NRXN3

neurexin 3, the group of Neurexins

Basic information

Region (hg38): 14:78170372-79868291

Previous symbols: [ "C14orf60" ]

Links

ENSG00000021645 ∙ NCBI:9369 ∙ OMIM:600567 ∙ HGNC:8010 ∙ Uniprot:Q9HDB5, Q9Y4C0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• autism (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NRXN3 gene.

• not provided (28 variants)
• Inborn genetic diseases (17 variants)
• NRXN3-related condition (3 variants)
• Autism spectrum disorder (2 variants)
• Autism (1 variants)
• not specified (1 variants)
• Autism;Intellectual disability (1 variants)
• Relative macrocephaly;Short stature (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NRXN3 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				10	5	15
missense			25	2	1	28
nonsense						0
start loss						0
frameshift				1		1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1	2		3
non coding			2	2	1	5
Total	0	0	27	15	7

Variants in NRXN3

This is a list of pathogenic ClinVar variants found in the NRXN3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
14-78243144-G-A		NRXN3-related disorder	Likely benign (Mar 01, 2019)
14-78243275-C-T		NRXN3-related disorder	Uncertain significance (Feb 21, 2024)
14-78243303-C-T		NRXN3-related disorder	Likely benign (May 31, 2019)
14-78243345-C-T		NRXN3-related disorder	Likely benign (May 21, 2019)
14-78243375-C-T			Likely benign (Jan 01, 2024)
14-78243384-C-T		NRXN3-related disorder	Likely benign (Oct 24, 2022)
14-78243456-G-A		NRXN3-related disorder	Likely benign (Dec 16, 2021)
14-78243471-T-C			Benign (Jun 19, 2018)
14-78243561-A-T			Likely benign (Nov 01, 2022)
14-78243701-G-A			Benign (Jun 19, 2018)
14-78278672-T-G		NRXN3-related disorder	Likely benign (Feb 20, 2019)
14-78484862-G-A		Autism	Benign (Dec 01, 2022)
14-78645154-A-T		NRXN3-related disorder	Benign (Jan 31, 2022)
14-78645187-G-A		NRXN3-related disorder	Likely benign (Jun 11, 2019)
14-78645241-C-T		NRXN3-related disorder	Likely benign (Aug 09, 2019)
14-78645277-T-C		NRXN3-related disorder	Likely benign (Mar 25, 2019)
14-78645397-C-T		NRXN3-related disorder	Likely benign (Jun 22, 2023)
14-78651155-C-T		NRXN3-related disorder	Likely benign (Sep 30, 2022)
14-78651233-C-A			Benign/Likely benign (Dec 01, 2022)
14-78651308-C-T			Benign/Likely benign (Jul 01, 2022)
14-78709242-G-A			Uncertain significance (May 14, 2020)
14-78709277-A-T		not specified	Uncertain significance (Jul 06, 2022)
14-78709298-G-A		not specified	Uncertain significance (Jun 07, 2023)
14-78709310-A-G		Relative macrocephaly;Short stature	Pathogenic (-)
14-78709378-C-T			Likely benign (Oct 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NRXN3	protein_coding	protein_coding	ENST00000554719	15	1622029

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000115	125741	0	4	125745	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.44	409	657	0.623	0.0000402	7030
Missense in Polyphen		156	271.62	0.57433		2865
Synonymous	0.565	243	254	0.955	0.0000164	2065
Loss of Function	5.90	1	42.5	0.0235	0.00000221	494

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000879	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Neuronal cell surface protein that may be involved in cell recognition and cell adhesion. May play a role in angiogenesis (By similarity). {ECO:0000250}.
• Pathway: Cell adhesion molecules (CAMs) - Homo sapiens (human);Neuronal System;Neurexins and neuroligins;Protein-protein interactions at synapses (Consensus)

Recessive Scores

• pRec: 0.119

Intolerance Scores

• loftool: 0.00234
• rvis_EVS: -1.55
• rvis_percentile_EVS: 3.27

Haploinsufficiency Scores

• pHI: 0.619
• hipred: Y
• hipred_score: 0.685
• ghis: 0.626

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.894

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Nrxn3
• Phenotype: respiratory system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: neuron cell-cell adhesion;axon guidance;learning;adult behavior;social behavior;vocalization behavior
• Cellular component: plasma membrane;integral component of plasma membrane
• Molecular function: signaling receptor activity;metal ion binding;cell adhesion molecule binding;neuroligin family protein binding