OR4K13

olfactory receptor family 4 subfamily K member 13, the group of Olfactory receptors, family 4

Basic information

Region (hg38): 14:20029399-20036038

Links

ENSG00000176253 ∙ NCBI:390433 ∙ ∙ HGNC:15351 ∙ Uniprot:Q8NH42 ∙ 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 OR4K13 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR4K13 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	2		19
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	2	0

Variants in OR4K13

This is a list of pathogenic ClinVar variants found in the OR4K13 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-20033872-G-A		not specified	Uncertain significance (Jun 23, 2023)
14-20033911-T-C		not specified	Uncertain significance (Feb 12, 2024)
14-20033918-G-A		not specified	Uncertain significance (Dec 03, 2021)
14-20033921-G-T		not specified	Uncertain significance (Jan 07, 2022)
14-20033949-A-C		not specified	Uncertain significance (Mar 30, 2024)
14-20033990-T-C		not specified	Uncertain significance (May 01, 2024)
14-20034065-G-C		not specified	Likely benign (Dec 28, 2022)
14-20034071-C-T		not specified	Uncertain significance (Mar 18, 2024)
14-20034133-A-G		not specified	Uncertain significance (Nov 10, 2022)
14-20034185-T-C		not specified	Uncertain significance (Jan 07, 2022)
14-20034244-T-C		not specified	Likely benign (Oct 13, 2023)
14-20034268-A-C		not specified	Uncertain significance (Aug 04, 2023)
14-20034283-T-C		not specified	Uncertain significance (Apr 07, 2023)
14-20034289-G-C		not specified	Uncertain significance (Jan 04, 2024)
14-20034290-A-T		not specified	Uncertain significance (Apr 08, 2022)
14-20034344-G-A		not specified	Uncertain significance (Nov 18, 2022)
14-20034374-G-A		not specified	Uncertain significance (Jan 26, 2023)
14-20034452-A-G		not specified	Uncertain significance (Dec 15, 2022)
14-20034586-G-T		not specified	Uncertain significance (Dec 06, 2023)
14-20034608-A-G		not specified	Uncertain significance (Sep 27, 2021)
14-20034653-C-A		not specified	Uncertain significance (Dec 19, 2023)
14-20034692-G-T		not specified	Uncertain significance (Sep 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR4K13	protein_coding	protein_coding	ENST00000315693	1	917

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.93e-8	0.0527	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.502	182	164	1.11	0.00000806	1968
Missense in Polyphen		47	50.874	0.92385		689
Synonymous	-1.08	72	61.2	1.18	0.00000295	633
Loss of Function	-1.14	9	5.99	1.50	4.03e-7	67

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)

Recessive Scores

• pRec: 0.0907

Intolerance Scores

• loftool: 0.740
• rvis_EVS: 0.37
• rvis_percentile_EVS: 75.43

Haploinsufficiency Scores

• pHI: 0.0984
• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0543

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