OR5D13

olfactory receptor family 5 subfamily D member 13, the group of Olfactory receptors, family 5

Basic information

Region (hg38): 11:55773438-55774382

Links

ENSG00000279761 ∙ NCBI:390142 ∙ ∙ HGNC:15280 ∙ Uniprot:Q8NGL4 ∙ 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 OR5D13 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR5D13 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			16	1		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	16	1	0

Variants in OR5D13

This is a list of pathogenic ClinVar variants found in the OR5D13 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-55773529-T-G		not specified	Uncertain significance (Aug 21, 2023)
11-55773541-T-C		not specified	Likely benign (Apr 19, 2023)
11-55773546-T-C		not specified	Uncertain significance (Mar 25, 2024)
11-55773598-A-G		not specified	Uncertain significance (Apr 19, 2023)
11-55773630-C-T		not specified	Uncertain significance (May 23, 2024)
11-55773679-C-G		not specified	Uncertain significance (Jun 28, 2022)
11-55773679-C-T		not specified	Uncertain significance (Jul 06, 2021)
11-55773694-A-G		not specified	Uncertain significance (Jun 13, 2024)
11-55773766-G-C		not specified	Uncertain significance (Aug 12, 2021)
11-55773778-C-T		not specified	Uncertain significance (Mar 30, 2024)
11-55773790-C-T		not specified	Uncertain significance (Oct 06, 2021)
11-55773807-C-G		not specified	Uncertain significance (May 23, 2023)
11-55773861-C-T		not specified	Uncertain significance (May 25, 2022)
11-55773898-G-A		not specified	Uncertain significance (Jan 23, 2023)
11-55774006-C-T		not specified	Uncertain significance (Feb 06, 2024)
11-55774033-G-A		not specified	Uncertain significance (Feb 28, 2023)
11-55774041-T-A		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
11-55774059-A-T		not specified	Uncertain significance (Dec 21, 2022)
11-55774209-C-T		not specified	Uncertain significance (Jun 28, 2022)
11-55774253-A-G		not specified	Uncertain significance (Aug 16, 2022)
11-55774281-G-A		not specified	Uncertain significance (Jun 01, 2023)
11-55774300-A-G		not specified	Uncertain significance (Apr 01, 2024)
11-55774329-G-A		not specified	Uncertain significance (Mar 29, 2023)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Odorant receptor. {ECO:0000305}.
• Pathway: Olfactory transduction - Homo sapiens (human);Signaling by GPCR;Signal Transduction;Olfactory Signaling Pathway;G alpha (s) signalling events;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.0875

Intolerance Scores

• loftool: 0.744
• rvis_EVS: 0.95
• rvis_percentile_EVS: 90.01

Haploinsufficiency Scores

• pHI: 0.0559
• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00576

Gene Damage Prediction

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

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;odorant binding