OR5A1

olfactory receptor family 5 subfamily A member 1, the group of Olfactory receptors, family 5

Basic information

Region (hg38): 11:59436469-59451380

Previous symbols: [ "OR5A1P" ]

Links

ENSG00000172320 ∙ NCBI:219982 ∙ ∙ HGNC:8319 ∙ Uniprot:Q8NGJ0 ∙ 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 OR5A1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR5A1 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			16		1	17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	0	1

Variants in OR5A1

This is a list of pathogenic ClinVar variants found in the OR5A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-59443173-C-T		not specified	Uncertain significance (Jul 26, 2021)
11-59443202-G-T		not specified	Uncertain significance (Feb 17, 2024)
11-59443205-A-G		not specified	Uncertain significance (Aug 26, 2024)
11-59443303-C-A		not specified	Uncertain significance (Mar 06, 2023)
11-59443335-C-T		not specified	Uncertain significance (Mar 25, 2024)
11-59443398-C-T		not specified	Uncertain significance (Sep 09, 2024)
11-59443407-T-C		not specified	Uncertain significance (Sep 29, 2023)
11-59443449-C-T		not specified	Uncertain significance (Jun 23, 2021)
11-59443583-A-G		not specified	Uncertain significance (Nov 08, 2024)
11-59443604-C-T		not specified	Uncertain significance (Aug 09, 2021)
11-59443628-G-T		not specified	Uncertain significance (Mar 18, 2024)
11-59443629-G-A		not specified	Uncertain significance (Dec 13, 2022)
11-59443638-T-C		not specified	Uncertain significance (Jun 03, 2022)
11-59443678-C-G		not specified	Uncertain significance (Jan 24, 2024)
11-59443715-G-A			Benign (Jul 15, 2020)
11-59443761-G-A		not specified	Uncertain significance (Dec 01, 2022)
11-59443796-G-A		not specified	Uncertain significance (Oct 11, 2024)
11-59443830-A-G		not specified	Uncertain significance (Aug 17, 2022)
11-59443878-G-A		not specified	Uncertain significance (May 08, 2023)
11-59443896-C-T		not specified	Uncertain significance (Oct 05, 2023)
11-59444022-T-A		not specified	Uncertain significance (Sep 25, 2023)
11-59444061-A-G		not specified	Uncertain significance (Mar 25, 2024)
11-59444088-T-C		not specified	Uncertain significance (Mar 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR5A1	protein_coding	protein_coding	ENST00000302030	1	1051

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000880	0.333	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.801	192	163	1.18	0.00000858	2037
Missense in Polyphen		58	46.665	1.2429		631
Synonymous	-1.45	85	69.6	1.22	0.00000398	672
Loss of Function	0.203	8	8.64	0.926	6.44e-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;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: 0.843
• rvis_EVS: 0.93
• rvis_percentile_EVS: 89.79

Haploinsufficiency Scores

• pHI: 0.153
• hipred: N
• hipred_score: 0.170

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.151

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Olfr76

Gene ontology

• Biological process: G protein-coupled receptor signaling pathway;sensory perception of smell;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;odorant binding