OR4C46

olfactory receptor family 4 subfamily C member 46, the group of Olfactory receptors, family 4

Basic information

Region (hg38): 11:54603069-54603998

Links

ENSG00000185926 ∙ NCBI:119749 ∙ OMIM:614273 ∙ HGNC:31271 ∙ Uniprot:A6NHA9 ∙ 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 OR4C46 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR4C46 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			47	3	2	52
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	47	3	2

Variants in OR4C46

This is a list of pathogenic ClinVar variants found in the OR4C46 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-54603080-C-T		not specified	Uncertain significance (Sep 12, 2023)
11-54603089-C-T			Likely benign (Dec 01, 2022)
11-54603094-C-G		not specified	Uncertain significance (Jun 10, 2024)
11-54603115-G-A		not specified	Uncertain significance (Nov 07, 2022)
11-54603130-G-A		not specified	Uncertain significance (May 17, 2023)
11-54603135-C-A		not specified	Uncertain significance (Jun 05, 2023)
11-54603136-T-C			Benign (Jun 26, 2018)
11-54603145-T-C		not specified	Uncertain significance (Mar 11, 2022)
11-54603155-G-A		not specified	Uncertain significance (Dec 02, 2021)
11-54603161-A-C		not specified	Uncertain significance (Mar 20, 2023)
11-54603179-T-C		not specified	Uncertain significance (Nov 10, 2021)
11-54603190-G-A		not specified	Uncertain significance (Jan 16, 2024)
11-54603223-G-T		not specified	Uncertain significance (Oct 05, 2023)
11-54603242-T-C		not specified	Uncertain significance (Jun 05, 2023)
11-54603251-C-A		not specified	Uncertain significance (Jul 26, 2022)
11-54603255-G-C		not specified	Uncertain significance (Aug 28, 2023)
11-54603334-G-T		not specified	Uncertain significance (Jan 04, 2024)
11-54603337-C-A		not specified	Uncertain significance (Dec 19, 2023)
11-54603406-G-A		not specified	Uncertain significance (Jun 24, 2022)
11-54603418-T-C		not specified	Likely benign (Jun 13, 2022)
11-54603424-A-T		not specified	Uncertain significance (Jan 11, 2023)
11-54603428-G-A		not specified	Uncertain significance (Jan 26, 2022)
11-54603430-G-A		not specified	Uncertain significance (Sep 21, 2023)
11-54603443-C-T		not specified	Uncertain significance (Jan 04, 2024)
11-54603470-A-C		not specified	Uncertain significance (Jun 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR4C46	protein_coding	protein_coding	ENST00000328188	1	930

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.52e-8	0.0151	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-5.54	354	158	2.24	0.00000720	2028
Missense in Polyphen		82	35.975	2.2793		563
Synonymous	-6.42	123	59.8	2.06	0.00000279	607
Loss of Function	-3.69	8	2.15	3.71	9.08e-8	37

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)

Intolerance Scores

• loftool: 0.910
• rvis_EVS: 1.47
• rvis_percentile_EVS: 95.28

Haploinsufficiency Scores

• pHI: 0.173
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Olfr1258

Gene ontology

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