LYST (Lysosomal-trafficking regulator) variants and mutations
LYST (also known as Lysosomal-trafficking regulator) is a human protein-coding gene encoding a lysosomal-trafficking regulator protein. It controls size, trafficking, and exocytosis of lysosome-related organelles in immune cells, melanocytes, and other tissues. Biallelic loss-of-function variants cause Chediak-Higashi syndrome with partial albinism, recurrent infection, bleeding, and risk of hemophagocytic lymphohistiocytosis. This analysis covers 4,472 LYST variants and mutations. Of these, 72% have computational variant effect predictions. Disease context includes Chediak-Higashi syndrome, Chédiak-Higashi syndrome, and Parkinson disease. Example LYST variants include M1?, T3I, and T3N.
Variant analysis overview
- Gene: LYST
- Protein: Lysosomal-trafficking regulator
- UniProt accession: Q99698
- Organism: Homo sapiens
- Variants analyzed: 4472
- Variant scope: all variants
- Completed: 2026-08-22
Variant and mutation evidence
- Variant composition: 4,289 unspecified-consequence records; 76 synonymous variants; 78 missense variants; 10 frameshift variants; 6 stop-gained variants; 5 in-frame deletions; 7 splice-region variants; 1 in-frame insertions
- Prediction scores: 3,222 variants have prediction scores (72% of the analyzed set).
Clinical, disease, and population context
- Disease context: 25 disease associations are represented. Top associations: Chediak-Higashi syndrome, Chédiak-Higashi syndrome, Parkinson disease, hereditary disease, Spastic paraplegia, Parkinsonism, peripheral neuropathy, hair color, systemic lupus erythematosus, attenuated Chédiak-Higashi syndrome, autoinflammatory syndrome, albinism.
Protein structure and variant hotspots
- Protein features: 2 domains; 10 post-translational modification sites.
- Structural context: 385 variants have structural context.
- PTM context: 11 variants overlap post-translational modification sites.
Data sources
Evidence in this analysis draws on EBI Proteins Variation, UniProt, gnomAD v4, EuropePMC, 3D Hotspot Analysis, Interaction Network Analysis, AlphaFold DB, gnomAD constraint, Open Targets, ClinGen, MaveDB, LitVar.
Notable LYST variants
Examples include M1?, T3I, T3N, D4E, D4N, S5N, N6D, N6K. Listed records include available protein-change notation, database identifiers, clinical classifications, computational predictions, population evidence, experimental measurements, and disease context.
- M1?, NCI-TCGA Cosmic COSV6771, cosmic curated COSV67710, Variant assessed as somatic; high impact.
- T3I (p.Thr3Ile), cosmic curated COSV10972, 1000Genomes rs548589202, ExAC rs548589202, TOPMed rs548589202, REVEL 0.06, CADD 19.20, Uncertain significance
- T3N (p.Thr3Asn), rs548589202, ClinGen CA344969506, ClinVar RCV002944225, ClinVar RCV004526952, REVEL 0.06, CADD 17.90, Uncertain significance, Chédiak-Higashi syndrome; not specified
- D4E (p.Asp4Glu), TOPMed rs928840637, gnomAD rs928840637, REVEL 0.14, CADD 19.60
- D4N (p.Asp4Asn), rs141312203, ClinGen CA1467756, cosmic curated COSV10108, ClinVar RCV001877008, REVEL 0.09, CADD 18.10, Uncertain significance, Chédiak-Higashi syndrome
- S5N (p.Ser5Asn), NCI-TCGA Cosmic COSV6771, Variant assessed as somatic; moderate impact.
- N6D (p.Asn6Asp), NCI-TCGA Cosmic COSV1010, cosmic curated COSV10108, Variant assessed as somatic; moderate impact.
