OR4K1

olfactory receptor family 4 subfamily K member 1, the group of Olfactory receptors, family 4

Basic information

Region (hg38): 14:19930916-19936757

Links

ENSG00000155249 ∙ NCBI:79544 ∙ ∙ HGNC:14726 ∙ Uniprot:Q8NGD4 ∙ 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 OR4K1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR4K1 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				1		1
missense			23	1		24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	2	0

Variants in OR4K1

This is a list of pathogenic ClinVar variants found in the OR4K1 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-19935670-G-T		not specified	Uncertain significance (Apr 25, 2022)
14-19935686-C-T		not specified	Uncertain significance (May 07, 2024)
14-19935694-T-A		not specified	Uncertain significance (Mar 22, 2023)
14-19935715-C-T		not specified	Uncertain significance (Dec 05, 2022)
14-19935806-T-C		not specified	Uncertain significance (Jul 07, 2022)
14-19935838-C-T		not specified	Uncertain significance (May 02, 2024)
14-19935843-G-A		not specified	Uncertain significance (Jan 29, 2024)
14-19935869-T-G		not specified	Uncertain significance (Aug 30, 2021)
14-19935875-A-T		not specified	Uncertain significance (Jul 06, 2021)
14-19935877-A-G		not specified	Uncertain significance (Jan 08, 2024)
14-19935898-A-C		not specified	Uncertain significance (May 18, 2023)
14-19935979-C-T		not specified	Uncertain significance (Sep 17, 2021)
14-19935992-G-C		not specified	Uncertain significance (May 05, 2023)
14-19936005-G-C		not specified	Uncertain significance (Mar 20, 2024)
14-19936007-T-C		not specified	Uncertain significance (May 09, 2022)
14-19936018-A-G		not specified	Uncertain significance (May 30, 2023)
14-19936021-G-A		not specified	Uncertain significance (Aug 16, 2021)
14-19936039-G-A		not specified	Uncertain significance (Mar 25, 2024)
14-19936081-A-G		not specified	Uncertain significance (Jun 06, 2023)
14-19936123-G-A		not specified	Likely benign (Jun 10, 2022)
14-19936123-G-T		not specified	Uncertain significance (Mar 02, 2023)
14-19936171-T-G		not specified	Uncertain significance (Oct 05, 2023)
14-19936231-T-C		not specified	Uncertain significance (Feb 02, 2023)
14-19936269-G-A			Likely benign (Apr 01, 2023)
14-19936270-A-C		not specified	Uncertain significance (Nov 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR4K1	protein_coding	protein_coding	ENST00000285600	1	1076

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.95e-8	0.0428	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.21	235	157	1.50	0.00000765	2005
Missense in Polyphen		102	57.457	1.7752		828
Synonymous	-2.13	78	57.5	1.36	0.00000288	601
Loss of Function	-1.34	9	5.59	1.61	3.24e-7	78

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: 0.0864

Intolerance Scores

• loftool: 0.841
• rvis_EVS: 1.38
• rvis_percentile_EVS: 94.53

Haploinsufficiency Scores

• pHI: 0.0777
• hipred: N
• hipred_score: 0.144

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0149

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Olfr728

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