OR4D10

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

Basic information

Region (hg38): 11:59473314-59479361

Previous symbols: [ "OR4D10P" ]

Links

ENSG00000254466 ∙ NCBI:390197 ∙ ∙ HGNC:15173 ∙ Uniprot:Q8NGI6 ∙ 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 OR4D10 gene.

• Inborn genetic diseases (17 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR4D10 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			14	3		17
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	4	0

Variants in OR4D10

This is a list of pathogenic ClinVar variants found in the OR4D10 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-59477460-G-A		not specified	Uncertain significance (Sep 20, 2023)
11-59477471-C-T			Likely benign (Aug 01, 2022)
11-59477472-C-T		not specified	Uncertain significance (Jul 15, 2021)
11-59477490-C-T		not specified	Likely benign (Aug 17, 2022)
11-59477491-G-A		not specified	Likely benign (May 18, 2022)
11-59477554-A-G		not specified	Uncertain significance (May 04, 2022)
11-59477584-A-C		not specified	Uncertain significance (Jun 07, 2023)
11-59477599-C-T		not specified	Uncertain significance (Nov 18, 2022)
11-59477619-C-T		not specified	Uncertain significance (Dec 19, 2022)
11-59477620-A-G		not specified	Likely benign (Dec 28, 2022)
11-59477730-A-G		not specified	Uncertain significance (Sep 14, 2023)
11-59477740-T-A		not specified	Uncertain significance (Jun 07, 2023)
11-59477745-C-T		not specified	Uncertain significance (Jan 30, 2024)
11-59477748-A-C		not specified	Likely benign (Jan 03, 2024)
11-59477783-G-A		not specified	Uncertain significance (Jan 30, 2024)
11-59477919-C-T		not specified	Uncertain significance (Jan 30, 2024)
11-59477929-C-G		not specified	Uncertain significance (Feb 11, 2022)
11-59477941-C-A		not specified	Uncertain significance (Jun 27, 2022)
11-59477989-T-C		not specified	Uncertain significance (Sep 17, 2021)
11-59477997-A-G		not specified	Uncertain significance (Jun 29, 2023)
11-59478012-C-T		not specified	Uncertain significance (Dec 15, 2023)
11-59478026-G-T		not specified	Uncertain significance (Oct 29, 2021)
11-59478049-C-A		not specified	Uncertain significance (Aug 22, 2023)
11-59478112-A-C		not specified	Uncertain significance (May 30, 2023)
11-59478145-C-T		not specified	Uncertain significance (Jan 03, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR4D10	protein_coding	protein_coding	ENST00000530162	1	1024

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00391	0.661	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.569	188	167	1.12	0.00000855	1997
Missense in Polyphen		42	40.927	1.0262		568
Synonymous	-0.933	80	70.1	1.14	0.00000361	672
Loss of Function	0.583	4	5.47	0.731	2.96e-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: 0.578
• rvis_EVS: -0.34
• rvis_percentile_EVS: 30.56

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.146
• ghis: 0.423

Essentials

• essential_gene_CRISPR2: N
• 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: Olfr1426

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