NLGN3 — neuroligin 3

5 sources retrieved · Most recent: April 2026 · Index updated 3 months ago

69PubMed Papers

#6,842 · top 35% of 19K genes

21Diseases

top 17%

0Drugs

12Pathogenic Variants

top 49%

OMIM Disease GeneExperimental GO EvidenceSwiss-Prot Reviewed

vocalization behaviorlearningsynapse organizationexcitatory synapseautismautism spectrum disordergenetic disorderIntellectual disability

AI Summary

AI summary not yet available. Showing NCBI Gene summary.

neuroligin 3

⚠Limited data available — This gene has 0 indexed publications. Summary and analysis may be incomplete.

Disease Associations21

autismOpen Targets

0.64Moderate

autism spectrum disorderOpen Targets

0.57Moderate

genetic disorderOpen Targets

0.45Moderate

Intellectual disabilityOpen Targets

0.43Moderate

neurodegenerative diseaseOpen Targets

0.37Weak

Asperger syndromeOpen Targets

0.37Weak

X-linked complex neurodevelopmental disorderOpen Targets

0.34Weak

Autistic behaviorOpen Targets

0.34Weak

hypogonadotropic hypogonadismOpen Targets

0.34Weak

complex neurodevelopmental disorderOpen Targets

0.12Weak

gliomaOpen Targets

0.11Weak

attention deficit hyperactivity disorderOpen Targets

0.10Weak

glioblastoma multiformeOpen Targets

0.10Weak

hereditary attention deficit-hyperactivity disorderOpen Targets

0.09Suggestive

attention deficit-hyperactivity disorder 8Open Targets

0.09Suggestive

schizophrenia 15Open Targets

0.09Suggestive

intellectual disability, autosomal recessive 59Open Targets

0.08Suggestive

Tourette syndromeOpen Targets

0.08Suggestive

intellectual disability, autosomal dominant 50Open Targets

0.08Suggestive

Potocki-Lupski syndromeOpen Targets

0.08Suggestive

Autism, X-linked 1UniProt

Pathogenic Variants12

NM_181303.2(NLGN3):c.422_423del (p.Cys141fs)Likely pathogenic

Autism, susceptibility to, X-linked 1

★☆☆☆2024→ Residue 141

NM_181303.2(NLGN3):c.622G>A (p.Gly208Arg)Likely pathogenic

Autism, susceptibility to, X-linked 1|Melanoma

★☆☆☆2024→ Residue 208

NM_181303.2(NLGN3):c.1978C>T (p.Arg660Cys)Likely pathogenic

X-linked complex neurodevelopmental disorder

★☆☆☆2023→ Residue 660

NM_181303.2(NLGN3):c.366G>A (p.Trp122Ter)Pathogenic

Hypogonadotropic hypogonadism

★☆☆☆2023→ Residue 122

NM_181303.2(NLGN3):c.2222T>G (p.Leu741Arg)Likely pathogenic

Autism, susceptibility to, X-linked 1

★☆☆☆2022→ Residue 741

NM_181303.2(NLGN3):c.1600C>T (p.Pro534Ser)Pathogenic

Intellectual disability;Autistic behavior

★☆☆☆2019→ Residue 534

NM_181303.2(NLGN3):c.214dup (p.Val72fs)Pathogenic

Inborn genetic diseases

★☆☆☆2016→ Residue 72

NM_181303.2(NLGN3):c.577+1G>ALikely pathogenic

Inborn genetic diseases

★☆☆☆2014

NM_181303.2(NLGN3):c.1849C>T (p.Arg617Trp)Likely pathogenic

Intellectual disability

★☆☆☆2014→ Residue 617

NM_181303.2(NLGN3):c.913+1G>ALikely pathogenic

Autism, susceptibility to, X-linked 1

☆☆☆☆2022

NM_181303.2(NLGN3):c.1672A>G (p.Met558Val)Likely pathogenic

Autism, susceptibility to, X-linked 1

☆☆☆☆→ Residue 558

NM_181303.2(NLGN3):c.611T>C (p.Val204Ala)Pathogenic

Autism, susceptibility to, X-linked 1

☆☆☆☆→ Residue 204

Tissue Expression6 tissues

Brain

100%

Bone Marrow

49%

Ovary

24%

Heart

Lung

Liver

Gene Interaction Network6 neighbors

Click a node to explore

Structure1 PDB hit

Preparing viewer…

PDB8GS3 · 3.90 Å · EM

View on RCSB

ConstraintgnomAD v4.1

LOEUFⓘ

0.42Moderately Constrained

pLIⓘ

1.00Intolerant

Observed/Expected LoF0.26 [0.16–0.42]

Rankings3 dim

Where NLGN3 stands among ~20K protein-coding genes

#6,824of 20,598
Most Researched69
#2,699of 5,509
Most Pathogenic Variants12
#2,257of 17,882
Most Constrained (LOEUF)0.42 · top quartile

Meta

Genes detectedNLGN3

Sources retrieved5 papers

Response time—

Sources5

The structure and expression of the human neuroligin-3 gene.

PMID: 10767552

Gene · 2000

0.95

Prediction of the coding sequences of unidentified human genes. XVII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro.

PMID: 10819331

DNA Res · 2000

0.95

The making of neurexins.

