NRXN3

neurexin 3, the group of Neurexins

Basic information

Region (hg38): 14:78170373-79868291

Previous symbols: [ "C14orf60" ]

Links

∙ 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_specified (103 variants)
NRXN3-related_disorder (36 variants)
not_provided (31 variants)
Relative_macrocephaly (2 variants)
Short_stature (2 variants)
Autism_spectrum_disorder (2 variants)
Autism (1 variants)
NRXN3-associated_neurodevelopmental_disorder (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. These statistics are base on transcript: NM_001330195.2. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				30 clinvar	4 clinvar	34
missense	1 clinvar		113 clinvar	4 clinvar		118
nonsense			1 clinvar			1
start loss						0
frameshift				1 clinvar		1
splice donor/acceptor (+/-2bp)						0
Total	1	0	114	35	4

Highest pathogenic variant AF is 0.00000185878

Loading clinvar variants...

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