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Protein

PHD finger protein 6

Gene

PHF6

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Transcriptional regulator that associates with ribosomal RNA promoters and suppresses ribosomal RNA (rRNA) transcription.1 Publication

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri14 – 52C2HC pre-PHD-type 1PROSITE-ProRule annotationAdd BLAST39
Zinc fingeri80 – 132PHD-type 1PROSITE-ProRule annotationAdd BLAST53
Zinc fingeri209 – 249C2HC pre-PHD-type 2PROSITE-ProRule annotationAdd BLAST41
Zinc fingeri278 – 330PHD-type 2PROSITE-ProRule annotationAdd BLAST53

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionDNA-binding
Biological processTranscription, Transcription regulation
LigandMetal-binding, Zinc

Enzyme and pathway databases

SIGNORiQ8IWS0

Names & Taxonomyi

Protein namesi
Recommended name:
PHD finger protein 6
Alternative name(s):
PHD-like zinc finger protein
Gene namesi
Name:PHF6
Synonyms:CENP-31, KIAA1823
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome X

Organism-specific databases

EuPathDBiHostDB:ENSG00000156531.16
HGNCiHGNC:18145 PHF6
MIMi300414 gene
neXtProtiNX_Q8IWS0

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

Centromere, Chromosome, Kinetochore, Nucleus

Pathology & Biotechi

Involvement in diseasei

Boerjeson-Forssman-Lehmann syndrome (BFLS)3 Publications
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA X-linked recessive disorder characterized by moderate to severe mental retardation, epilepsy, hypogonadism, hypometabolism, obesity with marked gynecomastia, swelling of subcutaneous tissue of the face, narrow palpebral fissure and large but not deformed ears.
See also OMIM:301900
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_01763345C → Y in BFLS; Loss of interaction with UBTF. 2 PublicationsCorresponds to variant dbSNP:rs132630299EnsemblClinVar.1
Natural variantiVAR_01763499C → F in BFLS; Loss of interaction with UBTF. 2 PublicationsCorresponds to variant dbSNP:rs132630298EnsemblClinVar.1
Natural variantiVAR_017635229H → R in BFLS. 1 PublicationCorresponds to variant dbSNP:rs104894918EnsemblClinVar.1
Natural variantiVAR_017636234K → E in BFLS. 1 PublicationCorresponds to variant dbSNP:rs104894917EnsemblClinVar.1
Natural variantiVAR_017637257R → G in BFLS. 1 PublicationCorresponds to variant dbSNP:rs104894919EnsemblClinVar.1
Natural variantiVAR_076933305C → F in BFLS. 1 PublicationCorresponds to variant dbSNP:rs587777489EnsemblClinVar.1

Keywords - Diseasei

Disease mutation, Epilepsy, Hypotrichosis, Mental retardation

Organism-specific databases

DisGeNETi84295
MalaCardsiPHF6
MIMi301900 phenotype
OpenTargetsiENSG00000156531
Orphaneti127 Borjeson-Forssman-Lehmann syndrome
PharmGKBiPA33263

Polymorphism and mutation databases

BioMutaiPHF6
DMDMi42559482

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedCombined sources
ChainiPRO_00000592932 – 365PHD finger protein 6Add BLAST364

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylserineCombined sources1
Modified residuei138PhosphoserineCombined sources1
Modified residuei145PhosphoserineCombined sources1
Modified residuei155PhosphoserineCombined sources1
Cross-linki173Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei183PhosphoserineBy similarity1
Modified residuei199PhosphoserineCombined sources1
Cross-linki227Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei358PhosphothreonineCombined sources1
Isoform 2 (identifier: Q8IWS0-2)
Modified residuei146PhosphoserineCombined sources1

Keywords - PTMi

Acetylation, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiQ8IWS0
MaxQBiQ8IWS0
PaxDbiQ8IWS0
PeptideAtlasiQ8IWS0
PRIDEiQ8IWS0
ProteomicsDBi70885
70886 [Q8IWS0-2]

PTM databases

iPTMnetiQ8IWS0
PhosphoSitePlusiQ8IWS0

Expressioni

Tissue specificityi

Ubiquitously expressed.1 Publication

Gene expression databases

BgeeiENSG00000156531 Expressed in 207 organ(s), highest expression level in female gonad
CleanExiHS_PHF6
ExpressionAtlasiQ8IWS0 baseline and differential
GenevisibleiQ8IWS0 HS

Organism-specific databases

HPAiHPA001023

Interactioni

Subunit structurei

Interacts with UBTF. Interacts with the NuRD complex component RBBP4 (via the nucleolar localization motif), the interaction mediates transcriptional repression activity.2 Publications

