OR52A1

olfactory receptor family 52 subfamily A member 1, the group of Olfactory receptors, family 52

Basic information

Region (hg38): 11:5146823-5154757

Links

ENSG00000182070 ∙ NCBI:23538 ∙ ∙ HGNC:8318 ∙ Uniprot:Q9UKL2 ∙ 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 OR52A1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR52A1 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			22			22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	0	0

Variants in OR52A1

This is a list of pathogenic ClinVar variants found in the OR52A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-5151463-G-A		not specified	Uncertain significance (Jan 30, 2024)
11-5151508-G-A		not specified	Uncertain significance (Feb 28, 2024)
11-5151511-G-C		not specified	Uncertain significance (Oct 27, 2022)
11-5151538-G-C		not specified	Uncertain significance (Dec 22, 2023)
11-5151549-T-C		not specified	Uncertain significance (Jan 22, 2024)
11-5151550-A-G		not specified	Uncertain significance (May 28, 2024)
11-5151598-C-T		not specified	Uncertain significance (Jan 10, 2022)
11-5151624-C-T		not specified	Uncertain significance (Apr 08, 2022)
11-5151634-C-A		not specified	Uncertain significance (Feb 03, 2022)
11-5151636-A-G		not specified	Uncertain significance (Oct 10, 2023)
11-5151645-T-C		not specified	Uncertain significance (Nov 17, 2023)
11-5151678-A-G		not specified	Uncertain significance (Mar 26, 2024)
11-5151763-A-T		not specified	Uncertain significance (Mar 06, 2023)
11-5151802-G-C		not specified	Uncertain significance (Jun 02, 2023)
11-5151816-A-G		not specified	Uncertain significance (Apr 08, 2024)
11-5151849-G-T		not specified	Uncertain significance (Apr 13, 2022)
11-5151868-G-A		not specified	Uncertain significance (Dec 28, 2022)
11-5152095-G-A		not specified	Uncertain significance (Mar 18, 2024)
11-5152104-A-C		not specified	Uncertain significance (Jan 29, 2024)
11-5152114-T-C		not specified	Uncertain significance (Sep 16, 2021)
11-5152149-G-A		not specified	Uncertain significance (Sep 20, 2023)
11-5152167-A-G		not specified	Uncertain significance (Jul 17, 2023)
11-5152168-G-C		not specified	Uncertain significance (Oct 25, 2023)
11-5152195-C-T		not specified	Uncertain significance (Mar 14, 2023)
11-5152237-A-C		not specified	Uncertain significance (Mar 25, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR52A1	protein_coding	protein_coding	ENST00000380367	1	35374

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00413	0.673	125715	1	17	125733	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.277	179	169	1.06	0.00000812	2062
Missense in Polyphen		34	35.563	0.95605		531
Synonymous	-0.432	64	59.8	1.07	0.00000265	634
Loss of Function	0.617	4	5.57	0.718	2.35e-7	79

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000247	0.000246
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000616	0.0000615
Middle Eastern	0.000163	0.000163
South Asian	0.000131	0.0000980
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: 0.0883

Intolerance Scores

• loftool: 0.676
• rvis_EVS: 0.55
• rvis_percentile_EVS: 81.48

Haploinsufficiency Scores

• pHI: 0.0622
• hipred: N
• hipred_score: 0.146
• ghis: 0.413

Essentials

• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.160

Gene Damage Prediction

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

Gene ontology

• Biological process: signal transduction;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 plasma membrane
• Molecular function: transmembrane signaling receptor activity;G protein-coupled receptor activity;olfactory receptor activity