OR4X1

protein-coding

olfactory receptor family 4 subfamily X member 1, the group of Olfactory receptors, family 4

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. This olfactory receptor gene is a segregating pseudogene, where some individuals have an allele that encodes a functional olfactory receptor, while other individuals have an allele encoding a protein that is predicted to be non-functional. [provided by RefSeq, Jul 2015]

MANE transcript

NM_001004726.1

Inheritance

—

ClinVar variants

U:50B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.3

Max pathogenic AF

—

Genomic locus

chr11:48,263,861-48,264,778

External References & Databases

Ensembl (ENSG00000176567)

Transcript & Mutation Effects

hg38 • Region Span ~0.9 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 OR4X1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 54

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001004726.1. 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				2 clinvar		2
missense			50 clinvar	4 clinvar		54
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	50	6	0	56

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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_001004726.1	RefSeq	NP_001004726.1	1	MANE Select
ENST00000320048.1	Ensembl	ENSP00000321506.1	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: ENST00000320048
Coding exons: 1
Length: 918
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	-2.58	254	162	1.57	0.00000750	2013
Missense (PolyPhen)		79	53.522	1.476		729
Synonymous	-1.72	84	66.2	1.27	0.00000343	625
Loss of Function	-0.654	7	5.37	1.30	3.11e-7	63

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: 0.638
RVIS EVS: 2.07
RVIS percentile EVS: 97.79

Essentials

Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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