OR52D1

olfactory receptor family 52 subfamily D member 1, the group of Olfactory receptors, family 52

Basic information

Region (hg38): 11:5488685-5489749

Links

ENSG00000181609 ∙ NCBI:390066 ∙ ∙ HGNC:15212 ∙ Uniprot:Q9H346 ∙ 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 OR52D1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR52D1 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	2		17
nonsense						0
start loss						0
frameshift						0
inframe indel				1		1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	3	0

Variants in OR52D1

This is a list of pathogenic ClinVar variants found in the OR52D1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-5488887-C-A		not specified	Uncertain significance (Oct 04, 2024)
11-5488890-A-G		not specified	Uncertain significance (Sep 09, 2024)
11-5488927-T-C		not specified	Uncertain significance (Sep 13, 2023)
11-5488988-G-T		not specified	Uncertain significance (Mar 06, 2023)
11-5489008-T-C		not specified	Uncertain significance (Dec 20, 2023)
11-5489023-G-A		not specified	Uncertain significance (Dec 01, 2022)
11-5489034-A-G		not specified	Uncertain significance (Aug 28, 2024)
11-5489127-C-T		not specified	Uncertain significance (Dec 07, 2022)
11-5489188-C-T		not specified	Uncertain significance (May 15, 2023)
11-5489209-G-A		not specified	Likely benign (Jan 30, 2024)
11-5489229-C-T		not specified	Uncertain significance (Aug 02, 2021)
11-5489245-C-A		not specified	Uncertain significance (Jun 19, 2024)
11-5489247-T-A		not specified	Uncertain significance (Nov 09, 2022)
11-5489253-G-A		not specified	Uncertain significance (Jan 09, 2024)
11-5489290-T-G		not specified	Uncertain significance (Dec 28, 2022)
11-5489331-G-T		not specified	Uncertain significance (Dec 09, 2024)
11-5489358-G-A		not specified	Uncertain significance (Sep 03, 2024)
11-5489395-A-G		not specified	Likely benign (Jul 06, 2021)
11-5489468-C-G		not specified	Uncertain significance (Feb 28, 2024)
11-5489479-CCTT-C			Likely benign (Jan 01, 2023)
11-5489517-G-A		not specified	Uncertain significance (Jan 19, 2024)
11-5489518-A-C		not specified	Uncertain significance (Oct 27, 2023)
11-5489602-G-A		not specified	Uncertain significance (Aug 21, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR52D1	protein_coding	protein_coding	ENST00000322641	1	1065

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000556	0.483	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.04	208	170	1.22	0.00000828	2056
Missense in Polyphen		85	64.976	1.3082		834
Synonymous	-0.897	74	64.8	1.14	0.00000297	701
Loss of Function	0.201	5	5.51	0.908	4.06e-7	61

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: 0.705
• rvis_EVS: 0.55
• rvis_percentile_EVS: 81.55

Haploinsufficiency Scores

• pHI: 0.215
• hipred: N
• hipred_score: 0.144

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0197

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Olfr646

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