- N6K (p.Asn6Lys), rs563310448, ClinGen CA344969483, ClinVar RCV003331676, ClinVar RCV005655255, REVEL 0.26, CADD 24.40, Uncertain significance, Inborn genetic diseases; not specified
- N6S (p.Asn6Ser), gnomAD rs1254846711, REVEL 0.29, CADD 25.00
- L8P (p.Leu8Pro), TOPMed rs1313658431, gnomAD rs1313658431, REVEL 0.68, CADD 27.10
- L8R (p.Leu8Arg), TOPMed rs1313658431, gnomAD rs1313658431, REVEL 0.65, CADD 26.90
- L8V (p.Leu8Val), rs2527303164, ClinGen CA344969476, ClinVar RCV002958831, REVEL 0.35, CADD 15.80, Uncertain significance, Chédiak-Higashi syndrome
- A9T (p.Ala9Thr), Ensembl rs1572394507
- A9V (p.Ala9Val), ExAC rs752805538, gnomAD rs752805538, REVEL 0.36, CADD 27.10
- R10C (p.Arg10Cys), rs767877661, ClinGen CA1467754, cosmic curated COSV67705, ClinVar RCV001323183, REVEL 0.24, CADD 29.00, Uncertain significance, Inborn genetic diseases; Chédiak-Higashi syndrome
- R10H (p.Arg10His), ESP rs145439907, ExAC rs145439907, TOPMed rs145439907, gnomAD rs145439907, REVEL 0.29, CADD 26.60
- E11* (p.Glu11Ter), NCI-TCGA TCGA novel, Variant assessed as somatic; high impact.
- D15A (p.Asp15Ala), ExAC rs773170266, gnomAD rs773170266
- D15G (p.Asp15Gly), rs773170266, NCI-TCGA Cosmic COSV6770, ExAC rs773170266, gnomAD rs773170266, REVEL 0.71, CADD 26.80, Variant assessed as somatic; moderate impact.
- D15H (p.Asp15His), ESP rs372774380, ExAC rs372774380, TOPMed rs372774380, gnomAD rs372774380, Uncertain significance
- D15N (p.Asp15Asn), rs372774380, ClinGen CA1467750, cosmic curated COSV67702, ClinVar RCV001368388, REVEL 0.42, CADD 25.90, Uncertain significance, Chédiak-Higashi syndrome
- N17D (p.Asn17Asp), ExAC rs747677876, gnomAD rs747677876, REVEL 0.18, CADD 22.80
- N17S (p.Asn17Ser), rs1177000208, ClinGen CA344969379, ClinVar RCV001223072, ClinVar RCV004629494, REVEL 0.15, CADD 21.60, Uncertain significance, Inborn genetic diseases; Chédiak-Higashi syndrome
- R18Q (p.Arg18Gln), rs768197548, ClinGen CA1467745, ClinVar RCV001369196, ExAC rs768197548, REVEL 0.03, CADD 17.50, Uncertain significance, Chédiak-Higashi syndrome
- R18W (p.Arg18Trp), rs780640186, ClinGen CA1467746, ClinVar RCV000801674, ExAC rs780640186, REVEL 0.31, CADD 29.70, Uncertain significance, Chédiak-Higashi syndrome
- C20F (p.Cys20Phe), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- C20G (p.Cys20Gly), gnomAD rs556924327, REVEL 0.79, CADD 27.30
- N21S (p.Asn21Ser), gnomAD rs1256066587, REVEL 0.09, CADD 21.50
- A22V (p.Ala22Val), rs1268630145, NCI-TCGA Cosmic COSV6771, cosmic curated COSV67713, Ensembl rs1268630145, AlphaMissense 0.23, MetaLR 0.58, Variant assessed as somatic; moderate impact.
