OR2A25

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

Basic information

Region (hg38): 7:144069811-144075870

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

Links

ENSG00000221933NCBI:392138HGNC:19562Uniprot:A4D2G3AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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
clinvar
1
missense
18
clinvar
3
clinvar
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)3302634
7-144074347-C-T not specified Uncertain significance (May 26, 2024)3302635
7-144074430-G-C not specified Uncertain significance (Mar 12, 2024)3205001
7-144074434-G-A not specified Likely benign (May 03, 2023)2510665
7-144074455-A-G not specified Uncertain significance (May 03, 2023)2569602
7-144074484-A-G not specified Uncertain significance (Jun 10, 2024)2345268
7-144074542-A-G not specified Uncertain significance (Dec 07, 2021)2357992
7-144074547-G-C not specified Uncertain significance (Apr 27, 2023)2541544
7-144074565-G-T not specified Likely benign (Jul 21, 2021)2350080
7-144074589-G-A not specified Uncertain significance (Oct 12, 2022)2410260
7-144074670-G-A not specified Uncertain significance (Feb 07, 2023)2480675
7-144074693-T-G not specified Uncertain significance (Sep 16, 2021)3205002
7-144074740-A-G not specified Uncertain significance (Mar 07, 2024)3205003
7-144074766-G-T not specified Uncertain significance (Aug 02, 2021)2222663
7-144074785-C-T not specified Likely benign (Oct 26, 2021)2223182
7-144074809-T-A not specified Uncertain significance (Jun 01, 2023)2554804
7-144074811-G-C not specified Uncertain significance (Mar 31, 2024)3302633
7-144074827-T-C not specified Uncertain significance (Oct 26, 2022)2220145
7-144074883-T-C not specified Uncertain significance (Jul 16, 2021)2358858
7-144074884-G-T not specified Uncertain significance (May 24, 2023)2537953
7-144074995-T-C not specified Uncertain significance (Feb 27, 2024)3205004
7-144075058-T-C not specified Uncertain significance (Mar 01, 2023)2492696
7-144075090-C-T not specified Uncertain significance (Aug 20, 2023)2619678
7-144075125-G-A Benign (Mar 29, 2018)781116
7-144075144-A-T not specified Uncertain significance (Jun 09, 2022)2294522

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
OR2A25protein_codingprotein_codingENST00000408898 11014
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.001000.60800000.00
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.7491861591.170.000008032010
Missense in Polyphen6255.5641.1158759
Synonymous-1.788667.41.280.00000372658
Loss of Function0.53256.460.7743.68e-790

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000.00
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

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

pHI
hipred
N
hipred_score
0.131
ghis

Essentials

essential_gene_CRISPR
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.0702

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Olfr447
Phenotype

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