OR52M1

olfactory receptor family 52 subfamily M member 1, the group of Olfactory receptors, family 52

Basic information

Region (hg38): 11:4545191-4546144

Previous symbols: [ "OR52M1P" ]

Links

ENSG00000197790 ∙ NCBI:119772 ∙ ∙ HGNC:15225 ∙ Uniprot:Q8NGK5 ∙ 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 OR52M1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR52M1 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					2	2
missense			31	3		34
nonsense						0
start loss						0
frameshift					2	2
inframe indel				1		1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	4	4

Variants in OR52M1

This is a list of pathogenic ClinVar variants found in the OR52M1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-4545218-G-A		not specified	Uncertain significance (Oct 12, 2022)
11-4545229-CT-C		OR52M1-related disorder	Benign (Jun 10, 2020)
11-4545239-A-G		not specified	Uncertain significance (Aug 05, 2023)
11-4545278-T-G		not specified	Uncertain significance (Dec 21, 2022)
11-4545283-C-A		OR52M1-related disorder	Benign (Jul 11, 2023)
11-4545311-G-A		not specified	Uncertain significance (Oct 25, 2023)
11-4545350-G-A		not specified	Uncertain significance (Feb 03, 2022)
11-4545371-A-G		not specified	Uncertain significance (May 02, 2024)
11-4545374-T-C		not specified	Uncertain significance (Dec 06, 2021)
11-4545380-T-C		not specified	Uncertain significance (Apr 18, 2024)
11-4545390-T-C		not specified	Uncertain significance (May 27, 2022)
11-4545444-G-C		not specified	Uncertain significance (Feb 23, 2023)
11-4545471-T-C		not specified	Uncertain significance (Jul 16, 2021)
11-4545473-G-A		not specified	Uncertain significance (May 20, 2024)
11-4545481-C-T		OR52M1-related disorder	Benign (Jul 11, 2023)
11-4545485-T-A		not specified	Uncertain significance (Jan 10, 2023)
11-4545491-G-A		not specified	Uncertain significance (Aug 26, 2022)
11-4545503-C-T		not specified	Uncertain significance (May 26, 2024)
11-4545510-A-G		not specified	Uncertain significance (Feb 28, 2024)
11-4545566-G-A		OR52M1-related disorder	Likely benign (May 31, 2022)
11-4545585-T-C		OR52M1-related disorder	Uncertain significance (Jun 06, 2023)
11-4545648-G-A		OR52M1-related disorder	Likely benign (Oct 27, 2022)
11-4545654-T-C		not specified	Uncertain significance (Oct 02, 2023)
11-4545693-G-A		not specified	Uncertain significance (Oct 26, 2021)
11-4545705-A-G		not specified	Uncertain significance (Apr 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR52M1	protein_coding	protein_coding	ENST00000360213	1	954

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.56e-9	0.0188	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.43	280	186	1.50	0.0000102	2038
Missense in Polyphen		88	63.256	1.3912		799
Synonymous	-4.19	114	69.5	1.64	0.00000351	704
Loss of Function	-1.81	10	5.44	1.84	3.14e-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: 0.0834

Intolerance Scores

• loftool: 0.944
• rvis_EVS: 0.16
• rvis_percentile_EVS: 64.85

Haploinsufficiency Scores

• pHI: 0.0711
• hipred: N
• hipred_score: 0.170

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0615

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Olfr554

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