OR4D1

olfactory receptor family 4 subfamily D member 1, the group of Olfactory receptors, family 4

Basic information

Region (hg38): 17:58148384-58159585

Previous symbols: [ "OR4D3" ]

Links

ENSG00000141194 ∙ NCBI:26689 ∙ ∙ HGNC:8293 ∙ Uniprot:Q15615 ∙ 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 OR4D1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR4D1 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			15	1		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	15	1	0

Variants in OR4D1

This is a list of pathogenic ClinVar variants found in the OR4D1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-58155251-T-C		not specified	Uncertain significance (Apr 25, 2023)
17-58155323-C-T		not specified	Uncertain significance (Dec 08, 2023)
17-58155412-C-A		not specified	Uncertain significance (Jan 24, 2023)
17-58155449-C-G		not specified	Uncertain significance (Sep 27, 2021)
17-58155479-G-A		not specified	Uncertain significance (Apr 28, 2022)
17-58155517-C-T		not specified	Uncertain significance (Apr 07, 2022)
17-58155518-G-A		not specified	Uncertain significance (Aug 02, 2023)
17-58155521-A-G		not specified	Uncertain significance (Jan 09, 2024)
17-58155537-G-T		not specified	Uncertain significance (Nov 17, 2022)
17-58155575-G-A		not specified	Uncertain significance (May 03, 2023)
17-58155604-G-C		not specified	Uncertain significance (Jan 30, 2024)
17-58155706-C-G		not specified	Uncertain significance (Nov 09, 2023)
17-58155726-T-A		not specified	Uncertain significance (Mar 29, 2022)
17-58155743-T-A		not specified	Uncertain significance (Sep 01, 2021)
17-58155938-T-A		not specified	Uncertain significance (Sep 14, 2022)
17-58156045-A-G		not specified	Uncertain significance (Jun 19, 2024)
17-58156079-G-A		not specified	Likely benign (Dec 16, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR4D1	protein_coding	protein_coding	ENST00000268912	1	1024

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000172	0.470	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.360	150	163	0.921	0.00000799	2008
Missense in Polyphen		47	46.48	1.0112		662
Synonymous	-0.191	68	66.0	1.03	0.00000325	656
Loss of Function	0.300	6	6.85	0.876	3.79e-7	78

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: 0.638
• rvis_EVS: 0.88
• rvis_percentile_EVS: 89.07

Haploinsufficiency Scores

• pHI: 0.153
• hipred: N
• hipred_score: 0.162
• ghis: 0.425

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.000341

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Olfr464

Gene ontology

• Biological process: G protein-coupled receptor signaling pathway;sensory perception of smell;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