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10 sources retrieved · Most recent: April 2026 · Index updated 14 days ago
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LYST
lysosomal trafficking regulator
Chromosome 1 · 1q42.3
NCBI Gene: 1130Ensembl: ENSG00000143669.16HGNC: HGNC:1968UniProt: Q99698
67PubMed Papers
21Diseases
0Drugs
272Pathogenic Variants
FUNCTIONAL ROLE
Transporter
RESEARCH IMPACT
Variant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
nucleoplasmnatural killer cell mediated cytotoxicityprotein bindingmicrotubule cytoskeletonChediak-Higashi syndromeChédiak-Higashi syndromeoculocutaneous albinismgenetic disorder
✦AI Summary

LYST (lysosomal trafficking regulator) is an adapter protein that regulates intracellular vesicle trafficking, particularly the fusion and fission of lysosomes and lysosome-related organelles 1. In cytotoxic T cells and natural killer cells, LYST controls the size, number, and exocytosis of lytic granules, critical for immune cytotoxicity 2. LYST also regulates phagosome maturation in macrophages and dendritic cells, and modulates TLR3/TLR4-induced inflammatory responses by controlling endosomal signaling pathways 2. Additionally, LYST plays a prominent role in autophagosome-lysosome reformation for lysosomal homeostasis maintenance 2. Mutations in LYST cause Chediak-Higashi syndrome (CHS), a rare autosomal recessive immunodeficiency characterized by congenital immunodeficiency, partial oculocutaneous albinism, bleeding diathesis, and progressive neurodegeneration 23. Mutation type correlates with disease severity: nonsense/frameshift mutations cause classic CHS with severe early-onset immunodeficiency and high hemophagocytic lymphohistiocytosis (HLH) risk, while missense mutations cause milder immunologic symptoms but inevitable neurological progression 3. LYST mutations also contribute to broader HLH disease spectrum, with degranulation defects including LYST variants representing >50% of genetic HLH cases 4. Hematopoietic stem cell transplantation effectively treats hematologic and immune defects but does not prevent progressive neurological complications 2.

Sources cited
1
LYST regulates membrane dynamics and intracellular trafficking of lysosomes and lysosome-related organelles
PMID: 38774881
2
LYST controls granule size, number, and exocytosis in NK cells; regulates autophagosome-lysosome reformation; mutations cause Chediak-Higashi syndrome with immunodeficiency and neurodegeneration
PMID: 37254856
3
LYST mutations cause CHS with mutation type correlating to disease severity; nonsense/frameshift mutations cause early severe disease with HLH risk; missense mutations cause milder early symptoms with inevitable neurological progression
PMID: 39622608
4
LYST mutations are among degranulation defects genes collectively representing >50% of genetic HLH cases in a large North American cohort
PMID: 32542393
⚠Limited data available — This gene has 4 indexed publications. Summary and analysis may be incomplete.
Disease Associationsⓘ21
Chediak-Higashi syndromeOpen Targets
0.84Strong
Chédiak-Higashi syndromeOpen Targets
0.82Strong
oculocutaneous albinismOpen Targets
0.50Moderate
genetic disorderOpen Targets
0.47Moderate
Spastic paraplegiaOpen Targets
0.46Moderate
Parkinson diseaseOpen Targets
0.46Moderate
ParkinsonismOpen Targets
0.46Moderate
peripheral neuropathyOpen Targets
0.46Moderate
hair colorOpen Targets
0.45Moderate
systemic lupus erythematosusOpen Targets
0.41Moderate
autoinflammatory syndromeOpen Targets
0.38Weak
albinismOpen Targets
0.37Weak
attenuated Chédiak-Higashi syndromeOpen Targets
0.37Weak
cyclic hematopoiesisOpen Targets