PMID: 9751164

J Neurochem · 1998

0.95

Binding of neuroligins to PSD-95.

PMID: 9278515

Science · 1997

0.95

Structures, alternative splicing, and neurexin binding of multiple neuroligins.

PMID: 8576240

J Biol Chem · 1996

0.95

View all 69 papers on PubMed →

Loading gene record…

5 sources retrieved · Most recent: April 2026 · Index updated 3 months ago

69PubMed Papers

#6,842 · top 35% of 19K genes

21Diseases

top 17%

0Drugs

12Pathogenic Variants

top 49%

OMIM Disease GeneExperimental GO EvidenceSwiss-Prot Reviewed

vocalization behaviorlearningsynapse organizationexcitatory synapseautismautism spectrum disordergenetic disorderIntellectual disability

AI Summary

AI summary not yet available. Showing NCBI Gene summary.

neuroligin 3

⚠Limited data available — This gene has 0 indexed publications. Summary and analysis may be incomplete.

Disease Associations21

autismOpen Targets

0.64Moderate

autism spectrum disorderOpen Targets

0.57Moderate

genetic disorderOpen Targets

0.45Moderate

Intellectual disabilityOpen Targets

0.43Moderate

neurodegenerative diseaseOpen Targets

0.37Weak

Asperger syndromeOpen Targets

0.37Weak

X-linked complex neurodevelopmental disorderOpen Targets

0.34Weak

Autistic behaviorOpen Targets

0.34Weak

hypogonadotropic hypogonadismOpen Targets

0.34Weak

complex neurodevelopmental disorderOpen Targets

0.12Weak

gliomaOpen Targets

0.11Weak

attention deficit hyperactivity disorderOpen Targets

0.10Weak

glioblastoma multiformeOpen Targets

0.10Weak

hereditary attention deficit-hyperactivity disorderOpen Targets

0.09Suggestive

attention deficit-hyperactivity disorder 8Open Targets

0.09Suggestive

schizophrenia 15Open Targets

0.09Suggestive

intellectual disability, autosomal recessive 59Open Targets

0.08Suggestive

Tourette syndromeOpen Targets

0.08Suggestive

intellectual disability, autosomal dominant 50Open Targets

0.08Suggestive

Potocki-Lupski syndromeOpen Targets

0.08Suggestive

Autism, X-linked 1UniProt

Pathogenic Variants12

NM_181303.2(NLGN3):c.422_423del (p.Cys141fs)Likely pathogenic

Autism, susceptibility to, X-linked 1

★☆☆☆2024→ Residue 141

NM_181303.2(NLGN3):c.622G>A (p.Gly208Arg)Likely pathogenic

Autism, susceptibility to, X-linked 1|Melanoma

★☆☆☆2024→ Residue 208

NM_181303.2(NLGN3):c.1978C>T (p.Arg660Cys)Likely pathogenic

X-linked complex neurodevelopmental disorder

★☆☆☆2023→ Residue 660

NM_181303.2(NLGN3):c.366G>A (p.Trp122Ter)Pathogenic

Hypogonadotropic hypogonadism

★☆☆☆2023→ Residue 122

NM_181303.2(NLGN3):c.2222T>G (p.Leu741Arg)Likely pathogenic

Autism, susceptibility to, X-linked 1

★☆☆☆2022→ Residue 741

NM_181303.2(NLGN3):c.1600C>T (p.Pro534Ser)Pathogenic

Intellectual disability;Autistic behavior

★☆☆☆2019→ Residue 534

NM_181303.2(NLGN3):c.214dup (p.Val72fs)Pathogenic

Inborn genetic diseases

★☆☆☆2016→ Residue 72

NM_181303.2(NLGN3):c.577+1G>ALikely pathogenic

Inborn genetic diseases

★☆☆☆2014

NM_181303.2(NLGN3):c.1849C>T (p.Arg617Trp)Likely pathogenic

Intellectual disability

★☆☆☆2014→ Residue 617

NM_181303.2(NLGN3):c.913+1G>ALikely pathogenic

Autism, susceptibility to, X-linked 1

☆☆☆☆2022

NM_181303.2(NLGN3):c.1672A>G (p.Met558Val)Likely pathogenic

Autism, susceptibility to, X-linked 1

☆☆☆☆→ Residue 558

NM_181303.2(NLGN3):c.611T>C (p.Val204Ala)Pathogenic

Autism, susceptibility to, X-linked 1

☆☆☆☆→ Residue 204

Tissue Expression6 tissues

Brain

100%

Bone Marrow

49%

Ovary

24%

Heart

Lung

Liver

Gene Interaction Network6 neighbors

Click a node to explore

Structure1 PDB hit

Preparing viewer…

PDB8GS3 · 3.90 Å · EM

View on RCSB

ConstraintgnomAD v4.1

LOEUFⓘ

0.42Moderately Constrained

pLIⓘ

1.00Intolerant

Observed/Expected LoF0.26 [0.16–0.42]

Rankings3 dim

Where NLGN3 stands among ~20K protein-coding genes

#6,824of 20,598
Most Researched69
#2,699of 5,509
Most Pathogenic Variants12
#2,257of 17,882
Most Constrained (LOEUF)0.42 · top quartile