OR1A2

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

Basic information

Region (hg38): 17:3197519-3198448

Links

ENSG00000172150 ∙ NCBI:26189 ∙ OMIM:618047 ∙ HGNC:8180 ∙ Uniprot:Q9Y585 ∙ 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 OR1A2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR1A2 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					1	1
missense			25	4	2	31
nonsense						0
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	4	4

Variants in OR1A2

This is a list of pathogenic ClinVar variants found in the OR1A2 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-3197570-A-C		not specified	Uncertain significance (May 23, 2024)
17-3197574-G-A		not specified	Uncertain significance (Nov 08, 2024)
17-3197627-A-T		not specified	Uncertain significance (Aug 10, 2021)
17-3197642-AATCTGCTCATC-A			Benign (Dec 31, 2019)
17-3197724-T-C		not specified	Uncertain significance (Feb 13, 2025)
17-3197729-A-G		not specified	Uncertain significance (Dec 21, 2023)
17-3197732-A-T		not specified	Likely benign (Dec 15, 2023)
17-3197790-T-C		not specified	Likely benign (Oct 02, 2023)
17-3197791-C-A		not specified	Uncertain significance (Jan 18, 2025)
17-3197815-G-T		not specified	Uncertain significance (May 28, 2024)
17-3197847-C-A			Benign (Dec 31, 2019)
17-3197868-C-T		not specified	Uncertain significance (Feb 28, 2023)
17-3197878-C-T			Benign (Dec 31, 2019)
17-3197879-G-A		not specified	Uncertain significance (Jun 11, 2021)
17-3197882-C-G		not specified	Uncertain significance (Dec 08, 2023)
17-3197910-A-G		not specified	Uncertain significance (Feb 22, 2025)
17-3197925-T-C		not specified	Uncertain significance (Jan 20, 2025)
17-3197958-G-C		not specified	Uncertain significance (Jan 22, 2025)
17-3197961-C-G		not specified	Uncertain significance (Nov 10, 2022)
17-3197970-T-C		not specified	Uncertain significance (Apr 22, 2024)
17-3198059-A-G		not specified	Likely benign (Mar 27, 2023)
17-3198081-C-T		not specified	Uncertain significance (Feb 13, 2025)
17-3198083-T-C		not specified	Uncertain significance (Apr 08, 2024)
17-3198086-T-C		not specified	Uncertain significance (Aug 16, 2021)
17-3198090-A-T		not specified	Uncertain significance (Nov 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR1A2	protein_coding	protein_coding	ENST00000381951	1	930

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0272	0.807	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.857	135	166	0.813	0.00000790	2026
Missense in Polyphen		44	47.781	0.92087		658
Synonymous	-0.221	67	64.7	1.03	0.00000320	623
Loss of Function	1.05	3	5.71	0.525	3.03e-7	78

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Odorant receptor. {ECO:0000305}.
• Pathway: Olfactory transduction - Homo sapiens (human);Olfactory receptor activity;GPCRs, Class A Rhodopsin-like;Signaling by GPCR;Signal Transduction;Olfactory Signaling Pathway;G alpha (s) signalling events;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.0948

Intolerance Scores

• loftool: 0.572
• rvis_EVS: 1.35
• rvis_percentile_EVS: 94.35

Haploinsufficiency Scores

• pHI: 0.0323
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0998

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Gene ontology

• Biological process: G protein-coupled receptor signaling pathway;positive regulation of cytokinesis;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