0.37Weak
breast cancerOpen Targets
0.32Weak
crush injuryOpen Targets
0.31Weak
spastic ataxiaOpen Targets
0.31Weak
ThrombocytopeniaOpen Targets
0.30Weak
COVID-19Open Targets
0.30Weak
Abnormal bleedingOpen Targets
0.30Weak
Chediak-Higashi syndromeUniProt
Pathogenic Variants272
NM_000081.4(LYST):c.1507C>T (p.Arg503Ter)Pathogenic
not provided|Chédiak-Higashi syndrome
★★☆☆2026→ Residue 503
NM_000081.4(LYST):c.9874G>T (p.Glu3292Ter)Pathogenic
Chédiak-Higashi syndrome
★★☆☆2026→ Residue 3292
NM_000081.4(LYST):c.3433del (p.His1145fs)Pathogenic
Chédiak-Higashi syndrome|not provided
★★☆☆2026→ Residue 1145
NM_000081.4(LYST):c.148C>T (p.Arg50Ter)Pathogenic
CHEDIAK-HIGASHI SYNDROME, CHILDHOOD TYPE|Chédiak-Higashi syndrome
★★☆☆2025→ Residue 50
NM_000081.4(LYST):c.484C>T (p.Gln162Ter)Pathogenic
Chédiak-Higashi syndrome
★★☆☆2025→ Residue 162
NM_000081.4(LYST):c.9377_9389del (p.Gly3126fs)Pathogenic
Chédiak-Higashi syndrome
★★☆☆2025→ Residue 3126
NM_000081.4(LYST):c.1540C>T (p.Arg514Ter)Pathogenic
Chédiak-Higashi syndrome
★★☆☆2025→ Residue 514
NM_000081.4(LYST):c.5061T>A (p.Tyr1687Ter)Pathogenic
Chédiak-Higashi syndrome
★★☆☆2025→ Residue 1687
NM_000081.4(LYST):c.10883dup (p.Tyr3628Ter)Pathogenic
Chédiak-Higashi syndrome
★★☆☆2025→ Residue 3628
NM_000081.4(LYST):c.8358+2T>GLikely pathogenic
Chédiak-Higashi syndrome
★★☆☆2025
NM_000081.4(LYST):c.5956C>T (p.Arg1986Ter)Pathogenic
Chédiak-Higashi syndrome
★★☆☆2025→ Residue 1986
NM_000081.4(LYST):c.8425G>T (p.Glu2809Ter)Pathogenic
not provided|Chédiak-Higashi syndrome
★★☆☆2025→ Residue 2809
NM_000081.4(LYST):c.11002G>T (p.Glu3668Ter)Pathogenic
Chédiak-Higashi syndrome
★★☆☆2025→ Residue 3668
NM_000081.4(LYST):c.1897A>T (p.Lys633Ter)Pathogenic
Chédiak-Higashi syndrome|not provided
★★☆☆2025→ Residue 633
NM_000081.4(LYST):c.9219_9222del (p.Glu3074fs)Pathogenic
Chédiak-Higashi syndrome
★★☆☆2025→ Residue 3074
NM_000081.4(LYST):c.3996del (p.Asp1333fs)Pathogenic
Chédiak-Higashi syndrome
★★☆☆2025→ Residue 1333
NM_000081.4(LYST):c.9784+1G>TLikely pathogenic
Chédiak-Higashi syndrome
★★☆☆2025
NM_000081.4(LYST):c.3085C>T (p.Gln1029Ter)Pathogenic
CHEDIAK-HIGASHI SYNDROME, CHILDHOOD TYPE|Chédiak-Higashi syndrome|not provided
★★☆☆2025→ Residue 1029
NM_000081.4(LYST):c.4863-1G>CLikely pathogenic
Chédiak-Higashi syndrome
★★☆☆2025
NM_000081.4(LYST):c.9838C>T (p.Arg3280Ter)Pathogenic
Chédiak-Higashi syndrome
★★☆☆2024→ Residue 3280
View on ClinVar ↗
Related Genes
VTA1Protein interaction95%HPS3Protein interaction93%HPS5Protein interaction83%STXBP2Protein interaction78%RAB27AProtein interaction77%STX11Protein interaction76%
Tissue Expression6 tissues
Bone Marrow
100%
Lung
16%
Ovary
10%
Liver
8%
Brain
7%
Heart
6%
Gene Interaction Network
Click a node to explore
LYSTVTA1HPS3HPS5STXBP2RAB27ASTX11
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted · UniProt Q99698
View on AlphaFold ↗
Constraintⓘ
LOEUFⓘ
0.51Moderately Constrained
pLIⓘ
0.00Tolerant
Observed/Expected LoF0.44 [0.38–0.51]
RankingsWhere LYST stands among ~20K protein-coding genes
  • #6,996of 20,598
    Most Researched67
  • #230of 5,498
    Most Pathogenic Variants272 · top 5%
  • #3,060of 17,882
    Most Constrained (LOEUF)0.51 · top quartile
Genes detectedLYST
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
Pediatric hemophagocytic lymphohistiocytosis.
PMID: 32107531
Blood · 2020
1.00
2
Chediak-Higashi syndrome.
PMID: 37254856
Curr Opin Hematol · 2023
0.90
3
Chediak-Higashi syndrome.
PMID: 18043242
Curr Opin Hematol · 2008
0.80
4
PMID: 20301751
0.70
5
Frequency and spectrum of disease-causing variants in 1892 patients with suspected genetic HLH disorders.
PMID: 32542393
Blood Adv · 2020
0.60