CYSLTR2

cysteinyl leukotriene receptor 2, the group of Leukotriene receptors

Basic information

Region (hg38): 13:48653711-48711226

Links

ENSG00000152207 ∙ NCBI:57105 ∙ OMIM:605666 ∙ HGNC:18274 ∙ Uniprot:Q9NS75 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CYSLTR2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CYSLTR2 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				1	3	4
missense			18	6	4	28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	7	7

Variants in CYSLTR2

This is a list of pathogenic ClinVar variants found in the CYSLTR2 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-48706844-A-T		not specified	Likely benign (Dec 20, 2022)
13-48706857-G-A		not specified	Likely benign (May 23, 2023)
13-48706873-C-T		not specified	Uncertain significance (Dec 20, 2023)
13-48706918-A-C		not specified	Uncertain significance (Jun 30, 2024)
13-48706932-G-C			Benign (Jul 20, 2018)
13-48706965-T-G			Likely benign (Mar 01, 2023)
13-48707013-C-T		not specified	Uncertain significance (Apr 20, 2023)
13-48707016-T-C		not specified	Uncertain significance (Dec 21, 2023)
13-48707016-T-G		not specified	Uncertain significance (Mar 20, 2023)
13-48707067-G-A		not specified	Uncertain significance (Aug 16, 2021)
13-48707087-G-A			Benign (Apr 10, 2018)
13-48707122-C-T		not specified	Uncertain significance (Aug 20, 2024)
13-48707125-A-G			Likely benign (Mar 01, 2023)
13-48707139-G-T		not specified	Uncertain significance (Apr 23, 2024)
13-48707149-G-C		not specified	Uncertain significance (Dec 12, 2023)
13-48707166-T-C		not specified	Uncertain significance (Jun 14, 2024)
13-48707170-T-C		not specified	Uncertain significance (Jan 31, 2024)
13-48707208-G-A		not specified	Uncertain significance (Aug 30, 2021)
13-48707212-T-G		not specified	Uncertain significance (Jan 23, 2024)
13-48707280-G-A		not specified	Uncertain significance (May 23, 2023)
13-48707314-T-C		not specified	Likely benign (Nov 13, 2024)
13-48707334-C-T		not specified	Uncertain significance (Oct 27, 2022)
13-48707361-G-A		not specified	Uncertain significance (May 27, 2022)
13-48707415-A-G		not specified	Uncertain significance (Aug 20, 2024)
13-48707418-A-G		not specified	Uncertain significance (Oct 04, 2015)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CYSLTR2	protein_coding	protein_coding	ENST00000282018	1	2548

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000998	0.367	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.117	175	179	0.975	0.00000927	2255
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

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.
• Pathway: Calcium signaling pathway - Homo sapiens (human);Neuroactive ligand-receptor interaction - Homo sapiens (human);Lung fibrosis;GPCRs, Class A Rhodopsin-like;Signaling by GPCR;Signal Transduction;eicosanoid metabolism;Eicosanoid ligand-binding receptors;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;Leukotriene receptors;G alpha (q) signalling events;GPCR downstream signalling;Endothelins (Consensus)

Recessive Scores

• pRec: 0.102

Intolerance Scores

• loftool: 0.805
• rvis_EVS: 1.31
• rvis_percentile_EVS: 94

Haploinsufficiency Scores

• pHI: 0.135
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.192

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cysltr2
• Phenotype: respiratory system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); homeostasis/metabolism phenotype; immune system phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan)

Gene ontology

• Biological process: immune response;G protein-coupled receptor signaling pathway;neuropeptide signaling pathway;leukotriene signaling pathway
• Cellular component: cellular_component;plasma membrane;integral component of plasma membrane
• Molecular function: galanin receptor activity;leukotriene receptor activity;protein binding;G protein-coupled peptide receptor activity