LYST

Chr 1

lysosomal trafficking regulator

Also known as: CHS, CHS1, Mauve

NCBI Gene: 1130ENSG00000143669UniProt: Q99698

This gene encodes a protein that regulates intracellular protein trafficking in endosomes, and may be involved in pigmentation. Mutations in this gene are associated with Chediak-Higashi syndrome, a lysosomal storage disorder. Alternative splicing results in multiple transcript variants, though the full-length nature of some of these variants has not been determined. [provided by RefSeq, Apr 2013]

GeneReviewsResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

UniProtChediak-Higashi syndrome

Clinical highlights

Gene-disease validity (ClinGen)
Chediak-Higashi syndrome · ARDefinitivesufficient evidence for diagnostic panels
Interpreting a novel variant
Loss of function is the curated mechanism (Gene2Phenotype) and the gene is intolerant of it in the population — truncating, frameshift and canonical splice variants carry more prior weight here than missense.Curated gene-level mechanism — a prior for triage, not a per-variant call.
1
Active trials
39
Pubs (1 yr)
—
P/LP submissions
—
P/LP missense
0.31
LOEUF· LoF intol.
LOF
Mechanism· G2P
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GeneReview available — LYST
Authoritative clinical overview · Recommended first read
Open GeneReview ↗
Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
LoF intolerant — likely haploinsufficient
LoF Constraint?
0.31LOEUF
pLI 0.015
Z-score 9.58
OE 0.24 (0.19–0.31)
Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint?
1.41Z-score
OE missense 0.91 (0.87–0.95)
1758 obs / 1932.1 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?
LoF OE?0.24 (0.19–0.31)
0≤0.351.4
Missense OE?0.91 (0.87–0.95)
0≤0.61.4
Synonymous OE?1.01
0≤1.21.6
LoF obs/exp: 44 / 184.4Missense obs/exp: 1758 / 1932.1Syn Z: -0.23

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

LYST · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients