CYSLTR1

protein-coding

cysteinyl leukotriene receptor 1, the group of Leukotriene receptors

Gene summary

This gene encodes a member of the G-protein coupled receptor 1 family. The encoded protein is a receptor for cysteinyl leukotrienes, and is involved in mediating bronchoconstriction via activation of a phosphatidylinositol-calcium second messenger system. Activation of the encoded receptor results in contraction and proliferation of bronchial smooth muscle cells, eosinophil migration, and damage to the mucus layer in the lung. Upregulation of this gene is associated with asthma and dysregulation may also be implicated in cancer. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]

MANE transcript

NM_006639.4

Inheritance

—

ClinVar variants

U:55B:2

Top phenotype

Prostate cancer

gnomAD constraint

pLI —, LoF o/e 0.74

Max pathogenic AF

—

Genomic locus

chrX:78,271,468-78,327,691

External References & Databases

Ensembl (ENSG00000173198)

Transcript & Mutation Effects

hg38 • Region Span ~56.2 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 CYSLTR1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 41

not providedTotal: 2

Prostate cancerTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006639.4. 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	1 clinvar		3
missense			50 clinvar	1 clinvar		51
nonsense			1 clinvar			1
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	55	2	0	57

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 14 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_006639.4	RefSeq	NP_006630.1	1	MANE Select
ENST00000373304.4	Ensembl	ENSP00000362401.3	1	MANE Select
NM_001282186.2	RefSeq	NP_001269115.1	1	Standard
NM_001282187.2	RefSeq	NP_001269116.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Calcium signaling pathway - Homo sapiens (human)
Neuroactive ligand-receptor interaction - Homo sapiens (human)
Leukotriene modifiers pathway, Pharmacodynamics
GPCRs, Class A Rhodopsin-like
Signaling by GPCR

Biological Process

inflammatory response to antigenic stimulus
calcium ion transport
chemotaxis
defense response
cell surface receptor signaling pathway

Molecular Function

galanin receptor activity
leukotriene receptor activity
protein binding
G protein-coupled peptide receptor activity

Cellular Component

plasma membrane
integral component of plasma membrane
membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000373304
Coding exons: 1
Length: 56088
Individuals with no LoFs: 125655
Homozygous LoFs: 9
Heterozygous LoFs: 11
Defined: 125675
p: 0.0000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.768	148	124	1.19	0.00000898	2245
Missense (PolyPhen)		43	49.43	0.86992		798
Synonymous	-2.66	67	44.4	1.51	0.00000311	653
Loss of Function	0.492	3	4.07	0.737	2.52e-7	107

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000076	0.000062	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0.00014	0.000099	rare
East Asian	0.000072	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00018	0.00013	rare
South Asian	0.00011	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Receptor for cysteinyl leukotrienes mediating bronchoconstriction of individuals with and without asthma. Stimulation by LTD4 results in the contraction and proliferation of smooth muscle, edema, eosinophil migration and damage to the mucus layer in the lung. This response is mediated via a G-protein that activates a phosphatidylinositol-calcium second messenger system. The rank order of affinities for the leukotrienes is LTD4 >> LTE4 = LTC4 >> LTB4.;

Recessive Scores

pRec: 0.158

Intolerance Scores

LoFtool: 0.657
RVIS EVS: -0.23
RVIS percentile EVS: 37.11

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.159

Gene Damage Prediction

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