OR4A47

olfactory receptor family 4 subfamily A member 47, the group of Olfactory receptors, family 4

Basic information

Region (hg38): 11:48488792-48489722

Links

ENSG00000237388 ∙ NCBI:403253 ∙ ∙ HGNC:31266 ∙ Uniprot:Q6IF82 ∙ 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 OR4A47 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR4A47 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			18	1		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	1	0

Variants in OR4A47

This is a list of pathogenic ClinVar variants found in the OR4A47 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-48488827-T-C		not specified	Uncertain significance (May 15, 2024)
11-48488865-C-A		not specified	Uncertain significance (Jan 27, 2022)
11-48488883-C-T			Likely benign (Feb 01, 2023)
11-48488911-A-G		not specified	Uncertain significance (Jul 21, 2021)
11-48488947-C-A		not specified	Uncertain significance (Apr 04, 2024)
11-48488962-T-C		not specified	Uncertain significance (Jan 09, 2024)
11-48489021-C-T		not specified	Uncertain significance (Apr 09, 2022)
11-48489064-C-T		not specified	Uncertain significance (Feb 27, 2023)
11-48489075-T-C		not specified	Uncertain significance (Apr 24, 2024)
11-48489205-T-C		not specified	Uncertain significance (Apr 25, 2023)
11-48489364-A-G		not specified	Uncertain significance (Apr 04, 2024)
11-48489456-T-C		not specified	Uncertain significance (Nov 17, 2022)
11-48489468-C-T		not specified	Uncertain significance (Sep 01, 2021)
11-48489480-G-C		not specified	Uncertain significance (Mar 04, 2024)
11-48489493-C-A		not specified	Uncertain significance (Apr 28, 2022)
11-48489499-C-T		not specified	Uncertain significance (Jun 30, 2023)
11-48489505-G-A		not specified	Uncertain significance (Aug 28, 2023)
11-48489554-T-A		not specified	Uncertain significance (Oct 14, 2023)
11-48489558-T-C		not specified	Uncertain significance (Oct 10, 2023)
11-48489559-A-C		not specified	Uncertain significance (May 16, 2023)
11-48489622-C-G		not specified	Uncertain significance (Jun 05, 2023)
11-48489627-A-G		not specified	Uncertain significance (Oct 04, 2022)
11-48489718-C-T		not specified	Uncertain significance (Mar 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR4A47	protein_coding	protein_coding	ENST00000446524	1	1064

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.31e-8	0.0475	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.71	249	154	1.61	0.00000695	2009
Missense in Polyphen		74	42.538	1.7396		625
Synonymous	-3.95	99	60.0	1.65	0.00000286	624
Loss of Function	-1.24	9	5.79	1.55	2.42e-7	97

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: 0.0867

Intolerance Scores

• loftool: 0.807
• rvis_EVS: 0.87
• rvis_percentile_EVS: 88.82

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.131

Essentials

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

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Olfr1256

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