GO - Molecular functioni

Protein-protein interaction databases

BioGridi124022, 47 interactors
IntActiQ8IWS0, 8 interactors
MINTiQ8IWS0
STRINGi9606.ENSP00000329097

Structurei

Secondary structure

1365
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliQ8IWS0
SMRiQ8IWS0
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni14 – 132Extended PHD1 domain (ePHD1)PROSITE-ProRule annotationAdd BLAST119
Regioni209 – 330Extended PHD2 domain (ePHD2)PROSITE-ProRule annotationAdd BLAST122

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi13 – 16Nuclear localization signalSequence analysis4
Motifi129 – 133Nuclear localization signalSequence analysis5
Motifi157 – 169Nucleolar localization signalSequence analysisAdd BLAST13

Domaini

The PHD-type zinc finger 1 mediates both nucleolar localization and interaction with UBTF.
The ePHD2 domain folds as an integrated structural module comprizing the C2HC pre-PHD-type 2 zinc finger and the PHD-type 2 zinc finger. It mediates non-specific binding to dsDNA, but doesn't bind histones in contrast to many PHD-type zinc fingers.

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri14 – 52C2HC pre-PHD-type 1PROSITE-ProRule annotationAdd BLAST39
Zinc fingeri80 – 132PHD-type 1PROSITE-ProRule annotationAdd BLAST53
Zinc fingeri209 – 249C2HC pre-PHD-type 2PROSITE-ProRule annotationAdd BLAST41
Zinc fingeri278 – 330PHD-type 2PROSITE-ProRule annotationAdd BLAST53

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiENOG410IPTE Eukaryota
ENOG410XS42 LUCA
GeneTreeiENSGT00530000063780
HOGENOMiHOG000026798
HOVERGENiHBG049389
InParanoidiQ8IWS0
PhylomeDBiQ8IWS0
TreeFamiTF325426

Family and domain databases

Gene3Di3.30.40.10, 2 hits
InterProiView protein in InterPro
IPR034732 EPHD
IPR001965 Znf_PHD
IPR013083 Znf_RING/FYVE/PHD
SMARTiView protein in SMART
SM00249 PHD, 2 hits
PROSITEiView protein in PROSITE
PS51805 EPHD, 2 hits

Sequences (5+)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 5 isoformsi produced by alternative splicing. AlignAdd to basket

This entry has 5 described isoforms and 2 potential isoforms that are computationally mapped.iShow all

Isoform 1 (identifier: Q8IWS0-1) [UniParc]FASTAAdd to basket
Also known as: PHF6a, PHF6b

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
MSSSVEQKKG PTRQRKCGFC KSNRDKECGQ LLISENQKVA AHHKCMLFSS
60 70 80 90 100
ALVSSHSDNE SLGGFSIEDV QKEIKRGTKL MCSLCHCPGA TIGCDVKTCH
110 120 130 140 150
RTYHYHCALH DKAQIREKPS QGIYMVYCRK HKKTAHNSEA DLEESFNEHE
160 170 180 190 200
LEPSSPKSKK KSRKGRPRKT NFKGLSEDTR STSSHGTDEM ESSSYRDRSP
210 220 230 240 250
HRSSPSDTRP KCGFCHVGEE ENEARGKLHI FNAKKAAAHY KCMLFSSGTV
260 270 280 290 300
QLTTTSRAEF GDFDIKTVLQ EIKRGKRMKC TLCSQPGATI GCEIKACVKT
310 320 330 340 350
YHYHCGVQDK AKYIENMSRG IYKLYCKNHS GNDERDEEDE ERESKSRGKV
360
EIDQQQLTQQ QLNGN
Length:365
Mass (Da):41,290
Last modified:March 1, 2003 - v1
Checksum:iE8E587909EF9701D
GO
Isoform 2 (identifier: Q8IWS0-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     140-140: A → AA
     279-311: KCTLCSQPGATIGCEIKACVKTYHYHCGVQDKA → VCSFYICYATLHLICCFKFRVHPKFIQSSENLK
     312-365: Missing.

Note: No experimental confirmation available.Combined sources
Show »
Length:312
Mass (Da):35,329
Checksum:i107F45F45063D7A0
GO
Isoform 3 (identifier: Q8IWS0-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     140-140: Missing.

