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Protein

Neuroligin-3

Gene

NLGN3

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Cell surface protein involved in cell-cell-interactions via its interactions with neurexin family members. Plays a role in synapse function and synaptic signal transmission, and may mediate its effects by clustering other synaptic proteins. May promote the initial formation of synapses, but is not essential for this. May also play a role in glia-glia or glia-neuron interactions in the developing peripheral nervous system (By similarity).By similarity1 Publication

GO - Molecular functioni

  • carboxylic ester hydrolase activity Source: GO_Central
  • cell adhesion molecule binding Source: BHF-UCL
  • neurexin family protein binding Source: BHF-UCL
  • receptor activity Source: BHF-UCL
  • scaffold protein binding Source: BHF-UCL

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

Cell adhesion

Enzyme and pathway databases

BioCyciZFISH:G66-30815-MONOMER.
ReactomeiR-HSA-6794361. Interactions of neurexins and neuroligins at synapses.

Protein family/group databases

ESTHERihuman-NLGN3. Neuroligin.
MEROPSiS09.987.

Names & Taxonomyi

Protein namesi
Recommended name:
Neuroligin-3
Alternative name(s):
Gliotactin homolog
Gene namesi
Name:NLGN3
Synonyms:KIAA1480, NL3
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome X

Organism-specific databases

HGNCiHGNC:14289. NLGN3.

Subcellular locationi

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini38 – 709ExtracellularSequence analysisAdd BLAST672
Transmembranei710 – 730HelicalSequence analysisAdd BLAST21
Topological domaini731 – 848CytoplasmicSequence analysisAdd BLAST118

GO - Cellular componenti

  • cell junction Source: UniProtKB-KW
  • cell surface Source: UniProtKB
  • endocytic vesicle Source: BHF-UCL
  • excitatory synapse Source: BHF-UCL
  • integral component of plasma membrane Source: GO_Central
  • integral component of postsynaptic membrane Source: BHF-UCL
  • synapse Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cell junction, Cell membrane, Membrane, Synapse

Pathology & Biotechi

Involvement in diseasei

Autism, X-linked 1 (AUTSX1)1 Publication
Disease susceptibility is associated with variations affecting the gene represented in this entry.
Disease descriptionA complex multifactorial, pervasive developmental disorder characterized by impairments in reciprocal social interaction and communication, restricted and stereotyped patterns of interests and activities, and the presence of developmental abnormalities by 3 years of age. Most individuals with autism also manifest moderate mental retardation.
See also OMIM:300425
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_015668451R → C in AUTSX1 and ASPGX1. 1 Publication1
Asperger syndrome, X-linked, 1 (ASPGX1)1 Publication
Disease susceptibility is associated with variations affecting the gene represented in this entry.
Disease descriptionA syndrome with features similar to autism. Affected individuals exhibit qualitative impairment in social interaction, as manifest by impairment in the use of non-verbal behaviors such as eye-to-eye gaze, facial expression, body postures, and gestures, failure to develop appropriate peer relationships, and lack of social sharing or reciprocity. Patients also exhibit restricted, repetitive and stereotyped patterns of behavior, interests, and activities, including abnormal preoccupation with certain activities and inflexible adherence to routines or rituals. Asperger syndrome is primarily distinguished from autism by the higher cognitive abilities and a more normal and timely development of language and communicative phrases.
See also OMIM:300494
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_015668451R → C in AUTSX1 and ASPGX1. 1 Publication1

Keywords - Diseasei

Asperger syndrome, Autism, Autism spectrum disorder, Disease mutation

Organism-specific databases

DisGeNETi54413.
MalaCardsiNLGN3.
MIMi300425. phenotype.
300494. phenotype.
OpenTargetsiENSG00000196338.
Orphaneti1162. Asperger syndrome.
106. Autism.
PharmGKBiPA31649.

Polymorphism and mutation databases

BioMutaiNLGN3.
DMDMi31076855.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 37Sequence analysisAdd BLAST37
ChainiPRO_000000864538 – 848Neuroligin-3Add BLAST811

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Glycosylationi98N-linked (GlcNAc...)Sequence analysis1
Disulfide bondi106 ↔ 141By similarity
Disulfide bondi340 ↔ 351By similarity
Disulfide bondi510 ↔ 544By similarity
Glycosylationi545N-linked (GlcNAc...)Sequence analysis1
Modified residuei745PhosphoserineBy similarity1
Modified residuei792PhosphotyrosineBy similarity1

Keywords - PTMi

Disulfide bond, Glycoprotein, Phosphoprotein

Proteomic databases

PaxDbiQ9NZ94.
PeptideAtlasiQ9NZ94.
PRIDEiQ9NZ94.

