OR1A1

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

Basic information

Region (hg38): 17:3207539-3218896

Links

ENSG00000172146 ∙ NCBI:8383 ∙ OMIM:618046 ∙ HGNC:8179 ∙ Uniprot:Q9P1Q5 ∙ 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 OR1A1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR1A1 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	2
missense			19		1	20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	1	2

Variants in OR1A1

This is a list of pathogenic ClinVar variants found in the OR1A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-3215636-C-A		not specified	Uncertain significance (Apr 18, 2024)
17-3215663-C-A		not specified	Uncertain significance (Sep 08, 2024)
17-3215742-G-C		not specified	Uncertain significance (Mar 07, 2024)
17-3215745-A-G		not specified	Uncertain significance (Apr 25, 2023)
17-3215808-T-G		not specified	Uncertain significance (Jul 20, 2022)
17-3215855-C-A		not specified	Uncertain significance (Sep 11, 2024)
17-3215879-T-G		not specified	Uncertain significance (Apr 06, 2023)
17-3215886-G-A		not specified	Uncertain significance (Oct 16, 2023)
17-3215916-C-T		not specified	Uncertain significance (Sep 14, 2022)
17-3215918-C-A		not specified	Uncertain significance (Jun 29, 2023)
17-3215981-G-A		not specified	Uncertain significance (Aug 20, 2024)
17-3215994-C-A		not specified	Uncertain significance (Aug 08, 2023)
17-3216002-C-T		not specified	Uncertain significance (Jan 24, 2023)
17-3216036-G-A		not specified	Uncertain significance (Apr 13, 2022)
17-3216084-A-G		not specified	Uncertain significance (May 15, 2024)
17-3216185-T-G		not specified	Uncertain significance (Apr 13, 2022)
17-3216191-G-C		not specified	Uncertain significance (Sep 29, 2023)
17-3216221-C-T			Benign (May 16, 2018)
17-3216269-T-C		not specified	Uncertain significance (Aug 16, 2022)
17-3216276-G-A		not specified	Uncertain significance (Jul 10, 2024)
17-3216356-G-A		not specified	Uncertain significance (Nov 19, 2024)
17-3216378-C-T		not specified	Uncertain significance (Jul 02, 2024)
17-3216390-C-G		not specified	Uncertain significance (Sep 14, 2022)
17-3216399-G-A		not specified	Uncertain significance (Nov 06, 2024)
17-3216450-C-G		not specified	Uncertain significance (Apr 22, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR1A1	protein_coding	protein_coding	ENST00000304094	1	930

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000116	0.394	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.596	187	165	1.13	0.00000899	2019
Missense in Polyphen		40	41.767	0.9577		595
Synonymous	-0.844	75	66.3	1.13	0.00000359	643
Loss of Function	0.0994	6	6.27	0.957	3.83e-7	82

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: 0.0905

Intolerance Scores

• loftool: 0.489
• rvis_EVS: 0.6
• rvis_percentile_EVS: 82.66

Haploinsufficiency Scores

• pHI: 0.0703
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.149

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Olfr43

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