OR2Y1

olfactory receptor family 2 subfamily Y member 1, the group of Olfactory receptors, family 2

Basic information

Region (hg38): 5:180739123-180740058

Links

ENSG00000174339 ∙ NCBI:134083 ∙ ∙ HGNC:14837 ∙ Uniprot:Q8NGV0 ∙ 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 OR2Y1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR2Y1 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			18	1		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	1	0

Variants in OR2Y1

This is a list of pathogenic ClinVar variants found in the OR2Y1 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-180739146-A-G		not specified	Uncertain significance (Jan 04, 2024)
5-180739152-C-T		not specified	Uncertain significance (Dec 15, 2021)
5-180739217-G-A		not specified	Uncertain significance (Jul 25, 2023)
5-180739229-T-C		not specified	Uncertain significance (Apr 25, 2023)
5-180739368-C-A		not specified	Uncertain significance (Feb 16, 2023)
5-180739500-C-T		not specified	Uncertain significance (Dec 16, 2023)
5-180739526-C-T		not specified	Uncertain significance (Mar 25, 2024)
5-180739544-C-T		not specified	Likely benign (Sep 16, 2021)
5-180739607-G-A		not specified	Uncertain significance (Jul 14, 2021)
5-180739662-T-C		not specified	Uncertain significance (Nov 28, 2023)
5-180739668-G-T		not specified	Uncertain significance (May 17, 2023)
5-180739694-C-T		not specified	Uncertain significance (Jan 04, 2022)
5-180739736-C-T		not specified	Uncertain significance (Mar 06, 2023)
5-180739800-C-T		not specified	Uncertain significance (Jul 11, 2022)
5-180739827-C-T		not specified	Uncertain significance (Jan 31, 2023)
5-180739882-C-T		not specified	Uncertain significance (Dec 19, 2022)
5-180739898-C-T		not specified	Uncertain significance (Nov 20, 2023)
5-180739959-A-C		not specified	Uncertain significance (Nov 09, 2021)
5-180739986-G-A		not specified	Uncertain significance (Oct 13, 2021)
5-180739997-G-T		not specified	Uncertain significance (Mar 12, 2024)
5-180740007-A-T		not specified	Uncertain significance (May 07, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR2Y1	protein_coding	protein_coding	ENST00000307832	1	1058

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	-0.348	189	176	1.07	0.00000958	2002
Missense in Polyphen		59	49.182	1.1996		690
Synonymous	-1.22	85	71.9	1.18	0.00000412	683
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: Odorant receptor. {ECO:0000305}.
• Pathway: Olfactory transduction - Homo sapiens (human);Olfactory receptor activity;Signaling by GPCR;Signal Transduction;Olfactory Signaling Pathway;G alpha (s) signalling events;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.101

Intolerance Scores

• loftool: 0.753
• rvis_EVS: 1.64
• rvis_percentile_EVS: 96.13

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.170

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0541

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Olfr1393

Gene ontology

• Biological process: G protein-coupled receptor signaling pathway;detection of chemical stimulus involved in sensory perception of smell
• Cellular component: plasma membrane;integral component of membrane
• Molecular function: G protein-coupled receptor activity;olfactory receptor activity