OR2T4

protein-coding

olfactory receptor family 2 subfamily T member 4, the group of Olfactory receptors, family 2

Gene summary

Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. [provided by RefSeq, Jul 2008]

MANE transcript

NM_001004696.2

Inheritance

—

ClinVar variants

U:43

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.3

Max pathogenic AF

—

Genomic locus

chr1:248,361,665-248,362,627

External References & Databases

Ensembl (ENSG00000196944)

Transcript & Mutation Effects

hg38 • Region Span ~1.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to OR2T4 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 43

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001004696.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			43 clinvar			43
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	43	0	0	43

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001004696.2	RefSeq	NP_001004696.2	1	MANE Select
ENST00000366473.4	Ensembl	ENSP00000355429.3	1	MANE Select

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Olfactory transduction - Homo sapiens (human)
Olfactory receptor activity
Signaling by GPCR
Signal Transduction
Olfactory Signaling Pathway

Biological Process

G protein-coupled receptor signaling pathway
detection of chemical stimulus involved in sensory perception of smell

Molecular Function

G protein-coupled receptor activity
olfactory receptor activity

Cellular Component

plasma membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000366475
Coding exons: 1
Length: 1047
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.881	211	178	1.19	0.00000913	2255
Missense (PolyPhen)		47	44.234	1.0625		669
Synonymous	-1.67	85	67.5	1.26	0.00000363	675
Loss of Function	1.69	2	6.72	0.298	2.95e-7	92

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Odorant receptor. {ECO:0000305}.;

Intolerance Scores

LoFtool: 0.571
RVIS EVS: 2.15
RVIS percentile EVS: 98

Essentials

Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0209

Gene Damage Prediction

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