OR52I2

olfactory receptor family 52 subfamily I member 2, the group of Olfactory receptors, family 52

Basic information

Region (hg38): 11:4581743-4593340

Links

ENSG00000226288 ∙ NCBI:143502 ∙ ∙ HGNC:15221 ∙ Uniprot:Q8NH67 ∙ 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 OR52I2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR52I2 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	4		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	24	4	0

Variants in OR52I2

This is a list of pathogenic ClinVar variants found in the OR52I2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-4586831-C-T		not specified	Uncertain significance (Mar 17, 2023)
11-4586871-G-A		not specified	Uncertain significance (Oct 20, 2024)
11-4586973-A-C		not specified	Uncertain significance (Feb 12, 2024)
11-4587024-G-A		not specified	Uncertain significance (Dec 10, 2024)
11-4587030-C-T		not specified	Uncertain significance (Aug 28, 2024)
11-4587044-G-A		not specified	Uncertain significance (Feb 12, 2024)
11-4587066-G-A		not specified	Uncertain significance (Jun 22, 2023)
11-4587095-G-A		not specified	Uncertain significance (Oct 25, 2022)
11-4587150-G-A		not specified	Likely benign (Oct 04, 2024)
11-4587159-G-T		not specified	Uncertain significance (Nov 07, 2023)
11-4587235-G-T		not specified	Uncertain significance (Nov 07, 2024)
11-4587237-C-T		not specified	Uncertain significance (Mar 11, 2022)
11-4587302-A-G		not specified	Uncertain significance (May 15, 2024)
11-4587308-C-T		not specified	Uncertain significance (Nov 07, 2022)
11-4587333-T-G		not specified	Uncertain significance (Feb 23, 2023)
11-4587344-A-G			Likely benign (Dec 01, 2022)
11-4587359-A-G		not specified	Likely benign (Sep 01, 2021)
11-4587363-T-C		not specified	Likely benign (Dec 01, 2022)
11-4587365-G-T		not specified	Conflicting classifications of pathogenicity (Dec 01, 2022)
11-4587366-C-T		not specified	Conflicting classifications of pathogenicity (Dec 01, 2022)
11-4587370-A-G			Likely benign (Dec 01, 2022)
11-4587377-C-A		not specified	Uncertain significance (Oct 09, 2024)
11-4587392-A-G		not specified	Uncertain significance (Dec 14, 2023)
11-4587401-C-G		not specified	Uncertain significance (Sep 20, 2023)
11-4587440-G-A		not specified	Uncertain significance (Dec 03, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR52I2	protein_coding	protein_coding	ENST00000312614	1	1115

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.443	0.531	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.923	219	184	1.19	0.00000949	2261
Missense in Polyphen		53	55.827	0.94937		783
Synonymous	-1.24	84	70.8	1.19	0.00000378	739
Loss of Function	1.77	1	5.48	0.183	2.38e-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: 0.683
• rvis_EVS: 1.15
• rvis_percentile_EVS: 92.56

Haploinsufficiency Scores

• pHI: 0.0806
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0171

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Olfr556

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