OR13A1

olfactory receptor family 13 subfamily A member 1, the group of Olfactory receptors, family 13

Basic information

Region (hg38): 10:45302298-45315608

Links

ENSG00000256574 ∙ NCBI:79290 ∙ ∙ HGNC:14772 ∙ Uniprot:Q8NGR1 ∙ 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 OR13A1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR13A1 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
missense			28	1		29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	2	0

Variants in OR13A1

This is a list of pathogenic ClinVar variants found in the OR13A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-45303485-T-C		not specified	Uncertain significance (Mar 28, 2023)
10-45303508-G-A			Likely benign (Jun 01, 2022)
10-45303557-C-T		not specified	Uncertain significance (Jul 26, 2022)
10-45303596-G-A		not specified	Uncertain significance (Mar 16, 2022)
10-45303606-C-T		not specified	Uncertain significance (Apr 17, 2023)
10-45303609-C-T		not specified	Uncertain significance (Jun 02, 2023)
10-45303641-G-A		not specified	Uncertain significance (Oct 12, 2021)
10-45303651-T-C		not specified	Uncertain significance (Feb 07, 2023)
10-45303687-C-A		not specified	Uncertain significance (Oct 26, 2021)
10-45303693-G-C		not specified	Uncertain significance (Oct 10, 2023)
10-45303716-T-C		not specified	Uncertain significance (Nov 10, 2022)
10-45303754-G-T		not specified	Uncertain significance (Jan 02, 2024)
10-45303764-G-T		not specified	Uncertain significance (Nov 29, 2023)
10-45303854-T-C		not specified	Uncertain significance (Jun 02, 2023)
10-45303864-A-C		not specified	Uncertain significance (Nov 18, 2022)
10-45303881-A-T		not specified	Uncertain significance (Jun 26, 2023)
10-45303904-G-T		not specified	Uncertain significance (Mar 14, 2023)
10-45303927-C-A		not specified	Uncertain significance (May 28, 2024)
10-45303932-G-A		not specified	Uncertain significance (Aug 08, 2023)
10-45303942-C-T		not specified	Uncertain significance (May 15, 2024)
10-45303945-T-C		not specified	Uncertain significance (Jun 03, 2022)
10-45304082-C-A		not specified	Uncertain significance (Jul 17, 2023)
10-45304112-A-C		not specified	Uncertain significance (Sep 14, 2023)
10-45304194-T-C		not specified	Uncertain significance (Apr 26, 2023)
10-45304200-C-T		not specified	Likely benign (Nov 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR13A1	protein_coding	protein_coding	ENST00000553795	1	12955

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00157	0.705	118369	154	7224	125747	0.0298

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.10	243	199	1.22	0.0000115	2145
Missense in Polyphen		63	42.715	1.4749		591
Synonymous	-2.53	126	94.7	1.33	0.00000688	676
Loss of Function	0.780	5	7.27	0.688	3.08e-7	87

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0780	0.0778
Ashkenazi Jewish	0.0673	0.0681
East Asian	0.000163	0.000163
Finnish	0.0254	0.0254
European (Non-Finnish)	0.0352	0.0349
Middle Eastern	0.000163	0.000163
South Asian	0.0122	0.0121
Other	0.0426	0.0426

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)

Intolerance Scores

• loftool: 0.560
• rvis_EVS: 0.38
• rvis_percentile_EVS: 75.51

Haploinsufficiency Scores

• pHI: 0.149
• hipred: N
• hipred_score: 0.170
• ghis: 0.394

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.115

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Olfr211

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