CYSLTR2

protein-coding

cysteinyl leukotriene receptor 2, the group of Leukotriene receptors

Gene summary

The cysteinyl leukotrienes LTC4, LTD4, and LTE4 are important mediators of human bronchial asthma. Pharmacologic studies have determined that cysteinyl leukotrienes activate at least 2 receptors, the protein encoded by this gene and CYSLTR1. This encoded receptor is a member of the superfamily of G protein-coupled receptors. It seems to play a major role in endocrine and cardiovascular systems. [provided by RefSeq, Jul 2008]

MANE transcript

NM_001308476.3

Inheritance

—

ClinVar variants

U:48B:15

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.99

Max pathogenic AF

—

Genomic locus

chr13:48,653,711-48,711,226

External References & Databases

Ensembl (ENSG00000152207)

Transcript & Mutation Effects

hg38 • Region Span ~57.5 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 CYSLTR2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 52

not providedTotal: 11

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001308476.3. 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				1 clinvar	3 clinvar	4
missense			48 clinvar	7 clinvar	4 clinvar	59
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	48	8	7	63

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 39 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001308476.3	RefSeq	NP_001295405.1	1	MANE Select
ENST00000682523.1	Ensembl	ENSP00000508181.1	1	MANE Select
NM_001308465.3	RefSeq	NP_001295394.1	1	Standard
NM_001308467.3	RefSeq	NP_001295396.1	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)
Lung fibrosis
GPCRs, Class A Rhodopsin-like
Signaling by GPCR

Biological Process

immune response
G protein-coupled receptor signaling pathway
neuropeptide signaling pathway
leukotriene signaling pathway

Molecular Function

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

Cellular Component

cellular_component
plasma membrane
integral component of plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000282018
Coding exons: 1
Length: 2548
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	0.117	175	179	0.975	0.00000927	2255
Missense (PolyPhen)		59	62.229	0.94812		822
Synonymous	0.561	67	73.1	0.916	0.00000387	706
Loss of Function	0.0209	6	6.06	0.991	2.61e-7	101

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: Receptor for cysteinyl leukotrienes. The response is mediated via a G-protein that activates a phosphatidylinositol- calcium second messenger system. Stimulation by BAY u9773, a partial agonist, induces specific contractions of pulmonary veins and might also have an indirect role in the relaxation of the pulmonary vascular endothelium. The rank order of affinities for the leukotrienes is LTC4 = LTD4 >> LTE4.;

Recessive Scores

pRec: 0.102

Intolerance Scores

LoFtool: 0.805
RVIS EVS: 1.31
RVIS percentile EVS: 94

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.192

Gene Damage Prediction

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