VN1R2

vomeronasal 1 receptor 2, the group of Vomeronasal receptors

Basic information

Region (hg38): 19:53258292-53261837

Links

ENSG00000196131 ∙ NCBI:317701 ∙ ∙ HGNC:19872 ∙ Uniprot:Q8NFZ6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the VN1R2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VN1R2 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						0
missense			17	1		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	1	0

Variants in VN1R2

This is a list of pathogenic ClinVar variants found in the VN1R2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-53258511-A-G		not specified	Uncertain significance (Aug 13, 2021)
19-53258520-C-T			Likely benign (Dec 01, 2022)
19-53258597-C-A		not specified	Uncertain significance (Apr 25, 2022)
19-53258685-A-C		not specified	Uncertain significance (Dec 13, 2023)
19-53258737-C-G		not specified	Uncertain significance (Dec 20, 2022)
19-53258773-T-C		not specified	Uncertain significance (Dec 15, 2022)
19-53258791-T-A		not specified	Uncertain significance (Nov 07, 2022)
19-53258844-G-T		not specified	Uncertain significance (Jan 31, 2022)
19-53258863-A-G		not specified	Uncertain significance (Feb 28, 2023)
19-53258875-A-G		not specified	Uncertain significance (Jun 07, 2024)
19-53259057-C-T		not specified	Uncertain significance (Feb 13, 2024)
19-53259064-A-G		not specified	Uncertain significance (Apr 04, 2024)
19-53259137-T-G		not specified	Uncertain significance (Apr 17, 2024)
19-53259157-T-C		not specified	Uncertain significance (Mar 21, 2023)
19-53259182-T-G		not specified	Uncertain significance (Dec 20, 2023)
19-53259183-G-A		not specified	Uncertain significance (Aug 08, 2023)
19-53259207-C-T		not specified	Uncertain significance (Jun 17, 2024)
19-53259442-T-C		not specified	Likely benign (Mar 19, 2024)
19-53259459-A-T		not specified	Uncertain significance (Jun 17, 2024)
19-53259504-C-T		not specified	Uncertain significance (Apr 19, 2023)
19-53259545-T-G		not specified	Uncertain significance (Aug 19, 2021)
19-53259546-G-T		not specified	Uncertain significance (Jul 27, 2022)
19-53259552-A-G		not specified	Uncertain significance (Oct 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VN1R2	protein_coding	protein_coding	ENST00000341702	1	3546

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p

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

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Putative pheromone receptor.

Intolerance Scores

• loftool: 0.855
• rvis_EVS: 0.62
• rvis_percentile_EVS: 83.36

Haploinsufficiency Scores

• pHI: 0.0307
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0265

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Vmn1r224

Gene ontology

• Biological process: G protein-coupled receptor signaling pathway;response to pheromone
• Cellular component: plasma membrane;integral component of membrane
• Molecular function: pheromone receptor activity