Note: No experimental confirmation available.
Show »
Length:364
Mass (Da):41,219
Checksum:i2BEB117AF92F7ECC
GO
Isoform 4 (identifier: Q8IWS0-4) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     140-140: Missing.
     279-311: KCTLCSQPGATIGCEIKACVKTYHYHCGVQDKA → VCSFYICYATLHLICCFKFRVHPKFIQSSENLK
     312-365: Missing.

Note: No experimental confirmation available.
Show »
Length:310
Mass (Da):35,187
Checksum:iB6091E6AC014F78A
GO
Isoform 5 (identifier: Q8IWS0-5) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     47-80: Missing.

Note: No experimental confirmation available.
Show »
Length:331
Mass (Da):37,628
Checksum:iCA296A2F39167444
GO

Computationally mapped potential isoform sequencesi

There are 2 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
Q5JRC6Q5JRC6_HUMAN
PHD finger protein 6, isoform CRA_d
PHF6 hCG_1783600
324Annotation score:
A0A0D9SGE8A0A0D9SGE8_HUMAN
PHD finger protein 6
PHF6
366Annotation score:

Sequence cautioni

The sequence BAB47452 differs from that shown. Reason: Erroneous initiation.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti126V → A in AAH05994 (PubMed:15489334).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_01763345C → Y in BFLS; Loss of interaction with UBTF. 2 PublicationsCorresponds to variant dbSNP:rs132630299EnsemblClinVar.1
Natural variantiVAR_01763499C → F in BFLS; Loss of interaction with UBTF. 2 PublicationsCorresponds to variant dbSNP:rs132630298EnsemblClinVar.1
Natural variantiVAR_017635229H → R in BFLS. 1 PublicationCorresponds to variant dbSNP:rs104894918EnsemblClinVar.1
Natural variantiVAR_017636234K → E in BFLS. 1 PublicationCorresponds to variant dbSNP:rs104894917EnsemblClinVar.1
Natural variantiVAR_017637257R → G in BFLS. 1 PublicationCorresponds to variant dbSNP:rs104894919EnsemblClinVar.1
Natural variantiVAR_076933305C → F in BFLS. 1 PublicationCorresponds to variant dbSNP:rs587777489EnsemblClinVar.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_05493747 – 80Missing in isoform 5. 1 PublicationAdd BLAST34
Alternative sequenceiVSP_009372140A → AA in isoform 2. 1 Publication1
Alternative sequenceiVSP_053441140Missing in isoform 3 and isoform 4. 1 Publication1
Alternative sequenceiVSP_009373279 – 311KCTLC…VQDKA → VCSFYICYATLHLICCFKFR VHPKFIQSSENLK in isoform 2 and isoform 4. 2 PublicationsAdd BLAST33
Alternative sequenceiVSP_009374312 – 365Missing in isoform 2 and isoform 4. 2 PublicationsAdd BLAST54

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY157622 mRNA Translation: AAO13214.1
AB058726 mRNA Translation: BAB47452.1 Different initiation.
AK290095 mRNA Translation: BAF82784.1
AK303369 mRNA Translation: BAG64426.1
AC004383 Genomic DNA No translation available.
AL591668 Genomic DNA No translation available.
CH471107 Genomic DNA Translation: EAX11762.1
CH471107 Genomic DNA Translation: EAX11763.1
CH471107 Genomic DNA Translation: EAX11766.1
BC005994 mRNA Translation: AAH05994.1
CCDSiCCDS14639.1 [Q8IWS0-1]
CCDS14640.1 [Q8IWS0-2]
RefSeqiNP_001015877.1, NM_001015877.1 [Q8IWS0-1]
NP_115711.2, NM_032335.3 [Q8IWS0-2]
NP_115834.1, NM_032458.2 [Q8IWS0-1]
UniGeneiHs.356501

Genome annotation databases

EnsembliENST00000332070; ENSP00000329097; ENSG00000156531 [Q8IWS0-1]
ENST00000370800; ENSP00000359836; ENSG00000156531 [Q8IWS0-2]
ENST00000370803; ENSP00000359839; ENSG00000156531 [Q8IWS0-1]
GeneIDi84295
KEGGihsa:84295
UCSCiuc004exh.4 human [Q8IWS0-1]

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

Entry informationi

Entry nameiPHF6_HUMAN
AccessioniPrimary (citable) accession number: Q8IWS0
Secondary accession number(s): A8K230
, B4E0G4, D3DTG3, E9PC97, Q5JRC7, Q5JRC8, Q96JK3, Q9BRU0
Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 16, 2004
Last sequence update: March 1, 2003
Last modified: September 12, 2018
This is version 149 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome
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Main funding by: National Institutes of Health

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