OR5A2

olfactory receptor family 5 subfamily A member 2, the group of Olfactory receptors, family 5

Basic information

Region (hg38): 11:59416968-59426413

Links

ENSG00000172324 ∙ NCBI:219981 ∙ ∙ HGNC:15249 ∙ Uniprot:Q8NGI9 ∙ 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 OR5A2 gene.

• Inborn genetic diseases (11 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR5A2 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			9	2		11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	2	0

Variants in OR5A2

This is a list of pathogenic ClinVar variants found in the OR5A2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-59422012-G-C		not specified	Uncertain significance (Oct 26, 2021)
11-59422023-C-T		not specified	Likely benign (Dec 02, 2022)
11-59422092-G-C		not specified	Uncertain significance (Feb 05, 2024)
11-59422101-C-T		not specified	Likely benign (Oct 12, 2022)
11-59422199-A-G		not specified	Uncertain significance (Nov 30, 2022)
11-59422226-G-T		not specified	Uncertain significance (Dec 16, 2023)
11-59422234-G-T		not specified	Uncertain significance (Nov 09, 2023)
11-59422251-T-C		not specified	Uncertain significance (Feb 01, 2023)
11-59422308-G-A		not specified	Uncertain significance (Apr 06, 2023)
11-59422313-A-T		not specified	Uncertain significance (Apr 19, 2023)
11-59422322-G-C		not specified	Uncertain significance (Jan 30, 2024)
11-59422322-G-T		not specified	Uncertain significance (May 27, 2022)
11-59422388-G-A		not specified	Uncertain significance (Apr 22, 2022)
11-59422398-G-C		not specified	Uncertain significance (May 15, 2023)
11-59422407-G-A		not specified	Uncertain significance (Jul 14, 2021)
11-59422440-G-T		not specified	Uncertain significance (Jan 03, 2024)
11-59422703-G-C		not specified	Uncertain significance (Jun 29, 2022)
11-59422778-G-A		not specified	Uncertain significance (Dec 13, 2022)
11-59422866-T-C		not specified	Likely benign (Dec 15, 2023)
11-59422940-C-T		not specified	Uncertain significance (Oct 30, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR5A2	protein_coding	protein_coding	ENST00000302040	1	1034

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	0.0218	178	179	0.995	0.00000862	2141
Missense in Polyphen		62	52.258	1.1864		692
Synonymous	-0.394	75	70.8	1.06	0.00000376	668
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: 0.0979

Intolerance Scores

• loftool: 0.772
• rvis_EVS: 0.42
• rvis_percentile_EVS: 77.06

Haploinsufficiency Scores

• pHI: 0.0961
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0193

Gene Damage Prediction

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

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