OR2C1

olfactory receptor family 2 subfamily C member 1, the group of Olfactory receptors, family 2

Basic information

Region (hg38): 16:3355888-3357306

Previous symbols: [ "OR2C2P" ]

Links

ENSG00000168158 ∙ NCBI:4993 ∙ ∙ HGNC:8242 ∙ Uniprot:O95371 ∙ 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 OR2C1 gene.

• Inborn genetic diseases (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR2C1 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			6	1		7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	1	0

Variants in OR2C1

This is a list of pathogenic ClinVar variants found in the OR2C1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-3355946-C-G		not specified	Likely benign (May 18, 2022)
16-3355947-G-A		not specified	Uncertain significance (Aug 16, 2022)
16-3356254-T-C		not specified	Uncertain significance (May 17, 2023)
16-3356310-G-T		not specified	Uncertain significance (Dec 17, 2023)
16-3356551-C-G		not specified	Uncertain significance (Aug 30, 2022)
16-3356583-G-A		not specified	Uncertain significance (Dec 19, 2023)
16-3356596-G-A		not specified	Uncertain significance (Feb 28, 2023)
16-3356650-C-T		not specified	Uncertain significance (Dec 21, 2022)
16-3356788-C-T		not specified	Uncertain significance (Sep 07, 2022)
16-3356812-C-G		not specified	Uncertain significance (Nov 09, 2023)
16-3356817-C-T		not specified	Uncertain significance (Oct 06, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR2C1	protein_coding	protein_coding	ENST00000304936	1	1036

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000381	0.394	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.527	199	179	1.11	0.00000994	1997
Missense in Polyphen		72	61.727	1.1664		787
Synonymous	-2.47	109	80.8	1.35	0.00000470	685
Loss of Function	0.234	7	7.70	0.909	4.11e-7	86

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)

Intolerance Scores

• loftool: 0.620
• rvis_EVS: 1.13
• rvis_percentile_EVS: 92.26

Haploinsufficiency Scores

• pHI: 0.108
• hipred: N
• hipred_score: 0.170

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0954

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Olfr15

Gene ontology

• Biological process: G protein-coupled receptor signaling pathway;detection of chemical stimulus involved in sensory perception of smell
• Cellular component: plasma membrane;cell cortex;integral component of membrane
• Molecular function: G protein-coupled receptor activity;olfactory receptor activity;odorant binding