OR13C9

olfactory receptor family 13 subfamily C member 9, the group of Olfactory receptors, family 13

Basic information

Region (hg38): 9:104617248-104618204

Links

ENSG00000136839 ∙ NCBI:286362 ∙ ∙ HGNC:15104 ∙ Uniprot:Q8NGT0 ∙ 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 OR13C9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR13C9 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			8			8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	0	0

Variants in OR13C9

This is a list of pathogenic ClinVar variants found in the OR13C9 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-104617429-T-C		not specified	Uncertain significance (Oct 17, 2023)
9-104617504-C-T		not specified	Uncertain significance (Apr 29, 2024)
9-104617541-T-C		not specified	Uncertain significance (Jan 26, 2022)
9-104617706-G-A		not specified	Uncertain significance (Oct 29, 2021)
9-104617775-T-C		not specified	Uncertain significance (Mar 28, 2023)
9-104617787-C-T		not specified	Uncertain significance (Aug 12, 2024)
9-104617832-C-A		not specified	Uncertain significance (Jun 02, 2023)
9-104617895-C-T		not specified	Uncertain significance (Oct 16, 2024)
9-104617967-A-G		not specified	Uncertain significance (Aug 05, 2023)
9-104618074-G-A		not specified	Uncertain significance (Feb 05, 2024)
9-104618172-T-A		not specified	Uncertain significance (Apr 24, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR13C9	protein_coding	protein_coding	ENST00000259362	1	957

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0206	0.763	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.156	172	166	1.03	0.00000739	2105
Missense in Polyphen		61	56.18	1.0858		761
Synonymous	-1.72	77	60.0	1.28	0.00000277	628
Loss of Function	0.867	3	5.12	0.586	2.12e-7	88

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: 0.879
• rvis_EVS: 1.22
• rvis_percentile_EVS: 93.16

Haploinsufficiency Scores

• pHI: 0.279
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0890

Gene Damage Prediction

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

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