OR2C3

olfactory receptor family 2 subfamily C member 3, the group of Olfactory receptors, family 2

Basic information

Region (hg38): 1:247524677-247536440

Previous symbols: [ "OR2C4", "OR2C5P" ]

Links

ENSG00000196242 ∙ NCBI:81472 ∙ ∙ HGNC:15005 ∙ Uniprot:Q8N628 ∙ 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 OR2C3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR2C3 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			16
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	0	0

Variants in OR2C3

This is a list of pathogenic ClinVar variants found in the OR2C3 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-247531599-T-C		not specified	Uncertain significance (Mar 29, 2023)
1-247531604-C-T		not specified	Uncertain significance (Jan 26, 2022)
1-247531605-G-A		not specified	Uncertain significance (Nov 03, 2023)
1-247531658-G-A		not specified	Uncertain significance (Dec 15, 2023)
1-247531661-G-T		not specified	Uncertain significance (Sep 29, 2022)
1-247531772-G-A		not specified	Uncertain significance (Dec 27, 2023)
1-247531904-G-C		not specified	Uncertain significance (Jun 06, 2023)
1-247531932-T-C		not specified	Uncertain significance (Dec 20, 2023)
1-247532027-G-C		not specified	Uncertain significance (Mar 07, 2023)
1-247532052-G-C		not specified	Uncertain significance (Oct 22, 2021)
1-247532144-C-T		not specified	Uncertain significance (Sep 25, 2023)
1-247532285-G-T		not specified	Uncertain significance (Mar 19, 2024)
1-247532342-T-C		not specified	Uncertain significance (Apr 12, 2023)
1-247532423-A-T		not specified	Uncertain significance (Jan 10, 2022)
1-247532424-T-C		not specified	Uncertain significance (Dec 17, 2023)
1-247532466-G-C		not specified	Uncertain significance (Mar 19, 2024)
1-247532493-C-T		not specified	Uncertain significance (Dec 16, 2023)
1-247532505-C-T		not specified	Uncertain significance (Sep 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR2C3	protein_coding	protein_coding	ENST00000366487	1	3708

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00595	0.747	125643	0	105	125748	0.000418

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0221	187	186	1.00	0.0000103	2086
Missense in Polyphen		50	48.792	1.0248		608
Synonymous	-1.18	95	81.4	1.17	0.00000502	690
Loss of Function	0.839	4	6.27	0.638	3.67e-7	62

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000547	0.000546
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.000508	0.000508
European (Non-Finnish)	0.000686	0.000686
Middle Eastern	0.000163	0.000163
South Asian	0.0000654	0.0000653
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: 0.840
• rvis_EVS: 0.93
• rvis_percentile_EVS: 89.79

Haploinsufficiency Scores

• pHI: 0.0909
• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0939

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;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