OR5M3

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

Basic information

Region (hg38): 11:56469274-56473352

Links

ENSG00000174937 ∙ NCBI:219482 ∙ ∙ HGNC:14806 ∙ Uniprot:Q8NGP4 ∙ 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 OR5M3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR5M3 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			20	2		22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	2	0

Variants in OR5M3

This is a list of pathogenic ClinVar variants found in the OR5M3 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-56469578-C-T		not specified	Uncertain significance (Nov 19, 2022)
11-56469599-A-G		not specified	Likely benign (Apr 26, 2023)
11-56469605-G-C		not specified	Uncertain significance (Jan 29, 2024)
11-56469632-C-T		not specified	Uncertain significance (Mar 01, 2024)
11-56469649-C-A		not specified	Uncertain significance (Nov 01, 2022)
11-56469720-G-A		not specified	Uncertain significance (Oct 20, 2021)
11-56469721-T-A		not specified	Uncertain significance (Feb 06, 2023)
11-56469726-G-C		not specified	Uncertain significance (Oct 30, 2023)
11-56469779-C-A		not specified	Uncertain significance (Sep 06, 2022)
11-56469819-G-A		not specified	Uncertain significance (Mar 16, 2022)
11-56469834-C-T		not specified	Uncertain significance (Jun 29, 2022)
11-56469854-G-C		not specified	Uncertain significance (Feb 16, 2023)
11-56469858-T-C		not specified	Uncertain significance (Apr 22, 2022)
11-56469897-C-T		not specified	Uncertain significance (Jun 13, 2024)
11-56469900-G-A		not specified	Uncertain significance (Feb 15, 2023)
11-56469933-C-T		not specified	Uncertain significance (Nov 30, 2022)
11-56469975-A-T		not specified	Uncertain significance (Mar 01, 2023)
11-56470011-C-A		not specified	Uncertain significance (Jan 26, 2022)
11-56470137-A-G		not specified	Uncertain significance (Mar 18, 2024)
11-56470145-A-G		not specified	Uncertain significance (Mar 18, 2024)
11-56470150-C-A		not specified	Uncertain significance (Aug 08, 2022)
11-56470185-G-C		not specified	Uncertain significance (Sep 14, 2022)
11-56470209-C-T		not specified	Uncertain significance (May 24, 2024)
11-56470256-T-C		not specified	Uncertain significance (Feb 28, 2023)
11-56470293-C-T		not specified	Uncertain significance (Apr 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR5M3	protein_coding	protein_coding	ENST00000312240	1	1051

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.58e-9	0.0279	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.928	200	166	1.20	0.00000824	2011
Missense in Polyphen		45	38.574	1.1666		558
Synonymous	-1.55	75	59.8	1.25	0.00000310	598
Loss of Function	-1.13	11	7.63	1.44	4.67e-7	95

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: 0.0917

Intolerance Scores

• loftool: 0.928
• rvis_EVS: 0.46
• rvis_percentile_EVS: 78.69

Haploinsufficiency Scores

• pHI: 0.142
• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0962

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Olfr1033

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