OR4D6

olfactory receptor family 4 subfamily D member 6, the group of Olfactory receptors, family 4

Basic information

Region (hg38): 11:59456960-59457905

Links

ENSG00000166884 ∙ NCBI:219983 ∙ ∙ HGNC:15175 ∙ Uniprot:Q8NGJ1 ∙ 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 OR4D6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR4D6 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			20	2		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	20	2	0

Variants in OR4D6

This is a list of pathogenic ClinVar variants found in the OR4D6 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-59457015-C-T		not specified	Uncertain significance (Jun 30, 2022)
11-59457016-G-A		not specified	Likely benign (Dec 17, 2023)
11-59457082-G-A		not specified	Uncertain significance (Aug 16, 2021)
11-59457142-T-C		not specified	Uncertain significance (Mar 31, 2024)
11-59457151-G-A		not specified	Uncertain significance (May 23, 2023)
11-59457155-C-A		not specified	Uncertain significance (Feb 10, 2022)
11-59457155-C-G		not specified	Uncertain significance (Feb 28, 2024)
11-59457192-G-A		not specified	Uncertain significance (Jun 04, 2024)
11-59457208-T-C		not specified	Uncertain significance (Apr 08, 2024)
11-59457217-T-C		not specified	Uncertain significance (May 13, 2024)
11-59457244-A-G		not specified	Uncertain significance (Dec 13, 2022)
11-59457309-G-A		not specified	Uncertain significance (Jun 22, 2023)
11-59457338-C-G		not specified	Uncertain significance (Jun 03, 2022)
11-59457352-A-C		not specified	Uncertain significance (Aug 10, 2023)
11-59457370-G-C		not specified	Uncertain significance (Jul 13, 2022)
11-59457378-G-A		not specified	Uncertain significance (Jun 03, 2022)
11-59457448-T-C		not specified	Uncertain significance (Apr 07, 2022)
11-59457450-C-T		not specified	Uncertain significance (Dec 27, 2023)
11-59457522-G-A		not specified	Uncertain significance (Jan 10, 2023)
11-59457534-A-G		not specified	Uncertain significance (Jun 11, 2024)
11-59457540-G-A		not specified	Uncertain significance (Dec 15, 2022)
11-59457567-A-G		not specified	Uncertain significance (Jul 06, 2022)
11-59457606-G-A		not specified	Uncertain significance (Sep 14, 2022)
11-59457651-G-A		not specified	Likely benign (Aug 15, 2023)
11-59457658-G-T		not specified	Uncertain significance (Jul 06, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR4D6	protein_coding	protein_coding	ENST00000300127	1	1054

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00509	0.716	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.203	179	172	1.04	0.00000924	2043
Missense in Polyphen		62	64.272	0.96465		827
Synonymous	-0.146	72	70.4	1.02	0.00000376	660
Loss of Function	0.744	4	5.96	0.671	3.41e-7	75

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: 0.748
• rvis_EVS: 2.89
• rvis_percentile_EVS: 99.14

Haploinsufficiency Scores

• pHI: 0.101
• hipred: N
• hipred_score: 0.144

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.000661

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Olfr1428

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