponds to variant dbSNP:rs1057519646Ensembl.1
Natural variantiVAR_078874135S → N in BAMS; no change in protein abundance; does not affect ATPase activity. 3 PublicationsCorresponds to variant dbSNP:rs1057519646Ensembl.1
Natural variantiVAR_078875136E → D in BAMS; no change in protein abundance. 1 PublicationCorresponds to variant dbSNP:rs1057519643Ensembl.1
Natural variantiVAR_078876136E → G in BAMS; has an increased ATPase activity. 1 Publication1
Natural variantiVAR_078877137G → E in BAMS and FSHD2; no change in protein abundance; strongly increased ATPase activity. 3 PublicationsCorresponds to variant dbSNP:rs1057519644Ensembl.1
Natural variantiVAR_078878138 – 2005Missing in FSHD2. 1 PublicationAdd BLAST1868
Natural variantiVAR_078879139N → H in BAMS; no change in protein abundance. 1 PublicationCorresponds to variant dbSNP:rs1135402739Ensembl.1
Natural variantiVAR_078880141L → F in BAMS; no change in protein abundance. 1 PublicationCorresponds to variant dbSNP:rs1057519641Ensembl.1
Natural variantiVAR_078881171F → V in BAMS; no change in protein abundance. 1 PublicationCorresponds to variant dbSNP:rs1135402740Ensembl.1
Natural variantiVAR_078882194L → F in FSHD2; decreased ATPase activity. 2 Publications1
Natural variantiVAR_078883195 – 2005Missing in FSHD2. 1 PublicationAdd BLAST1811
Natural variantiVAR_078884242A → G in BAMS; no change in protein abundance. 1 PublicationCorresponds to variant dbSNP:rs1135402741Ensembl.1
Natural variantiVAR_078885263H → D in FSHD2; decreased ATPase activity. 2 Publications1
Natural variantiVAR_080699275Missing in FSHD2; unknown pathological significance. 1 Publication1
Natural variantiVAR_080700283Y → C in FSHD2; does not affect ATPase activity. 1 PublicationCorresponds to variant dbSNP:rs886041921EnsemblClinVar.1
Natural variantiVAR_078886342W → S in BAMS; slightly decreased ATPase activity. 2 Publications1
Natural variantiVAR_078887344 – 2005Missing in FSHD2. 1 PublicationAdd BLAST1662
Natural variantiVAR_078888345Q → R in BAMS; no change in protein abundance. 1 PublicationCorresponds to variant dbSNP:rs1057519639Ensembl.1
Natural variantiVAR_078889348H → R in BAMS; no change in protein abundance; does not affect ATPase activity. 3 PublicationsCorresponds to variant dbSNP:rs1057519640Ensembl.1
Natural variantiVAR_069067353Y → C in FSHD2; decreased protein level in fibroblasts as compared to wild-type protein; abolished ATPase activity. 4 Publications1
Natural variantiVAR_078890400Q → L in BAMS; no change in protein abundance. 1 Publication