OR2A25

olfactory receptor family 2 subfamily A member 25, the group of Olfactory receptors, family 2

Basic information

Region (hg38): 7:144069810-144075870

Previous symbols: [ "OR2A25P", "OR2A27" ]

Links

ENSG00000221933 ∙ NCBI:392138 ∙ ∙ HGNC:19562 ∙ Uniprot:A4D2G3 ∙ 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 OR2A25 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR2A25 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					1	1
missense			18	3		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	3	1

Variants in OR2A25

This is a list of pathogenic ClinVar variants found in the OR2A25 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-144074272-T-C		not specified	Uncertain significance (Mar 20, 2024)
7-144074347-C-T		not specified	Uncertain significance (May 26, 2024)
7-144074430-G-C		not specified	Uncertain significance (Mar 12, 2024)
7-144074434-G-A		not specified	Likely benign (May 03, 2023)
7-144074455-A-G		not specified	Uncertain significance (May 03, 2023)
7-144074484-A-G		not specified	Uncertain significance (Jun 10, 2024)
7-144074542-A-G		not specified	Uncertain significance (Dec 07, 2021)
7-144074547-G-C		not specified	Uncertain significance (Apr 27, 2023)
7-144074565-G-T		not specified	Likely benign (Jul 21, 2021)
7-144074589-G-A		not specified	Uncertain significance (Oct 12, 2022)
7-144074670-G-A		not specified	Uncertain significance (Feb 07, 2023)
7-144074693-T-G		not specified	Uncertain significance (Sep 16, 2021)
7-144074740-A-G		not specified	Uncertain significance (Mar 07, 2024)
7-144074766-G-T		not specified	Uncertain significance (Aug 02, 2021)
7-144074785-C-T		not specified	Likely benign (Oct 26, 2021)
7-144074809-T-A		not specified	Uncertain significance (Jun 01, 2023)
7-144074811-G-C		not specified	Uncertain significance (Mar 31, 2024)
7-144074827-T-C		not specified	Uncertain significance (Oct 26, 2022)
7-144074883-T-C		not specified	Uncertain significance (Jul 16, 2021)
7-144074884-G-T		not specified	Uncertain significance (May 24, 2023)
7-144074995-T-C		not specified	Uncertain significance (Feb 27, 2024)
7-144075058-T-C		not specified	Uncertain significance (Mar 01, 2023)
7-144075090-C-T		not specified	Uncertain significance (Aug 20, 2023)
7-144075125-G-A			Benign (Mar 29, 2018)
7-144075144-A-T		not specified	Uncertain significance (Jun 09, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR2A25	protein_coding	protein_coding	ENST00000408898	1	1014

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00100	0.608	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.749	186	159	1.17	0.00000803	2010
Missense in Polyphen		62	55.564	1.1158		759
Synonymous	-1.78	86	67.4	1.28	0.00000372	658
Loss of Function	0.532	5	6.46	0.774	3.68e-7	90

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: 0.460
• rvis_EVS: 0.4
• rvis_percentile_EVS: 76.31

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.131

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0702

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Olfr447

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