- V24A (p.Val24Ala), rs151236654, ClinGen CA1467738, ClinVar RCV000704497, ClinVar RCV004792412, REVEL 0.10, CADD 21.60, Uncertain significance, Chédiak-Higashi syndrome; not provided
- V24F (p.Val24Phe), rs201023832, ClinGen CA1467739, ClinVar RCV002785418, ClinVar RCV002794972, REVEL 0.22, CADD 23.30, Uncertain significance, Chédiak-Higashi syndrome; Inborn genetic diseases
- V24G (p.Val24Gly), rs151236654, ClinGen CA344969258, ClinVar RCV001950349, REVEL 0.30, CADD 24.00, Uncertain significance, Chédiak-Higashi syndrome
- V24I (p.Val24Ile), 1000Genomes rs201023832, ESP rs201023832, ExAC rs201023832, TOPMed rs201023832, REVEL 0.10, CADD 22.70, Uncertain significance
- Q25R (p.Gln25Arg), rs767571020, ClinGen CA1467737, ClinVar RCV002624507, ExAC rs767571020, REVEL 0.17, CADD 23.10, Uncertain significance, Chédiak-Higashi syndrome
- E28G (p.Glu28Gly), rs887494891, ClinGen CA39625079, ClinVar RCV003092639, TOPMed rs887494891, REVEL 0.30, CADD 29.10, Uncertain significance, Chédiak-Higashi syndrome
- E28K (p.Glu28Lys), NCI-TCGA Cosmic COSV6770, cosmic curated COSV67705, Variant assessed as somatic; moderate impact.
- A29T (p.Ala29Thr), rs755173231, ClinGen CA1467736, cosmic curated COSV67708, ClinVar RCV001239042, REVEL 0.09, CADD 18.20, Uncertain significance, Autoinflammatory syndrome; Chédiak-Higashi syndrome
- A29V (p.Ala29Val), gnomAD rs1310444782, REVEL 0.19, CADD 23.60, Uncertain significance, not provided
- R30M (p.Arg30Met), gnomAD rs1394389379, REVEL 0.17, CADD 24.30
- R30S (p.Arg30Ser), ExAC rs751871167, gnomAD rs751871167, REVEL 0.13, CADD 23.10
- E31K (p.Glu31Lys), ExAC rs766509659, TOPMed rs766509659, gnomAD rs766509659, REVEL 0.20, CADD 26.80
- E32G (p.Glu32Gly), cosmic curated COSV67710, Ensembl rs1675822145, REVEL 0.20, CADD 29.00
- E33D (p.Glu33Asp), Ensembl rs2102996920
- E33G (p.Glu33Gly), rs772935284, ClinGen CA1467732, ClinVar RCV002943675, ExAC rs772935284, REVEL 0.17, CADD 25.80, Uncertain significance, Chédiak-Higashi syndrome
- E35G (p.Glu35Gly), gnomAD rs1185984907, REVEL 0.25, CADD 27.50, Uncertain significance, Inborn genetic diseases
- E35K (p.Glu35Lys), rs148788623, cosmic curated COSV10108, ESP rs148788623, ExAC rs148788623, REVEL 0.24, CADD 26.40, Variant assessed as somatic; moderate impact.
- E36* (p.Glu36Ter), rs2527301436, ClinGen CA344969042, ClinVar RCV003637117, Pathogenic
- T37A (p.Thr37Ala), rs776142039, ClinGen CA1467729, ClinVar RCV001966272, ClinVar RCV004044613, REVEL 0.16, CADD 20.00, Uncertain significance, Inborn genetic diseases; not provided; Chédiak-Higashi syndrome
- T37K (p.Thr37Lys), ESP rs375106444, ExAC rs375106444, TOPMed rs375106444, gnomAD rs375106444, REVEL 0.12, CADD 23.90, Uncertain significance
- T37M (p.Thr37Met), rs375106444, ClinGen CA1467728, cosmic curated COSV67713, ClinVar RCV000348659, REVEL 0.13, CADD 24.10, Uncertain significance, not provided; Chédiak-Higashi syndrome
- T37R (p.Thr37Arg), ESP rs375106444, ExAC rs375106444, TOPMed rs375106444, gnomAD rs375106444, Uncertain significance