PTM databases

iPTMnetiQ9NZ94.
PhosphoSitePlusiQ9NZ94.

Expressioni

Tissue specificityi

Expressed in the blood vessel walls (at protein level). Detected in throughout the brain and in spinal cord. Detected in brain, and at lower levels in pancreas islet beta cells.3 Publications

Gene expression databases

BgeeiENSG00000196338.
CleanExiHS_NLGN3.
ExpressionAtlasiQ9NZ94. baseline and differential.
GenevisibleiQ9NZ94. HS.

Organism-specific databases

HPAiHPA003183.

Interactioni

Subunit structurei

Interacts with NRXN1, NRXN2 and NRXN3. Interacts (via its C-terminus) with DLG4/PSD-95 (via PDZ domain 3) (By similarity). Homodimer, and heterodimer with NLGN1 and NLGN2 (By similarity).By similarity

GO - Molecular functioni

  • cell adhesion molecule binding Source: BHF-UCL
  • neurexin family protein binding Source: BHF-UCL
  • scaffold protein binding Source: BHF-UCL

Protein-protein interaction databases

BioGridi119944. 24 interactors.
IntActiQ9NZ94. 2 interactors.
MINTiMINT-199096.
STRINGi9606.ENSP00000351591.

Structurei

3D structure databases

DisProtiDP00553.
ProteinModelPortaliQ9NZ94.
SMRiQ9NZ94.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Keywords - Domaini

Signal, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiKOG1516. Eukaryota.
COG2272. LUCA.
GeneTreeiENSGT00760000118946.
HOVERGENiHBG008839.
InParanoidiQ9NZ94.
KOiK07378.
OMAiKPNKKIC.
OrthoDBiEOG091G0CHW.
PhylomeDBiQ9NZ94.
TreeFamiTF326187.

Family and domain databases

Gene3Di3.40.50.1820. 2 hits.
InterProiIPR029058. AB_hydrolase.
IPR002018. CarbesteraseB.
IPR019819. Carboxylesterase_B_CS.
IPR000460. Nlgn.
[Graphical view]
PfamiPF00135. COesterase. 1 hit.
[Graphical view]
PRINTSiPR01090. NEUROLIGIN.
SUPFAMiSSF53474. SSF53474. 2 hits.
PROSITEiPS00941. CARBOXYLESTERASE_B_2. 1 hit.
[Graphical view]

Sequences (3)i

Sequence statusi: Complete.

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

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9NZ94-1) [UniParc]FASTAAdd to basket
Also known as: HNL3s

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
MWLRLGPPSL SLSPKPTVGR SLCLTLWFLS LALRASTQAP APTVNTHFGK
60 70 80 90 100
LRGARVPLPS EILGPVDQYL GVPYAAPPIG EKRFLPPEPP PSWSGIRNAT
110 120 130 140 150
HFPPVCPQNI HTAVPEVMLP VWFTANLDIV ATYIQEPNED CLYLNVYVPT
160 170 180 190 200
EDVKRISKEC ARKPNKKICR KGGSGAKKQG EDLADNDGDE DEDIRDSGAK
210 220 230 240 250
PVMVYIHGGS YMEGTGNMID GSILASYGNV IVITLNYRVG VLGFLSTGDQ
260 270 280 290 300
AAKGNYGLLD QIQALRWVSE NIAFFGGDPR RITVFGSGIG ASCVSLLTLS
310 320 330 340 350
HHSEGLFQRA IIQSGSALSS WAVNYQPVKY TSLLADKVGC NVLDTVDMVD
360 370 380 390 400
CLRQKSAKEL VEQDIQPARY HVAFGPVIDG DVIPDDPEIL MEQGEFLNYD
410 420 430 440 450
IMLGVNQGEG LKFVEGVVDP EDGVSGTDFD YSVSNFVDNL YGYPEGKDTL
460 470 480 490 500
RETIKFMYTD WADRDNPETR RKTLVALFTD HQWVEPSVVT ADLHARYGSP
510 520 530 540 550
TYFYAFYHHC QSLMKPAWSD AAHGDEVPYV FGVPMVGPTD LFPCNFSKND
560 570 580 590 600
VMLSAVVMTY WTNFAKTGDP NKPVPQDTKF IHTKANRFEE VAWSKYNPRD
610 620 630 640 650
QLYLHIGLKP RVRDHYRATK VAFWKHLVPH LYNLHDMFHY TSTTTKVPPP
660 670 680 690 700
DTTHSSHITR RPNGKTWSTK RPAISPAYSN ENAQGSWNGD QDAGPLLVEN
710 720 730 740 750
PRDYSTELSV TIAVGASLLF LNVLAFAALY YRKDKRRQEP LRQPSPQRGA
760 770 780 790 800
GAPELGAAPE EELAALQLGP THHECEAGPP HDTLRLTALP DYTLTLRRSP
810 820 830 840
DDIPLMTPNT ITMIPNSLVG LQTLHPYNTF AAGFNSTGLP HSHSTTRV
Length:848
Mass (Da):93,895
Last modified:May 23, 2003 - v2
Checksum:iB3EE2FAB7E427C82
GO
Isoform 2 (identifier: Q9NZ94-2) [UniParc]FASTAAdd to basket
Also known as: HNL3

