OR52A5

olfactory receptor family 52 subfamily A member 5, the group of Olfactory receptors, family 52

Basic information

Region (hg38): 11:5128776-5138356

Links

ENSG00000171944 ∙ NCBI:390054 ∙ ∙ HGNC:19580 ∙ Uniprot:Q9H2C5 ∙ 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 OR52A5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR52A5 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			21			21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	0	0

Variants in OR52A5

This is a list of pathogenic ClinVar variants found in the OR52A5 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-5131696-G-A		not specified	Uncertain significance (Oct 26, 2021)
11-5131753-A-C		not specified	Uncertain significance (Jan 27, 2022)
11-5131805-A-T		not specified	Uncertain significance (Jun 07, 2024)
11-5131811-G-T		not specified	Uncertain significance (Sep 20, 2023)
11-5131831-A-G		not specified	Uncertain significance (Jan 31, 2023)
11-5131867-A-G		not specified	Uncertain significance (Apr 12, 2022)
11-5131868-A-C		not specified	Uncertain significance (Apr 12, 2022)
11-5131889-G-C		not specified	Uncertain significance (Dec 03, 2021)
11-5131953-C-A		not specified	Uncertain significance (Nov 18, 2022)
11-5132036-G-T		not specified	Uncertain significance (May 04, 2022)
11-5132041-T-C		not specified	Uncertain significance (Dec 28, 2022)
11-5132075-G-C		not specified	Uncertain significance (Jan 09, 2024)
11-5132081-C-T		not specified	Uncertain significance (Jan 22, 2024)
11-5132089-A-C		not specified	Uncertain significance (Jun 17, 2024)
11-5132209-T-C		not specified	Uncertain significance (Oct 12, 2021)
11-5132273-G-A		not specified	Uncertain significance (Jul 09, 2021)
11-5132322-G-C		not specified	Uncertain significance (Dec 08, 2023)
11-5132419-A-C		not specified	Uncertain significance (Mar 25, 2024)
11-5132470-T-C		not specified	Uncertain significance (Dec 18, 2023)
11-5132535-C-T		not specified	Uncertain significance (Mar 23, 2023)
11-5132582-C-T		not specified	Uncertain significance (May 04, 2022)
11-5132590-C-A		not specified	Uncertain significance (May 04, 2022)
11-5132620-A-G		not specified	Uncertain significance (Feb 05, 2024)
11-5132629-T-C		not specified	Uncertain significance (Jan 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR52A5	protein_coding	protein_coding	ENST00000307388	1	951

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000691	0.295	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.877	202	170	1.19	0.00000796	2074
Missense in Polyphen		57	45.193	1.2612		633
Synonymous	0.449	58	62.5	0.928	0.00000301	645
Loss of Function	0.102	8	8.32	0.962	6.02e-7	83

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: 0.0972

Intolerance Scores

• loftool: 0.895
• rvis_EVS: 1.24
• rvis_percentile_EVS: 93.35

Haploinsufficiency Scores

• pHI: 0.0492
• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.119

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Olfr69

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