- H38Y (p.His38Tyr), rs200935378, ClinGen CA1467726, ClinVar RCV000817010, ClinVar RCV005589902, REVEL 0.41, CADD 24.70, Uncertain significance, Chédiak-Higashi syndrome; Inborn genetic diseases; not provided
- M39K (p.Met39Lys), rs1364323740, ClinGen CA344968957, ClinVar RCV002876720, ClinVar RCV004571412, REVEL 0.65, CADD 25.50, Uncertain significance, Chédiak-Higashi syndrome; Inborn genetic diseases
- M39V (p.Met39Val), TOPMed rs1675815529, REVEL 0.23, CADD 21.00
- A40T (p.Ala40Thr), TOPMed rs906884088, gnomAD rs906884088, REVEL 0.23, CADD 23.80
- A40V (p.Ala40Val), rs538522923, ClinGen CA1467725, ClinVar RCV001944891, ExAC rs538522923, REVEL 0.15, CADD 22.90, Uncertain significance, Chédiak-Higashi syndrome
- T41A (p.Thr41Ala), ExAC rs749681929, TOPMed rs749681929, gnomAD rs749681929, REVEL 0.04, CADD 9.76
- T41N (p.Thr41Asn), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- T41S (p.Thr41Ser), ExAC rs749681929, TOPMed rs749681929, gnomAD rs749681929, REVEL 0.05, CADD 14.50
- L42P (p.Leu42Pro), rs2527300940, ClinGen CA344968878, ClinVar RCV002302955, Uncertain significance, Chédiak-Higashi syndrome
- L42V (p.Leu42Val), rs1229357698, ClinGen CA344968887, ClinVar RCV001878145, ClinVar RCV004793572, REVEL 0.38, CADD 25.40, Uncertain significance, Chédiak-Higashi syndrome; not provided
- G43D (p.Gly43Asp), rs2527300997, ClinGen CA2574025385, ClinVar RCV003469978, Likely pathogenic
- Q44* (p.Gln44Ter), rs756716492, ClinGen CA1467722, ClinVar RCV003523867, ExAC rs756716492, CADD 37.00, Pathogenic
- Q44H (p.Gln44His), Ensembl rs1572393935
- Q44R (p.Gln44Arg), rs1294045996, ClinGen CA344968822, ClinVar RCV001035778, gnomAD rs1294045996, REVEL 0.21, CADD 24.40, Uncertain significance, Chédiak-Higashi syndrome
- Y45H (p.Tyr45His), rs2527300776, ClinGen CA344968802, ClinVar RCV002044643, REVEL 0.80, CADD 27.10, Uncertain significance, Chédiak-Higashi syndrome
- L46F (p.Leu46Phe), rs2527300755, ClinGen CA344968776, ClinVar RCV002820508, REVEL 0.56, CADD 26.20, Uncertain significance, Chédiak-Higashi syndrome
- V47A (p.Val47Ala), gnomAD rs1409282900, REVEL 0.33, CADD 26.10
- V47F (p.Val47Phe), Ensembl rs1675810975
- V47I (p.Val47Ile), rs1675810975, ClinGen CA344968764, ClinVar RCV003268314, AlphaMissense 0.56, MetaLR 0.42, Uncertain significance, Inborn genetic diseases
- H48R (p.His48Arg), rs200132460, ClinGen CA1467721, ClinVar RCV000629222, ClinVar RCV001311684, REVEL 0.10, CADD 14.50, Conflicting interpretations, Chédiak-Higashi syndrome; not provided
- G49C (p.Gly49Cys), NCI-TCGA Cosmic COSV1010, cosmic curated COSV10109, Variant assessed as somatic; moderate impact.
- G49D (p.Gly49Asp), rs2527300575, ClinGen CA344968708, ClinVar RCV001232594, REVEL 0.43, CADD 25.00, Uncertain significance, Chédiak-Higashi syndrome
- R50* (p.Arg50Ter), rs80338643, ClinGen CA116450, ClinVar RCV000004017, ClinVar RCV000055722, AlphaMissense 0.87, MetaLR 0.63, Pathogenic
- R50G (p.Arg50Gly), rs80338643, ClinGen CA344968694, ClinVar RCV001047342, TOPMed rs80338643, REVEL 0.70, AlphaMissense 0.87, Uncertain significance, Chédiak-Higashi syndrome
- R50L (p.Arg50Leu), NCI-TCGA Cosmic COSV6771, cosmic curated COSV67713, Variant assessed as somatic; moderate impact.