The sequence of this isoform differs from the canonical sequence as follows:
     153-172: Missing.

Show »
Length:828
Mass (Da):91,570
Checksum:iB72E4F3472678692
GO
Isoform 3 (identifier: Q9NZ94-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     153-192: Missing.

Note: No experimental evidence available. Gene prediction based on EST data.
Show »
Length:808
Mass (Da):89,538
Checksum:iA0686FBADE342331
GO

Sequence cautioni

The sequence AAF71231 differs from that shown. Contaminating sequence. Potential poly-A sequence.Curated
The sequence BAA96004 differs from that shown. Reason: Erroneous initiation.Curated
The sequence BAC11226 differs from that shown. Reason: Erroneous initiation.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti224L → P in AAF71230 (PubMed:10767552).Curated1
Sequence conflicti274F → S in BAG37248 (PubMed:14702039).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_06888792S → Y.1 PublicationCorresponds to variant rs17854698dbSNPEnsembl.1
Natural variantiVAR_015668451R → C in AUTSX1 and ASPGX1. 1 Publication1
Natural variantiVAR_068888718L → I.1 PublicationCorresponds to variant rs17854697dbSNPEnsembl.1
Natural variantiVAR_068889751G → W.1 PublicationCorresponds to variant rs17857400dbSNPEnsembl.1
Natural variantiVAR_068890778G → S.1 PublicationCorresponds to variant rs17857401dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_053827153 – 192Missing in isoform 3. CuratedAdd BLAST40
Alternative sequenceiVSP_007534153 – 172Missing in isoform 2. 4 PublicationsAdd BLAST20

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF217411 mRNA. Translation: AAF71230.1.
AF217412 mRNA. Translation: AAF71231.1. Sequence problems.
AF217413 Genomic DNA. Translation: AAF71232.1.
AF217413 Genomic DNA. Translation: AAF71233.1.
GQ489207 mRNA. Translation: ADB12634.1.
AK074814 mRNA. Translation: BAC11226.1. Different initiation.
AK314699 mRNA. Translation: BAG37248.1.
AL590764 Genomic DNA. No translation available.
CH471132 Genomic DNA. Translation: EAX05307.1.
CH471132 Genomic DNA. Translation: EAX05308.1.
CH471132 Genomic DNA. Translation: EAX05309.1.
CH471132 Genomic DNA. Translation: EAX05310.1.
CH471132 Genomic DNA. Translation: EAX05312.1.
CH471132 Genomic DNA. Translation: EAX05313.1.
BC051715 mRNA. Translation: AAH51715.1.
AB040913 mRNA. Translation: BAA96004.1. Different initiation.
CCDSiCCDS14407.1. [Q9NZ94-2]
CCDS55441.1. [Q9NZ94-1]
CCDS55442.1. [Q9NZ94-3]
RefSeqiNP_001160132.1. NM_001166660.1. [Q9NZ94-3]
NP_001308205.1. NM_001321276.1.
NP_061850.2. NM_018977.3. [Q9NZ94-2]
NP_851820.1. NM_181303.1. [Q9NZ94-1]
UniGeneiHs.438877.

