Gene
LYST
lysosomal trafficking regulator
- HGNC 1968(opens in a new tab)
- Ensembl gene ENSG00000143669(opens in a new tab)
- NCBI Gene 1130(opens in a new tab)
Summary
- Cytogenetic location
- 1q42.3
- Coordinates
- Chromosome 1: 235,661,041–235,866,906 (GRCh38)
- Exons
- 53 exons across 205.9 kb
- Protein
- 3,801 amino acids
- Inheritance
- Autosomal recessive
- Also known as
- CHS, Mauve
- Previous symbols
- CHS1
- MANE Select transcript
- ENST00000389793.7NM_000081.4
- Locus type
- gene with protein product
Reference genomeGRCh38hg38
Positions on gene and variant pages follow this choice, in this browser.
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Chediak-Higashi syndrome
- Autosomal recessive
ChC)diak-Higashi syndrome (CHS) is a rare severe genetic disorder generally characterized by partial oculocutaneous albinism (OCA), severe immunodeficiency, mild bleeding, neurological dysfunction and lymphoproliferative disorder. A classic, early-onset form and an attenuated, later-onset form (Atypical CHS) have been described.
- ClinGen rates the link definitive
- 5 GenCC submitters rate it definitive or strong
Broader groupings
Other Inborn Errors of Immunity
- Inborn error of immunity
One of 114 genes linked to it
Inherited disorders of the immune system caused by changes in single genes, affecting how the body fights infection or regulates inflammation.
- ClinGen rates the link definitive
- 5 GenCC submitters rate it definitive or strong
Inheritance
- Autosomal recessive
- It takes a changed copy from each parent. With one, you are a carrier and usually unaffected; when both parents are carriers, each child has a one-in-four chance of inheriting two.
How LYST is laid out
- Coding sequence
- Untranslated region
- Intron
- Direction of transcription
- Known disease-causing sites
- Stretches short reads find hard
Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.
Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).
Nearby genes from Ensembl release 116, on GRCh38.
Exons make up 13.5 kb of the gene's 205.9 kb; 11,406 of those bases code for the protein.
How a genome test reads LYST
242
positions in LYST where ClinVar classes a change as pathogenic or likely pathogenic
None of them falls in a region short reads find hard.
A whole genome covers all 205.9 kb of LYST, introns included, not only the 13.5 kb of exons.
Traits linked to LYST
The Human Phenotype Ontology lists these as features of the rare conditions LYST can cause. Each trait's page lists the other genes linked to it.
Abnormality of the nervous system
- Intellectual disability
- Peripheral neuropathy
- Abnormal gait
- Abnormality of extrapyramidal motor function
- Abnormality of movement
- Abnormality of the nervous system
- Ataxia
- Brain degeneration
Show 18 more traits
- Cognitive impairment
- Cranial nerve paralysis
- Damage to nerves that sense feeling
- Decreased nerve conduction velocity
- Degeneration of cerebellum
- Degeneration of the spinal cord
- Dementia
- Epilepsy
- Inability to walk
- Incoordination
- Motor polyneuropathy
- Parkinsonism
- Somatic sensory dysfunction
- Specific learning disability
- Tremor
- Decreased reflex response
- Ongoing loss of nerve cells
- Progressive peripheral neuropathy
Abnormality of blood and blood-forming tissues
- Giant neutrophil granules
- Low number of red blood cells or hemoglobin
- Abnormal leukocyte morphology
- Abnormality of coagulation
- Abnormality of multiple cell lineages in the bone marrow
- Bleeding gums
- Bloody nose
- Bruising susceptibility
Show 15 more traits
- Hemophagocytosis
- Increased CD25+ mast cell proportion
- Vacuolated lymphocytes
- Abnormal natural killer cell morphology
- Abnormal neutrophil physiology
- Abnormal platelet function
- Bleeding tendency
- Hypofibrinogenemia
- Low blood cell count
- Low blood neutrophil count
- Low platelet count
- Abnormal dense granules
- Decreased blood leukocyte number
- Impaired neutrophil bactericidal activity
- Recurring nosebleed
Abnormality of the eye
- Absent pigmentation in the eye
- Abnormal retinal pigmentation
- Decreased clarity of vision
- Extreme sensitivity of the eyes to light
- Light eye color
- Rotary nystagmus
- Cross-eyed
- Horizontal nystagmus
Show 2 more traits
Abnormality of the immune system
- Decreased immune function
- Recurrent bacterial infections
- Recurrent infections
- Recurrent respiratory infections
- Recurrent bacterial skin infections
- Recurrent staphylococcal infections
- Recurrent streptococcal infections
- Skin rash
Show 1 more trait
Abnormality of the integument
- Loss of hair color
- Patchy lightened skin
- Silver-gray hair
- Fair skin
- Open skin sore
- Large clumps of pigment irregularly distributed along hair shaft
- Photosensitive skin
- Spotty increased pigmentation
Show 1 more trait
Laboratory abnormality
- Elevated serum ferritin
- Fever
- Decreased protein levels in blood
- Fluid around lungs
- Fluid retention
- High liver enzymes
- Increased circulating lactate dehydrogenase concentration
- Increased plasma triglycerides
Show 1 more trait
External links
Gene records
Transcript
Protein
Where this comes from
- HGNC: the gene's symbol, name, other symbols and location.
- MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
- GenCC and ClinGen, released 2026-10-16: which conditions the gene is linked to, and how strongly.
- The ACMG secondary findings list, SF v3.2.
- ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
- The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
- Data release 2026.10.16-c6eea6bf.
Cite this page
Dante Labs. (n.d.). LYST gene: lysosomal trafficking regulator. Retrieved 16 October 2026, from https://dantelabs.com/genes/lyst
Dante Labs. LYST gene: lysosomal trafficking regulator [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/lyst
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