- R50Q (p.Arg50Gln), rs368095341, ClinGen CA1467719, ClinVar RCV001360702, ESP rs368095341, REVEL 0.68, CADD 26.50, Uncertain significance, Chédiak-Higashi syndrome
- F52L (p.Phe52Leu), rs2527300405, ClinGen CA344968654, ClinVar RCV002042702, REVEL 0.30, CADD 23.90, Uncertain significance, Chédiak-Higashi syndrome
- L53I (p.Leu53Ile), ExAC rs758551378, TOPMed rs758551378, gnomAD rs758551378, REVEL 0.05, CADD 20.60, Likely benign
- L53Q (p.Leu53Gln), gnomAD rs1675805723, REVEL 0.22, CADD 25.30
- L55V (p.Leu55Val), rs1182404827, NCI-TCGA Cosmic COSV6770, cosmic curated COSV67707, gnomAD rs1182404827, AlphaMissense 0.75, MetaLR 0.62, Variant assessed as somatic; moderate impact.
- T56I (p.Thr56Ile), rs2527300081, ClinGen CA344968540, ClinVar RCV002031759, Uncertain significance, Chédiak-Higashi syndrome
- K57N (p.Lys57Asn), rs761573707, ClinGen CA344968494, ClinVar RCV003034220, Uncertain significance, Chédiak-Higashi syndrome
- S60P (p.Ser60Pro), Ensembl rs1675802846, REVEL 0.20, CADD 24.30
- I61M (p.Ile61Met), gnomAD rs1675802266, REVEL 0.11, CADD 18.70
- I61V (p.Ile61Val), rs776670065, ClinGen CA1467712, ClinVar RCV002942792, ExAC rs776670065, REVEL 0.04, CADD 14.60, Uncertain significance, Chédiak-Higashi syndrome
- I62V (p.Ile62Val), rs2527299782, ClinGen CA344968432, ClinVar RCV002988493, Uncertain significance, Chédiak-Higashi syndrome
- Q64* (p.Gln64Ter), NCI-TCGA Cosmic COSV1010, cosmic curated COSV10109, Variant assessed as somatic; high impact.
- Q64K (p.Gln64Lys), rs2527299738, ClinGen CA344968417, ClinVar RCV003371564, REVEL 0.42, CADD 27.30, Uncertain significance, Inborn genetic diseases
- A65G (p.Ala65Gly), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- T67I (p.Thr67Ile), rs1673632150, ClinGen CA344966120, ClinVar RCV002913148, gnomAD rs1673632150, REVEL 0.52, CADD 26.90, Uncertain significance, Chédiak-Higashi syndrome
- C68S (p.Cys68Ser), Ensembl rs1673631891, REVEL 0.71, CADD 26.60
- R69K (p.Arg69Lys), ESP rs371476919, REVEL 0.21, CADD 26.10
- E71A (p.Glu71Ala), ExAC rs747426872, gnomAD rs747426872, REVEL 0.56, CADD 32.00
- E71D (p.Glu71Asp), Ensembl rs1572347340
- L75V (p.Leu75Val), Ensembl rs2102906107, REVEL 0.41, CADD 24.80
- L76F (p.Leu76Phe), Ensembl rs1558289247, REVEL 0.38, CADD 32.00, Uncertain significance, Chédiak-Higashi syndrome
- L79F (p.Leu79Phe), TOPMed rs1173921496, gnomAD rs1173921496, Uncertain significance
- L79I (p.Leu79Ile), TOPMed rs1173921496, gnomAD rs1173921496, Uncertain significance
- L79V (p.Leu79Val), rs1173921496, ClinGen CA344965984, ClinVar RCV001372066, TOPMed rs1173921496, REVEL 0.44, CADD 24.50, Uncertain significance, Chédiak-Higashi syndrome
- P81A (p.Pro81Ala), NCI-TCGA Cosmic COSV6771, cosmic curated COSV67714, Variant assessed as somatic; moderate impact.
