CYSLTR1

cysteinyl leukotriene receptor 1, the group of Leukotriene receptors

Basic information

Region (hg38): X:78271468-78327691

Links

ENSG00000173198 ∙ NCBI:10800 ∙ OMIM:300201 ∙ HGNC:17451 ∙ Uniprot:Q9Y271 ∙ 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 CYSLTR1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CYSLTR1 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		1
missense			15	1		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	2	0

Variants in CYSLTR1

This is a list of pathogenic ClinVar variants found in the CYSLTR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-78272743-C-T		not specified	Uncertain significance (Jan 03, 2024)
X-78272747-T-G		not specified	Uncertain significance (Dec 05, 2024)
X-78272813-G-C		not specified	Uncertain significance (Jun 12, 2023)
X-78272865-T-C			Likely benign (Apr 01, 2022)
X-78272887-T-C		not specified	Uncertain significance (Dec 14, 2022)
X-78272951-G-A		not specified	Uncertain significance (Oct 25, 2023)
X-78272966-G-A		not specified	Uncertain significance (Jan 08, 2024)
X-78272989-C-T		not specified	Uncertain significance (Apr 22, 2024)
X-78273014-T-A		not specified	Uncertain significance (Jun 18, 2021)
X-78273035-C-T		not specified	Uncertain significance (Nov 17, 2023)
X-78273260-G-C		not specified	Uncertain significance (Apr 18, 2024)
X-78273292-A-T		not specified	Uncertain significance (May 04, 2023)
X-78273293-T-A		not specified	Uncertain significance (May 04, 2023)
X-78273386-G-A		not specified	Conflicting classifications of pathogenicity (Jul 14, 2024)
X-78273398-T-C		not specified	Uncertain significance (Jun 29, 2023)
X-78273457-C-T		not specified	Uncertain significance (Mar 20, 2024)
X-78273459-G-C		not specified	Uncertain significance (Mar 24, 2023)
X-78273511-C-A		not specified	Uncertain significance (Apr 17, 2023)
X-78273563-T-C		not specified	Uncertain significance (Dec 06, 2024)
X-78273584-T-G		not specified	Uncertain significance (Sep 03, 2024)
X-78273602-T-C		not specified	Uncertain significance (Jul 22, 2024)
X-78273678-AT-A		Malignant tumor of prostate	Uncertain significance (-)
X-78273682-C-T		not specified	Uncertain significance (Aug 04, 2024)
X-78273698-T-G		not specified	Uncertain significance (Dec 08, 2023)
X-78273725-T-C		not specified	Uncertain significance (Jul 31, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CYSLTR1	protein_coding	protein_coding	ENST00000373304	1	56088

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0120	0.660	125655	9	11	125675	0.0000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.768	148	124	1.19	0.00000898	2245
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000762	0.0000615
Ashkenazi Jewish	0.000135	0.0000992
East Asian	0.0000723	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000184	0.000132
Middle Eastern	0.0000723	0.0000544
South Asian	0.000108	0.0000653
Other	0.00	0.00

dbNSFP

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.
• Pathway: 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;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: 0.158

Intolerance Scores

• loftool: 0.657
• rvis_EVS: -0.23
• rvis_percentile_EVS: 37.11

Haploinsufficiency Scores

• pHI: 0.156
• hipred: N
• hipred_score: 0.253
• ghis: 0.515

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.159

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cysltr1
• 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); respiratory system phenotype; immune system phenotype; cellular phenotype

Gene ontology

• Biological process: inflammatory response to antigenic stimulus;calcium ion transport;chemotaxis;defense response;cell surface receptor signaling pathway;G protein-coupled receptor signaling pathway;positive regulation of cytosolic calcium ion concentration;neuropeptide signaling pathway;respiratory gaseous exchange;leukotriene signaling pathway
• Cellular component: plasma membrane;integral component of plasma membrane;membrane
• Molecular function: galanin receptor activity;leukotriene receptor activity;protein binding;G protein-coupled peptide receptor activity