OR10A4

olfactory receptor family 10 subfamily A member 4, the group of Olfactory receptors, family 10

Basic information

Region (hg38): 11:6876625-6877619

Previous symbols: [ "OR10A4P" ]

Links

ENSG00000170782 ∙ NCBI:283297 ∙ ∙ HGNC:15130 ∙ Uniprot:Q9H209 ∙ 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 OR10A4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR10A4 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			14		2	16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	0	2

Variants in OR10A4

This is a list of pathogenic ClinVar variants found in the OR10A4 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-6876685-T-C		not specified	Uncertain significance (Jun 17, 2024)
11-6876759-G-A		not specified	Uncertain significance (Feb 07, 2023)
11-6876958-T-C		not specified	Uncertain significance (Jan 10, 2022)
11-6877119-A-G		not specified	Uncertain significance (Jun 05, 2023)
11-6877181-C-G		not specified	Uncertain significance (Jan 23, 2024)
11-6877204-T-C		not specified	Uncertain significance (Dec 17, 2023)
11-6877272-C-G		not specified	Uncertain significance (Dec 27, 2023)
11-6877273-T-A		not specified	Uncertain significance (Apr 23, 2024)
11-6877283-C-A		not specified	Uncertain significance (Jan 30, 2024)
11-6877325-C-G		not specified	Uncertain significance (Nov 01, 2022)
11-6877383-C-T			Benign (Jun 01, 2018)
11-6877395-T-C		not specified	Uncertain significance (Jan 09, 2024)
11-6877473-T-C		not specified	Uncertain significance (Mar 28, 2024)
11-6877513-T-G		not specified	Uncertain significance (Jan 23, 2023)
11-6877522-G-C		not specified	Uncertain significance (Mar 30, 2024)
11-6877540-T-C		not specified	Uncertain significance (Feb 28, 2023)
11-6877545-G-C		not specified	Uncertain significance (Jul 05, 2022)
11-6877558-G-A			Benign (Apr 04, 2018)
11-6877573-C-A		not specified	Uncertain significance (Jul 30, 2023)
11-6877590-C-G		not specified	Uncertain significance (Jan 04, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR10A4	protein_coding	protein_coding	ENST00000379829	1	995

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000168	0.263	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.19	206	163	1.26	0.00000791	2046
Missense in Polyphen		59	47.082	1.2531		712
Synonymous	-0.568	74	68.0	1.09	0.00000345	679
Loss of Function	-0.149	7	6.59	1.06	3.65e-7	79

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 (Potential). May be involved in taste perception. {ECO:0000305}.
• Pathway: Olfactory transduction - Homo sapiens (human);Olfactory receptor activity;GPCRs, Class A Rhodopsin-like;Signaling by GPCR;Signal Transduction;Olfactory Signaling Pathway;G alpha (s) signalling events;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.169

Intolerance Scores

• loftool: 0.751
• rvis_EVS: 2.02
• rvis_percentile_EVS: 97.71

Haploinsufficiency Scores

• pHI: 0.315
• hipred: N
• hipred_score: 0.170

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0820

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Olfr17
• Phenotype: respiratory system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); growth/size/body region phenotype; taste/olfaction phenotype; craniofacial phenotype; cellular phenotype

Gene ontology

• Biological process: G protein-coupled receptor signaling pathway;axon guidance;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