- P81L (p.Pro81Leu), Ensembl rs2102906016
- V83I (p.Val83Ile), rs1673627982, ClinGen CA344965947, ClinVar RCV001236774, REVEL 0.26, CADD 24.60, Uncertain significance, Chédiak-Higashi syndrome
- V83L (p.Val83Leu), gnomAD rs1673627982, REVEL 0.24, CADD 23.50
- W84R (p.Trp84Arg), ESP rs150500390, ExAC rs150500390, TOPMed rs150500390, gnomAD rs150500390, REVEL 0.64, CADD 27.90
- K85E (p.Lys85Glu), rs1451315699, ClinGen CA344965915, ClinVar RCV002621604, TOPMed rs1451315699, REVEL 0.32, CADD 29.10, Uncertain significance, Chédiak-Higashi syndrome
- I86M (p.Ile86Met), gnomAD rs1673626284, REVEL 0.33, CADD 19.40
- I86T (p.Ile86Thr), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- P87L (p.Pro87Leu), NCI-TCGA Cosmic COSV6771, cosmic curated COSV67710, Variant assessed as somatic; moderate impact.
- P87T (p.Pro87Thr), rs779163949, ClinGen CA1467678, ClinVar RCV001935803, ClinVar RCV006280799, REVEL 0.59, CADD 26.00, Uncertain significance, Chédiak-Higashi syndrome; not provided
- E90* (p.Glu90Ter), NCI-TCGA TCGA novel, Variant assessed as somatic; high impact.
- E91Q (p.Glu91Gln), gnomAD rs1673625438, REVEL 0.04, CADD 19.60
- K92M (p.Lys92Met), ExAC rs757411778, gnomAD rs757411778, REVEL 0.20, CADD 24.00
- A93G (p.Ala93Gly), rs771549954, NCI-TCGA TCGA novel, ClinGen CA1467676, ClinVar RCV000820937, REVEL 0.17, CADD 24.20, Uncertain significance, Chédiak-Higashi syndrome
- A93T (p.Ala93Thr), gnomAD rs1441889423, REVEL 0.22, CADD 24.20
- T94A (p.Thr94Ala), rs886046182, ClinGen CA10610430, ClinVar RCV000278844, Ensembl rs886046182, REVEL 0.12, CADD 0.01, Uncertain significance, Chédiak-Higashi syndrome
- T94I (p.Thr94Ile), rs777389303, ClinGen CA205750, cosmic curated COSV67705, ClinVar RCV000192732, REVEL 0.13, CADD 17.30, Conflicting interpretations, Chédiak-Higashi syndrome; not specified; not provided
- D95E (p.Asp95Glu), rs747965676, ClinGen CA1467654, ClinVar RCV000706487, ClinVar RCV001759421, REVEL 0.26, CADD 22.60, Uncertain significance, Autoinflammatory syndrome; not provided; Chédiak-Higashi syndrome
- F96V (p.Phe96Val), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- N97K (p.Asn97Lys), NCI-TCGA Cosmic COSV1010, cosmic curated COSV10108, NCI-TCGA Cosmic COSV6770, REVEL 0.09, CADD 11.30, Variant assessed as somatic; moderate impact.
- L98R (p.Leu98Arg), TOPMed rs1673351594
- L98V (p.Leu98Val), TOPMed rs1274363445, gnomAD rs1274363445, Likely benign
- P99A (p.Pro99Ala), ESP rs375315039, TOPMed rs375315039, gnomAD rs375315039, REVEL 0.37, CADD 24.00
- P99L (p.Pro99Leu), rs781295135, ClinGen CA1467653, ClinVar RCV001050338, ExAC rs781295135, REVEL 0.43, CADD 25.00, Uncertain significance, Chédiak-Higashi syndrome
- L100F (p.Leu100Phe), ESP rs372351602, ExAC rs372351602, TOPMed rs372351602, gnomAD rs372351602, Uncertain significance, Chédiak-Higashi syndrome
- L100H (p.Leu100His), gnomAD rs1673350303, REVEL 0.14, CADD 24.30
- D103H (p.Asp103His), ExAC rs765939688, TOPMed rs765939688, gnomAD rs765939688, REVEL 0.12, CADD 23.20
- D103V (p.Asp103Val), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- D103Y (p.Asp103Tyr), ExAC rs765939688, TOPMed rs765939688, gnomAD rs765939688, REVEL 0.24, CADD 23.40
- I104T (p.Ile104Thr), TOPMed rs1349537073, gnomAD rs1349537073, REVEL 0.21, CADD 24.60
