OR5D16

olfactory receptor family 5 subfamily D member 16, the group of Olfactory receptors, family 5

Basic information

Region (hg38): 11:55838752-55839738

Links

ENSG00000205029 ∙ NCBI:390144 ∙ ∙ HGNC:15283 ∙ Uniprot:Q8NGK9 ∙ 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 OR5D16 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR5D16 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			19	4		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	4	0

Variants in OR5D16

This is a list of pathogenic ClinVar variants found in the OR5D16 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-55838863-G-A		not specified	Likely benign (May 23, 2023)
11-55838883-T-A		not specified	Uncertain significance (Feb 17, 2024)
11-55838884-C-G		not specified	Uncertain significance (May 23, 2023)
11-55838920-T-A		not specified	Uncertain significance (Dec 13, 2023)
11-55838930-C-G		not specified	Uncertain significance (Aug 17, 2021)
11-55838975-A-G		not specified	Uncertain significance (Mar 16, 2024)
11-55839066-C-A		not specified	Likely benign (Aug 12, 2021)
11-55839079-G-T		not specified	Uncertain significance (Dec 21, 2022)
11-55839128-T-A		not specified	Uncertain significance (Dec 21, 2022)
11-55839184-A-G		not specified	Uncertain significance (Dec 17, 2023)
11-55839235-G-A		not specified	Likely benign (Dec 21, 2021)
11-55839236-C-T		not specified	Uncertain significance (Oct 29, 2021)
11-55839300-A-T		not specified	Uncertain significance (Jul 27, 2023)
11-55839304-T-C		not specified	Uncertain significance (Jun 18, 2021)
11-55839316-C-G		not specified	Uncertain significance (Mar 13, 2023)
11-55839322-T-C		not specified	Uncertain significance (Aug 03, 2022)
11-55839359-C-G		not specified	Uncertain significance (Feb 07, 2023)
11-55839394-A-G		not specified	Uncertain significance (May 10, 2024)
11-55839461-G-A		not specified	Likely benign (Oct 25, 2023)
11-55839529-C-T		not specified	Uncertain significance (Oct 25, 2022)
11-55839562-C-A		not specified	Uncertain significance (Jul 14, 2021)
11-55839593-C-G		not specified	Uncertain significance (Jan 30, 2024)
11-55839595-G-A		not specified	Uncertain significance (Jul 19, 2023)
11-55839598-G-T		not specified	Uncertain significance (Sep 01, 2021)
11-55839662-G-A		not specified	Uncertain significance (Jun 17, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR5D16	protein_coding	protein_coding	ENST00000378396	1	987

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.61	228	169	1.35	0.00000797	2149
Missense in Polyphen		59	45.954	1.2839		672
Synonymous	-1.30	84	70.2	1.20	0.00000362	673
Loss of Function

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish
East Asian
Finnish
European (Non-Finnish)
Middle Eastern
South Asian
Other

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: 0.777
• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.54

Haploinsufficiency Scores

• pHI: 0.0763
• hipred: N
• hipred_score: 0.131

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0588

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Olfr1155

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