OR1D5

olfactory receptor family 1 subfamily D member 5, the group of Olfactory receptors, family 1

Basic information

Region (hg38): 17:3062669-3063607

Links

ENSG00000262628 ∙ NCBI:8386 ∙ ∙ HGNC:8186 ∙ Uniprot:P58170 ∙ 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 OR1D5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR1D5 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			24	1		25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	2	0

Variants in OR1D5

This is a list of pathogenic ClinVar variants found in the OR1D5 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-3062703-C-T		not specified	Uncertain significance (Aug 10, 2021)
17-3062708-C-T			Likely benign (Jul 01, 2022)
17-3062800-C-T		not specified	Uncertain significance (Dec 18, 2023)
17-3062801-C-A		not specified	Uncertain significance (Dec 18, 2023)
17-3062821-G-A		not specified	Uncertain significance (Nov 14, 2023)
17-3062845-G-A		not specified	Uncertain significance (Jun 23, 2023)
17-3062847-G-C		not specified	Uncertain significance (Sep 14, 2021)
17-3062875-A-T		not specified	Uncertain significance (Dec 20, 2023)
17-3062877-T-C		not specified	Uncertain significance (Dec 13, 2023)
17-3062892-G-C		not specified	Uncertain significance (Mar 25, 2024)
17-3062949-C-T		not specified	Uncertain significance (Aug 12, 2021)
17-3062959-A-G		not specified	Uncertain significance (Jun 07, 2024)
17-3062962-T-C		not specified	Uncertain significance (Dec 12, 2023)
17-3063009-A-G		not specified	Uncertain significance (Jan 07, 2022)
17-3063049-G-C		not specified	Uncertain significance (Apr 06, 2024)
17-3063057-A-G		not specified	Uncertain significance (Jan 04, 2024)
17-3063060-A-G		not specified	Uncertain significance (Jan 30, 2024)
17-3063083-G-T		not specified	Uncertain significance (Oct 25, 2022)
17-3063093-C-T		not specified	Uncertain significance (Jul 12, 2022)
17-3063153-G-A		not specified	Uncertain significance (May 11, 2022)
17-3063167-C-G		not specified	Uncertain significance (Apr 24, 2024)
17-3063252-G-A		not specified	Uncertain significance (Sep 01, 2021)
17-3063259-C-T		not specified	Likely benign (Nov 30, 2022)
17-3063381-T-C		not specified	Uncertain significance (Oct 26, 2022)
17-3063447-T-C		not specified	Likely benign (Apr 17, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR1D5	protein_coding	protein_coding	ENST00000575751	1	939

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0248	0.793	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.182	165	159	1.04	0.00000777	1977
Missense in Polyphen		63	54.631	1.1532		763
Synonymous	-0.834	76	67.3	1.13	0.00000327	638
Loss of Function	0.991	3	5.51	0.544	2.34e-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;GPCRs, Class A Rhodopsin-like;Signaling by GPCR;Signal Transduction;Olfactory Signaling Pathway;G alpha (s) signalling events;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.0846

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.255

Essentials

• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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