- I104V (p.Ile104Val), rs2102892270, ClinGen CA344965495, ClinVar RCV003131525, Ensembl rs2102892270, REVEL 0.04, CADD 13.70, Uncertain significance, Chédiak-Higashi syndrome
- I105T (p.Ile105Thr), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- I105V (p.Ile105Val), ExAC rs757904572, gnomAD rs757904572, REVEL 0.07, CADD 18.60
- T107N (p.Thr107Asn), rs750083768, ClinGen CA1467648, ClinVar RCV001973747, ExAC rs750083768, REVEL 0.09, CADD 19.10, Uncertain significance, Chédiak-Higashi syndrome
- K108T (p.Lys108Thr), TOPMed rs1673347955, gnomAD rs1673347955, REVEL 0.24, CADD 25.50
- E109V (p.Glu109Val), rs2527133455, ClinGen CA344965460, ClinVar RCV003523929, Uncertain significance, Chédiak-Higashi syndrome
- K110N (p.Lys110Asn), ExAC rs764938143, TOPMed rs764938143, gnomAD rs764938143, REVEL 0.10, CADD 17.90, Uncertain significance, Inborn genetic diseases
- N111Y (p.Asn111Tyr), NCI-TCGA Cosmic COSV6770, cosmic curated COSV67704, Variant assessed as somatic; moderate impact.
- S112* (p.Ser112Ter), NCI-TCGA TCGA novel, CADD 36.00, Variant assessed as somatic; high impact.
- S113G (p.Ser113Gly), rs1403594840, ClinGen CA344965435, ClinVar RCV003199491, TOPMed rs1403594840, REVEL 0.07, CADD 16.00, Uncertain significance, Inborn genetic diseases
- Q115* (p.Gln115Ter), NCI-TCGA TCGA novel, Variant assessed as somatic; high impact.
- Q115E (p.Gln115Glu), rs775773934, ClinGen CA1467645, ClinVar RCV002015289, ClinVar RCV005660310, REVEL 0.03, CADD 17.50, Uncertain significance, Inborn genetic diseases; Chédiak-Higashi syndrome
- R116G (p.Arg116Gly), NCI-TCGA Cosmic COSV6771, cosmic curated COSV67714, Variant assessed as somatic; moderate impact.
- T118I (p.Thr118Ile), rs1475563507, ClinGen CA344965396, ClinVar RCV003051428, TOPMed rs1475563507, REVEL 0.07, CADD 22.80, Uncertain significance, Chédiak-Higashi syndrome
- Q119* (p.Gln119Ter), NCI-TCGA Cosmic COSV1010, Variant assessed as somatic; high impact.
- Q119E (p.Gln119Glu), NCI-TCGA Cosmic COSV1010, Variant assessed as somatic; moderate impact.
- Q119K (p.Gln119Lys), NCI-TCGA Cosmic COSV1010, cosmic curated COSV10108, Variant assessed as somatic; moderate impact.
- E120G (p.Glu120Gly), Ensembl rs2102891913
- K121N (p.Lys121Asn), NCI-TCGA Cosmic COSV1010, cosmic curated COSV10108, Variant assessed as somatic; moderate impact.
- L122I (p.Leu122Ile), NCI-TCGA Cosmic COSV1010, cosmic curated COSV10108, Variant assessed as somatic; moderate impact.
- L122S (p.Leu122Ser), ExAC rs759993717, TOPMed rs759993717, gnomAD rs759993717, REVEL 0.08, CADD 17.40
- H123Q (p.His123Gln), TOPMed rs1462203583, gnomAD rs1462203583
- H123R (p.His123Arg), rs3768067, ClinGen CA1467642, cosmic curated COSV67704, ClinVar RCV000323413, CADD 17.80, Benign/Likely benign, Autoinflammatory syndrome; Chédiak-Higashi syndrome; not specified
- H123Y (p.His123Tyr), rs2527132957, ClinGen CA344965365, ClinVar RCV002638487, Uncertain significance, Chédiak-Higashi syndrome
- E125A (p.Glu125Ala), gnomAD rs1221276518, REVEL 0.08, CADD 22.90
- E125D (p.Glu125Asp), gnomAD rs1450462176, REVEL 0.05, CADD 17.80
- E125K (p.Glu125Lys), Ensembl rs957967518
- G126R (p.Gly126Arg), TOPMed rs1208650740, gnomAD rs1208650740, REVEL 0.08, CADD 17.80
- G126V (p.Gly126Val), NCI-TCGA TCGA novel, CADD 20.40, Variant assessed as somatic; high impact.
