OR5T2

olfactory receptor family 5 subfamily T member 2, the group of Olfactory receptors, family 5

Basic information

Region (hg38): 11:56231282-56234255

Links

ENSG00000181718NCBI:219464HGNC:15296Uniprot:Q8NGG2AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the OR5T2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR5T2 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
37
clinvar
5
clinvar
42
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
5
clinvar
5
Total 0 0 42 5 0

Variants in OR5T2

This is a list of pathogenic ClinVar variants found in the OR5T2 region.

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

Position Type Phenotype Significance ClinVar
11-56232119-T-G not specified Uncertain significance (Aug 19, 2024)2213807
11-56232135-T-A not specified Uncertain significance (Sep 15, 2021)2379484
11-56232154-A-C not specified Uncertain significance (Aug 28, 2023)2621823
11-56232188-T-C not specified Uncertain significance (Feb 15, 2023)2466864
11-56232197-C-A not specified Uncertain significance (Jan 09, 2025)3884110
11-56232198-T-C not specified Uncertain significance (Mar 01, 2023)2493025
11-56232207-C-T not specified Likely benign (Sep 27, 2021)3206405
11-56232211-A-T not specified Uncertain significance (Sep 15, 2021)2360159
11-56232242-A-T not specified Uncertain significance (May 17, 2023)2516339
11-56232251-A-G not specified Uncertain significance (Jun 21, 2023)2604788
11-56232253-C-T not specified Uncertain significance (Jul 06, 2024)3411971
11-56232321-T-C not specified Uncertain significance (May 23, 2023)2550292
11-56232324-A-G not specified Uncertain significance (Feb 16, 2023)2470468
11-56232342-C-T not specified Uncertain significance (May 18, 2023)2519621
11-56232377-G-A not specified Uncertain significance (Jun 18, 2024)3303260
11-56232437-A-G not specified Uncertain significance (Mar 03, 2022)2213868
11-56232449-T-C not specified Uncertain significance (Sep 27, 2024)3411970
11-56232452-A-G not specified Uncertain significance (Sep 22, 2023)3206404
11-56232513-C-G not specified Uncertain significance (Nov 06, 2023)3206403
11-56232548-A-T not specified Uncertain significance (Jun 22, 2023)2599820
11-56232558-C-A not specified Likely benign (Apr 24, 2023)2516733
11-56232560-C-T not specified Uncertain significance (Sep 06, 2022)2353448
11-56232596-A-G not specified Uncertain significance (May 23, 2023)2549895
11-56232597-T-C not specified Likely benign (Aug 11, 2024)3411966
11-56232629-G-A not specified Uncertain significance (Jul 26, 2024)2271624

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
OR5T2protein_codingprotein_codingENST00000313264 11248
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.0003780.40700000.00
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-2.082641851.430.000008442344
Missense in Polyphen5436.6951.4716568
Synonymous-0.5697669.91.090.00000338709
Loss of Function-0.027854.931.011.99e-792

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
0.807
rvis_EVS
1.29
rvis_percentile_EVS
93.84

Haploinsufficiency Scores

pHI
0.172
hipred
N
hipred_score
0.112
ghis
0.394

Essentials

essential_gene_CRISPR
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.0137

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Olfr1086
Phenotype

Gene ontology

Biological process
G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger;chemical synaptic transmission;detection of chemical stimulus involved in sensory perception of smell;G protein-coupled serotonin receptor signaling pathway
Cellular component
plasma membrane;integral component of plasma membrane;dendrite
Molecular function
G protein-coupled receptor activity;olfactory receptor activity;G protein-coupled serotonin receptor activity;neurotransmitter receptor activity