Genome annotation databases

EnsembliENST00000358741; ENSP00000351591; ENSG00000196338. [Q9NZ94-1]
ENST00000374051; ENSP00000363163; ENSG00000196338. [Q9NZ94-2]
ENST00000536169; ENSP00000445298; ENSG00000196338. [Q9NZ94-3]
GeneIDi54413.
KEGGihsa:54413.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF217411 mRNA. Translation: AAF71230.1.
AF217412 mRNA. Translation: AAF71231.1. Sequence problems.
AF217413 Genomic DNA. Translation: AAF71232.1.
AF217413 Genomic DNA. Translation: AAF71233.1.
GQ489207 mRNA. Translation: ADB12634.1.
AK074814 mRNA. Translation: BAC11226.1. Different initiation.
AK314699 mRNA. Translation: BAG37248.1.
AL590764 Genomic DNA. No translation available.
CH471132 Genomic DNA. Translation: EAX05307.1.
CH471132 Genomic DNA. Translation: EAX05308.1.
CH471132 Genomic DNA. Translation: EAX05309.1.
CH471132 Genomic DNA. Translation: EAX05310.1.
CH471132 Genomic DNA. Translation: EAX05312.1.
CH471132 Genomic DNA. Translation: EAX05313.1.
BC051715 mRNA. Translation: AAH51715.1.
AB040913 mRNA. Translation: BAA96004.1. Different initiation.
CCDSiCCDS14407.1. [Q9NZ94-2]
CCDS55441.1. [Q9NZ94-1]
CCDS55442.1. [Q9NZ94-3]
RefSeqiNP_001160132.1. NM_001166660.1. [Q9NZ94-3]
NP_001308205.1. NM_001321276.1.
NP_061850.2. NM_018977.3. [Q9NZ94-2]
NP_851820.1. NM_181303.1. [Q9NZ94-1]
UniGeneiHs.438877.

3D structure databases

DisProtiDP00553.
ProteinModelPortaliQ9NZ94.
SMRiQ9NZ94.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi119944. 24 interactors.
IntActiQ9NZ94. 2 interactors.
MINTiMINT-199096.
STRINGi9606.ENSP00000351591.

Protein family/group databases

ESTHERihuman-NLGN3. Neuroligin.
MEROPSiS09.987.

PTM databases

iPTMnetiQ9NZ94.
PhosphoSitePlusiQ9NZ94.

Polymorphism and mutation databases

BioMutaiNLGN3.
DMDMi31076855.

Proteomic databases

PaxDbiQ9NZ94.
PeptideAtlasiQ9NZ94.
PRIDEiQ9NZ94.

Protocols and materials databases

DNASUi54413.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000358741; ENSP00000351591; ENSG00000196338. [Q9NZ94-1]
ENST00000374051; ENSP00000363163; ENSG00000196338. [Q9NZ94-2]
ENST00000536169; ENSP00000445298; ENSG00000196338. [Q9NZ94-3]
GeneIDi54413.
KEGGihsa:54413.

Organism-specific databases

CTDi54413.
DisGeNETi54413.
GeneCardsiNLGN3.
GeneReviewsiNLGN3.
HGNCiHGNC:14289. NLGN3.
HPAiHPA003183.
MalaCardsiNLGN3.
MIMi300336. gene.
300425. phenotype.
300494. phenotype.
neXtProtiNX_Q9NZ94.
OpenTargetsiENSG00000196338.
Orphaneti1162. Asperger syndrome.
106. Autism.
PharmGKBiPA31649.
HUGEiSearch...
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG1516. Eukaryota.
COG2272. LUCA.
GeneTreeiENSGT00760000118946.
HOVERGENiHBG008839.
InParanoidiQ9NZ94.
KOiK07378.
OMAiKPNKKIC.
OrthoDBiEOG091G0CHW.
PhylomeDBiQ9NZ94.
TreeFamiTF326187.

Enzyme and pathway databases

BioCyciZFISH:G66-30815-MONOMER.
ReactomeiR-HSA-6794361. Interactions of neurexins and neuroligins at synapses.

Miscellaneous databases

ChiTaRSiNLGN3. human.
GeneWikiiNLGN3.
GenomeRNAii54413.
PROiQ9NZ94.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000196338.
CleanExiHS_NLGN3.
ExpressionAtlasiQ9NZ94. baseline and differential.
GenevisibleiQ9NZ94. HS.

Family and domain databases

Gene3Di3.40.50.1820. 2 hits.
InterProiIPR029058. AB_hydrolase.
IPR002018. CarbesteraseB.
IPR019819. Carboxylesterase_B_CS.
IPR000460. Nlgn.
[Graphical view]
PfamiPF00135. COesterase. 1 hit.
[Graphical view]
PRINTSiPR01090. NEUROLIGIN.
SUPFAMiSSF53474. SSF53474. 2 hits.
PROSITEiPS00941. CARBOXYLESTERASE_B_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiNLGN3_HUMAN
AccessioniPrimary (citable) accession number: Q9NZ94
Secondary accession number(s): B2RBK1
, D2X2H6, D3DVV0, D3DVV1, Q86V51, Q8NCD0, Q9NZ95, Q9NZ96, Q9NZ97, Q9P248
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 23, 2003
Last sequence update: May 23, 2003
Last modified: November 30, 2016
This is version 147 of the entry and version 2 of the sequence. [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

Complete proteome, Reference proteome

Documents

  1. Human chromosome X
    Human chromosome X: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.