VN1R2

protein-coding

vomeronasal 1 receptor 2, the group of Vomeronasal receptors

Gene summary

Predicted to enable pheromone binding activity. Predicted to be involved in G protein-coupled receptor signaling pathway; response to pheromone; and sensory perception of chemical stimulus. Predicted to be located in membrane. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_173856.2

Inheritance

—

ClinVar variants

U:49B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e —

Max pathogenic AF

—

Genomic locus

chr19:53,258,292-53,261,837

External References & Databases

Ensembl (ENSG00000196131)

Transcript & Mutation Effects

hg38 • Region Span ~3.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to VN1R2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 51

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_173856.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			49 clinvar	2 clinvar		51
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	49	3	0	52

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_173856.2	RefSeq	NP_776255.2	1	MANE Select
ENST00000341702.3	Ensembl	ENSP00000351244.2	1	MANE Select

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

G protein-coupled receptor signaling pathway
response to pheromone

Molecular Function

pheromone receptor activity

Cellular Component

plasma membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000341702
Coding exons: 1
Length: 3546

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.267	190	201	0.947	0.00000969	2580
Missense (PolyPhen)		37	41.254	0.89687		608
Synonymous	0.355	76	80.0	0.950	0.00000414	805
Loss of Function

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Putative pheromone receptor.;

Intolerance Scores

LoFtool: 0.855
RVIS EVS: 0.62
RVIS percentile EVS: 83.36

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0265

Gene Damage Prediction

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