OR5K3

olfactory receptor family 5 subfamily K member 3, the group of Olfactory receptors, family 5

Basic information

Region (hg38): 3:98390666-98391631

Links

ENSG00000206536 ∙ NCBI:403277 ∙ ∙ HGNC:31290 ∙ Uniprot:A6NET4 ∙ 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 OR5K3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR5K3 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			29	1		30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	1	0

Variants in OR5K3

This is a list of pathogenic ClinVar variants found in the OR5K3 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-98390732-C-A		not specified	Uncertain significance (Mar 01, 2024)
3-98390825-C-A		not specified	Uncertain significance (May 08, 2023)
3-98390835-C-T		not specified	Uncertain significance (Dec 13, 2021)
3-98390846-A-T		not specified	Uncertain significance (May 11, 2022)
3-98390901-C-T		not specified	Uncertain significance (Jul 11, 2023)
3-98390922-T-C		not specified	Uncertain significance (May 07, 2024)
3-98390927-G-A		not specified	Likely benign (Jan 03, 2024)
3-98390937-G-A		not specified	Uncertain significance (May 28, 2024)
3-98390949-A-G		not specified	Uncertain significance (Mar 19, 2024)
3-98390998-C-G		not specified	Uncertain significance (Jun 21, 2021)
3-98391005-C-A		not specified	Uncertain significance (Jul 09, 2021)
3-98391035-G-A		not specified	Uncertain significance (Oct 29, 2021)
3-98391078-A-C		not specified	Uncertain significance (Nov 09, 2023)
3-98391097-G-T		not specified	Uncertain significance (Aug 15, 2023)
3-98391141-A-T		not specified	Uncertain significance (Dec 28, 2022)
3-98391146-G-C		not specified	Uncertain significance (Jan 10, 2022)
3-98391148-G-C		not specified	Uncertain significance (Nov 29, 2023)
3-98391179-C-T		not specified	Uncertain significance (Nov 19, 2022)
3-98391206-G-A		not specified	Uncertain significance (Sep 26, 2022)
3-98391215-T-G		not specified	Uncertain significance (Jul 13, 2022)
3-98391267-T-A		not specified	Uncertain significance (Mar 31, 2023)
3-98391270-T-G		not specified	Uncertain significance (Mar 07, 2023)
3-98391338-A-G		not specified	Uncertain significance (Aug 08, 2023)
3-98391411-T-C		not specified	Uncertain significance (Dec 09, 2023)
3-98391452-G-T		not specified	Uncertain significance (Dec 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR5K3	protein_coding	protein_coding	ENST00000383695	1	966

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000804	0.331	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.44	210	159	1.32	0.00000714	2110
Missense in Polyphen		48	36.429	1.3176		521
Synonymous	-1.09	67	56.6	1.18	0.00000255	622
Loss of Function	-0.0938	6	5.76	1.04	2.83e-7	98

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: 0.807
• rvis_EVS: 1.89
• rvis_percentile_EVS: 97.27

Haploinsufficiency Scores

• pHI: 0.111
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00196

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Olfr195

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