Seroatlas · Human Serome Atlas

NLGN3

Neuroligin-3

Also known as: ASPGX1, AUTSX1, HNL3, KIAA1480, NLGN3_HUMAN

Cross-references: UniProt · Ensembl · Human Protein Atlas · GeneCards · NCBI Gene

Protein identityUniProt · HPA

UniProt accession
Q9NZ94
Gene
NLGN3
Ensembl
ENSG00000196338
Chromosome
X
Canonical length
848 aa
Protein class
Disease related genes, Human disease related genes, Potential drug targets, Predicted intracellular proteins, Predicted membrane proteins, Transporters
Subcellular location
Golgi apparatus,Cell Junctions
Secretome location
Intracellular and membrane
Quaternary structure
Homodimer

OverviewNCBI Gene

This gene encodes a member of a family of neuronal cell surface proteins. Members of this family may act as splice site-specific ligands for beta-neurexins and may be involved in the formation and remodeling of central nervous system synapses. Mutations in this gene may be associated with autism and Asperger syndrome. Multiple transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Oct 2009]

Canonical amino-acid sequenceUniProt

848 residues, UniProt reviewed canonical sequence.

>Q9NZ94|NLGN3
     1  MWLRLGPPSL SLSPKPTVGR SLCLTLWFLS LALRASTQAP APTVNTHFGK LRGARVPLPS
    61  EILGPVDQYL GVPYAAPPIG EKRFLPPEPP PSWSGIRNAT HFPPVCPQNI HTAVPEVMLP
   121  VWFTANLDIV ATYIQEPNED CLYLNVYVPT EDVKRISKEC ARKPNKKICR KGGSGAKKQG
   181  EDLADNDGDE DEDIRDSGAK PVMVYIHGGS YMEGTGNMID GSILASYGNV IVITLNYRVG
   241  VLGFLSTGDQ AAKGNYGLLD QIQALRWVSE NIAFFGGDPR RITVFGSGIG ASCVSLLTLS
   301  HHSEGLFQRA IIQSGSALSS WAVNYQPVKY TSLLADKVGC NVLDTVDMVD CLRQKSAKEL
   361  VEQDIQPARY HVAFGPVIDG DVIPDDPEIL MEQGEFLNYD IMLGVNQGEG LKFVEGVVDP
   421  EDGVSGTDFD YSVSNFVDNL YGYPEGKDTL RETIKFMYTD WADRDNPETR RKTLVALFTD
   481  HQWVEPSVVT ADLHARYGSP TYFYAFYHHC QSLMKPAWSD AAHGDEVPYV FGVPMVGPTD
   541  LFPCNFSKND VMLSAVVMTY WTNFAKTGDP NKPVPQDTKF IHTKANRFEE VAWSKYNPRD
   601  QLYLHIGLKP RVRDHYRATK VAFWKHLVPH LYNLHDMFHY TSTTTKVPPP DTTHSSHITR
   661  RPNGKTWSTK RPAISPAYSN ENAQGSWNGD QDAGPLLVEN PRDYSTELSV TIAVGASLLF
   721  LNVLAFAALY YRKDKRRQEP LRQPSPQRGA GAPELGAAPE EELAALQLGP THHECEAGPP
   781  HDTLRLTALP DYTLTLRRSP DDIPLMTPNT ITMIPNSLVG LQTLHPYNTF AAGFNSTGLP
   841  HSHSTTRV

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against NLGN3 can act on the native protein depends on physical access: surface and secreted proteins are reachable by circulating antibodies, intracellular proteins usually are not.

Antibody reachability
Cell surface
Secreted
No
Transmembrane segments
1
Mean surface accessibility (rSASA)
0.36
Highest tissue expression
32 nTPM

Expression across tissuesHPA

Tissue

  • cerebral cortex: 32 nTPM
  • seminal vesicle: 11 nTPM
  • epididymis: 6.4 nTPM
  • prostate: 5.5 nTPM
  • amygdala: 5.4 nTPM
  • adrenal gland: 5.3 nTPM

Single-cell type

  • oligodendrocyte progenitor cells: 145 nCPM
  • oligodendrocytes: 58 nCPM
  • bergmann glia: 58 nCPM
  • astrocytes: 35 nCPM
  • peritubular myoid cells: 34 nCPM
  • neutrophils: 23 nCPM

Immune cell

  • neutrophil: 1 nTPM
  • NK-cell: 0.4 nTPM
  • plasmacytoid DC: 0.4 nTPM
  • basophil: 0.3 nTPM
  • naive B-cell: 0.3 nTPM
  • classical monocyte: 0.1 nTPM

Brain region

  • amygdala: 60 nTPM
  • hippocampal formation: 59 nTPM
  • cerebral cortex: 58 nTPM
  • hypothalamus: 57 nTPM
  • medulla oblongata: 55 nTPM
  • basal ganglia: 53 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about NLGN3.

Disease | AllUniProt

Conditions NLGN3 is implicated in, by any mechanism.

Disease | GeneticClinVar

12 pathogenic / likely-pathogenic of 271 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

Genetic constraint and essentialitygnomAD · DepMap

Does the body need this protein intact? Low LOEUF or a strong DepMap dependency means loss or blockade of the protein is likely to be felt.

gnomAD LOEUF (loss-of-function intolerance)
0.31
gnomAD pLI
0.98
gnomAD missense Z
4.21
DepMap mean gene effect
-0.07
DepMap dependency class
selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 4% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

Molecular functions

Cellular components

Protein domainsUniProt · Pfam · InterPro

KeywordsUniProt

InteractionsUniProt · HPA

Protein binding partners of NLGN3 in the human serome: UniProt-annotated complex subunits plus reported interactors. Each links to its own Seroatlas record.

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads NLGN3 as an antibody target. Whether an autoantibody or antibody against NLGN3 could matter depends on whether native NLGN3 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

NLGN3 is annotated at the cell surface, where native NLGN3 is exposed to circulating antibodies and is a prime autoantibody target that could block, deplete, or overstimulate it.

Annotation status

The present source text does not explicitly label NLGN3 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

Canonical record: https://seroatlas.com/gene/NLGN3. Study-independent annotations aggregated from UniProt, Human Protein Atlas, PubMed, IEDB, Pfam, InterPro, Gene Ontology, AlphaFold, gnomAD, DepMap, ClinVar, TCGA. Catalog release seroatlas-reviewed-human-uniprot-20260313.

Seroatlas is the reference for exploring autoantibody and antibody serology at the human-protein level: the autoreactome and human serome, multiplex serology (HuProt, HuScan, VirScan, PhIP-Seq).

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