OR1C1

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

Basic information

Region (hg38): 1:247754846-247760556

Links

ENSG00000221888 ∙ NCBI:26188 ∙ ∙ HGNC:8182 ∙ Uniprot:Q15619 ∙ 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 OR1C1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR1C1 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	1		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	16	1	0

Variants in OR1C1

This is a list of pathogenic ClinVar variants found in the OR1C1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-247757478-A-T		not specified	Uncertain significance (Dec 27, 2023)
1-247757611-G-T		not specified	Uncertain significance (May 11, 2022)
1-247757635-C-T		not specified	Uncertain significance (Mar 18, 2024)
1-247757703-T-G		not specified	Uncertain significance (Sep 22, 2022)
1-247757705-C-A		not specified	Uncertain significance (May 27, 2022)
1-247757779-G-T		not specified	Uncertain significance (Sep 29, 2023)
1-247757797-C-G		not specified	Uncertain significance (May 23, 2023)
1-247757797-C-T		not specified	Uncertain significance (Apr 13, 2022)
1-247757835-T-A		not specified	Uncertain significance (Mar 08, 2024)
1-247757851-G-T		not specified	Uncertain significance (Mar 04, 2024)
1-247757860-G-A		not specified	Uncertain significance (Oct 05, 2021)
1-247757902-A-C		not specified	Uncertain significance (Nov 07, 2023)
1-247757996-G-T		not specified	Uncertain significance (Feb 16, 2023)
1-247758033-G-A		not specified	Uncertain significance (Nov 18, 2022)
1-247758202-C-A		not specified	Uncertain significance (Apr 18, 2023)
1-247758244-G-A		not specified	Uncertain significance (May 16, 2024)
1-247758267-G-A		not specified	Likely benign (Mar 16, 2022)
1-247758370-C-T		not specified	Uncertain significance (Apr 11, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR1C1	protein_coding	protein_coding	ENST00000408896	1	1307

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0574	0.726	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.390	187	173	1.08	0.00000867	2051
Missense in Polyphen		47	46.936	1.0014		600
Synonymous	-0.605	82	75.3	1.09	0.00000459	657
Loss of Function	0.776	2	3.59	0.558	1.49e-7	52

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: 0.281
• rvis_EVS: 0.51
• rvis_percentile_EVS: 80.1

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.140

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;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