OR5K4

olfactory receptor family 5 subfamily K member 4, the group of Olfactory receptors, family 5

Basic information

Region (hg38): 3:98353854-98354819

Links

ENSG00000196098 ∙ NCBI:403278 ∙ ∙ HGNC:31291 ∙ Uniprot:A6NMS3 ∙ 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 OR5K4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR5K4 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			23	2		25
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 OR5K4

This is a list of pathogenic ClinVar variants found in the OR5K4 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-98353860-A-G		not specified	Uncertain significance (May 30, 2024)
3-98353866-A-T		not specified	Uncertain significance (Aug 17, 2022)
3-98353886-A-T		not specified	Uncertain significance (Aug 19, 2024)
3-98353903-T-G		not specified	Uncertain significance (May 14, 2024)
3-98353905-A-G		not specified	Uncertain significance (Sep 16, 2021)
3-98353906-C-T		not specified	Uncertain significance (Jan 04, 2024)
3-98353939-T-C		not specified	Uncertain significance (Mar 07, 2024)
3-98353942-T-A		not specified	Uncertain significance (Feb 27, 2023)
3-98353957-A-G		not specified	Uncertain significance (Aug 19, 2023)
3-98353992-G-A		not specified	Uncertain significance (Aug 28, 2021)
3-98354007-G-A		not specified	Uncertain significance (Dec 02, 2021)
3-98354014-G-A		not specified	Likely benign (Dec 13, 2023)
3-98354098-T-C		not specified	Uncertain significance (Jan 17, 2023)
3-98354126-T-G		not specified	Likely benign (May 10, 2022)
3-98354151-C-A		not specified	Uncertain significance (Nov 17, 2023)
3-98354152-A-C		not specified	Uncertain significance (Jan 16, 2024)
3-98354200-C-A		not specified	Uncertain significance (Jul 22, 2024)
3-98354202-A-G		not specified	Likely benign (Jul 22, 2024)
3-98354218-G-A		not specified	Uncertain significance (Nov 08, 2022)
3-98354271-C-T		not specified	Uncertain significance (Feb 21, 2024)
3-98354272-T-C		not specified	Uncertain significance (Sep 13, 2023)
3-98354284-T-C		not specified	Uncertain significance (Jan 31, 2022)
3-98354292-G-A		not specified	Uncertain significance (Jun 04, 2024)
3-98354324-G-C		not specified	Uncertain significance (Mar 29, 2022)
3-98354350-T-C		not specified	Uncertain significance (Dec 21, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR5K4	protein_coding	protein_coding	ENST00000354924	1	966

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000396	0.121	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.940	203	169	1.20	0.00000831	2106
Missense in Polyphen		41	36.63	1.1193		527
Synonymous	-0.312	63	59.9	1.05	0.00000285	642
Loss of Function	-0.926	7	4.81	1.46	1.97e-7	93

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: 0.890
• rvis_EVS: 1.48
• rvis_percentile_EVS: 95.32

Haploinsufficiency Scores

• pHI: 0.0914
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.124

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Olfr180

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;odorant binding