- S127R (p.Ser127Arg), TOPMed rs1046482208, REVEL 0.04, CADD 17.40
- A128D (p.Ala128Asp), rs770962889, ClinGen CA1467641, ClinVar RCV002022608, ExAC rs770962889, REVEL 0.06, CADD 16.30, Uncertain significance, Chédiak-Higashi syndrome
- A128T (p.Ala128Thr), Ensembl rs1673341807, REVEL 0.03, CADD 13.70
- L129P (p.Leu129Pro), TOPMed rs1673341287, REVEL 0.04, CADD 11.90
- S130T (p.Ser130Thr), rs773369935, ClinGen CA1467639, ClinVar RCV001968568, ExAC rs773369935, REVEL 0.02, CADD 9.02, Uncertain significance, Chédiak-Higashi syndrome
- S131R (p.Ser131Arg), TOPMed rs1194287259, gnomAD rs1194287259, REVEL 0.04, CADD 19.00
- Q132H (p.Gln132His), gnomAD rs1229777043
- Q132R (p.Gln132Arg), rs2527132523, ClinGen CA344965304, ClinVar RCV003047738, ClinVar RCV003047739, REVEL 0.07, CADD 18.30, Uncertain significance, Inborn genetic diseases; Chédiak-Higashi syndrome
- V133A (p.Val133Ala), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- S134F (p.Ser134Phe), ExAC rs770004763, gnomAD rs770004763, REVEL 0.06, CADD 26.00
- S134P (p.Ser134Pro), NCI-TCGA Cosmic COSV1010, cosmic curated COSV10108, REVEL 0.01, CADD 20.90, Variant assessed as somatic; moderate impact.
- A135T (p.Ala135Thr), TOPMed rs1673339522
- K136E (p.Lys136Glu), rs2527132266, ClinGen CA344965283, ClinVar RCV002576229, REVEL 0.07, CADD 23.10, Uncertain significance, Chédiak-Higashi syndrome
- N138S (p.Asn138Ser), ExAC rs747965164, gnomAD rs747965164, REVEL 0.03, CADD 13.70
- V139G (p.Val139Gly), ExAC rs781096801, TOPMed rs781096801, gnomAD rs781096801, REVEL 0.03, CADD 12.70
- F140L (p.Phe140Leu), rs754991654, ClinGen CA1467635, ClinVar RCV001060555, ExAC rs754991654, REVEL 0.03, CADD 9.49, Uncertain significance, Chédiak-Higashi syndrome
- R141* (p.Arg141Ter), rs201847422, NCI-TCGA Cosmic COSV6770, cosmic curated COSV67707, 1000Genomes rs201847422, CADD 35.00, Variant assessed as somatic; high impact.
- R141Q (p.Arg141Gln), rs143601402, ClinGen CA1467633, ClinVar RCV000823752, ClinVar RCV004792542, REVEL 0.05, CADD 17.20, Uncertain significance, not provided; Chédiak-Higashi syndrome
- K142N (p.Lys142Asn), NCI-TCGA Cosmic COSV6771, cosmic curated COSV67715, Variant assessed as somatic; moderate impact.
- S143N (p.Ser143Asn), ExAC rs749936152, gnomAD rs749936152, REVEL 0.05, CADD 18.30, Uncertain significance, Inborn genetic diseases
- S143R (p.Ser143Arg), rs757912379, ClinGen CA1467632, ClinVar RCV001060556, ExAC rs757912379, REVEL 0.03, CADD 22.00, Uncertain significance, Chédiak-Higashi syndrome
Public LYST analysis runs
- LYST analysis run — LYST (4,472 variants) — completed 2026-08-22