OR12D3

olfactory receptor family 12 subfamily D member 3, the group of Olfactory receptors, family 12

Basic information

Region (hg38): 6:29373422-29375291

Links

ENSG00000112462 ∙ NCBI:81797 ∙ ∙ HGNC:13963 ∙ Uniprot:Q9UGF7 ∙ 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 OR12D3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR12D3 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			17			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	17	0	0

Variants in OR12D3

This is a list of pathogenic ClinVar variants found in the OR12D3 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-29374410-T-A		not specified	Uncertain significance (Jun 27, 2022)
6-29374545-C-T		not specified	Uncertain significance (Apr 13, 2023)
6-29374593-A-G		not specified	Uncertain significance (Jan 23, 2023)
6-29374647-A-G		not specified	Uncertain significance (Jul 12, 2023)
6-29374719-G-T		not specified	Uncertain significance (Mar 20, 2024)
6-29374746-G-A		not specified	Uncertain significance (Jul 21, 2021)
6-29374746-G-T		not specified	Uncertain significance (Jul 06, 2022)
6-29374828-C-T		not specified	Uncertain significance (Jan 23, 2024)
6-29374830-T-C		not specified	Uncertain significance (Sep 07, 2022)
6-29374866-A-T		not specified	Uncertain significance (Mar 02, 2023)
6-29374873-A-G		not specified	Uncertain significance (Jul 13, 2021)
6-29374876-C-A		not specified	Uncertain significance (Dec 12, 2023)
6-29374886-C-T		not specified	Uncertain significance (Aug 17, 2021)
6-29375004-C-T		not specified	Uncertain significance (Dec 21, 2022)
6-29375029-G-A		not specified	Uncertain significance (May 26, 2023)
6-29375103-C-T		not specified	Uncertain significance (Sep 12, 2023)
6-29375119-T-C		not specified	Uncertain significance (Dec 20, 2021)
6-29375184-A-G		not specified	Uncertain significance (Apr 27, 2024)
6-29375283-T-G		not specified	Uncertain significance (Nov 09, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR12D3	protein_coding	protein_coding	ENST00000396806	1	1869

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00785	0.570	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.774	146	175	0.835	0.00000887	2081
Missense in Polyphen		28	40.034	0.6994		537
Synonymous	0.430	60	64.4	0.932	0.00000329	641
Loss of Function	0.165	3	3.32	0.902	1.39e-7	46

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: 0.0939

Intolerance Scores

• loftool: 0.818
• rvis_EVS: 0.22
• rvis_percentile_EVS: 68.13

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.170

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.113

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Olfr109

Gene ontology

• Biological process: G protein-coupled receptor signaling pathway;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