ATP13A2 (Q9NQ11) variants and mutations
ATP13A2 (also known as Q9NQ11) is a human protein-coding gene encoding a polyamine-transporting ATPase 13A2 protein. It supports lysosomal and endolysosomal homeostasis and transports polyamines and other cationic substrates across intracellular membranes. Biallelic pathogenic variants cause Kufor-Rakeb syndrome and related early-onset parkinsonian-neurodegenerative phenotypes. This analysis covers 1,695 ATP13A2 variants and mutations. Of these, 81% have computational variant effect predictions. Disease context includes Kufor-Rakeb syndrome, autosomal recessive spastic paraplegia type 78, and parkinsonism due to ATP13A2 deficiency. Example ATP13A2 variants include S2C, S2N, and A3P.
Variant analysis overview
- Gene: ATP13A2
- Protein: Q9NQ11
- UniProt accession: Q9NQ11
- Organism: Homo sapiens
- Variants analyzed: 1695
- Variant scope: all variants
- Completed: 2026-08-20
Variant and mutation evidence
- Variant composition: 1,411 unspecified-consequence records; 1 stop retained variant; 2 stop lost; 79 synonymous variants; 157 missense variants; 27 frameshift variants; 7 stop-gained variants; 4 in-frame deletions; 1 splice-region variants; 1 protein altering variant; 5 substitution
- Prediction scores: 1,369 variants have prediction scores (81% of the analyzed set).
Clinical, disease, and population context
- Disease context: 25 disease associations are represented. Top associations: Kufor-Rakeb syndrome, autosomal recessive spastic paraplegia type 78, parkinsonism due to ATP13A2 deficiency, Spastic paraplegia, hereditary disease, Parkinson disease, neurodegeneration with brain iron accumulation, Hereditary late-onset Parkinson disease, Dystonia, complex hereditary spastic paraplegia, Abnormality of the skeletal system, Varicose veins.
Protein structure and variant hotspots
- Protein features: 10 transmembrane segments; 2 binding sites; 3 post-translational modification sites.
- Structural context: 316 variants have structural context.
- PTM context: 1 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, Protein Data Bank, AlphaFold DB, gnomAD constraint, Open Targets, ClinGen, MaveDB, LitVar.
Notable ATP13A2 variants
Examples include S2C, S2N, A3P, A3T, S5G, S5T, P7L, P7S. Listed records include available protein-change notation, database identifiers, clinical classifications, computational predictions, population evidence, experimental measurements, and disease context.
- S2C (p.Ser2Cys), rs2101432066, ClinGen CA338267563, ClinVar RCV001898394, Ensembl rs2101432066, Uncertain significance, Kufor-Rakeb syndrome; Autosomal recessive spastic paraplegia type 78
- S2N (p.Ser2Asn), Ensembl rs2077805596, REVEL 0.32, CADD 23.30
- A3P (p.Ala3Pro), rs549839037, ClinGen CA637809, ClinVar RCV000991571, ClinVar RCV001392172, REVEL 0.30, CADD 18.90, Conflicting interpretations, Inborn genetic diseases; Kufor-Rakeb syndrome; Autosomal recessive spastic parap
- A3T (p.Ala3Thr), rs549839037, ClinGen CA338267555, ClinVar RCV002692040, 1000Genomes rs549839037, REVEL 0.25, CADD 16.20, Uncertain significance, Inborn genetic diseases
- S5G (p.Ser5Gly), rs2101131465, ClinGen CA338265856, ClinVar RCV002027418, ClinVar RCV006327431, Uncertain significance, Inborn genetic diseases; Kufor-Rakeb syndrome; Autosomal recessive spastic parap
- S5T (p.Ser5Thr), TOPMed rs2077535998
- P7L (p.Pro7Leu), rs2077535736, ClinGen CA338265790, ClinVar RCV001939160, Ensembl rs2077535736, REVEL 0.10, CADD 18.60, Uncertain significance, Autosomal recessive spastic paraplegia type 78; Kufor-Rakeb syndrome
- P7S (p.Pro7Ser), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- V9M (p.Val9Met), rs143579092, ClinGen CA637792, ClinVar RCV002021661, ClinVar RCV003481253, REVEL 0.21, CADD 14.40, Uncertain significance, not provided; Autosomal recessive spastic paraplegia type 78; Kufor-Rakeb syndro
- G10D (p.Gly10Asp), rs1553172821, ClinGen CA338265724, ClinVar RCV000585147, Ensembl rs1553172821, REVEL 0.30, CADD 22.70, Uncertain significance, not provided
- G10S (p.Gly10Ser), gnomAD rs1162022004, REVEL 0.24, CADD 23.60
- T12M (p.Thr12Met), rs151117874, ClinGen CA637791, ClinVar RCV000801260, ClinVar RCV001097440, REVEL 0.50, CADD 22.10, Conflicting interpretations, Kufor-Rakeb syndrome; Autosomal recessive spastic paraplegia type 78; Inborn gen
- T12R (p.Thr12Arg), ESP rs151117874, ExAC rs151117874, TOPMed rs151117874, gnomAD rs151117874, REVEL 0.20, CADD 19.40, Likely benign, in KRS
- P13S (p.Pro13Ser), cosmic curated COSV58700, gnomAD rs1438068941
- P13T (p.Pro13Thr), gnomAD rs1438068941, REVEL 0.10, CADD 20.60
- G15A (p.Gly15Ala), rs1287774416, ClinGen CA338265601, ClinVar RCV002030731, ClinVar RCV006327400, REVEL 0.14, CADD 18.40, Uncertain significance, Kufor-Rakeb syndrome; Autosomal recessive spastic paraplegia type 78; Inborn gen
- G15D (p.Gly15Asp), gnomAD rs1287774416, REVEL 0.18, CADD 22.50, Uncertain significance
- G15S (p.Gly15Ser), rs763402910, ClinGen CA637787, ClinVar RCV003786470, ExAC rs763402910, REVEL 0.25, CADD 14.30, Uncertain significance, Kufor-Rakeb syndrome; Autosomal recessive spastic paraplegia type 78
- Y16C (p.Tyr16Cys), TOPMed rs1368656267, gnomAD rs1368656267, REVEL 0.49, CADD 26.90
- Y16F (p.Tyr16Phe), rs1368656267, ClinGen CA338265578, ClinVar RCV002337861, Uncertain significance, Inborn genetic diseases
- T18S (p.Thr18Ser), TOPMed rs1206896222, gnomAD rs1206896222, REVEL 0.23, CADD 23.50
- L19V (p.Leu19Val), gnomAD rs1259931850, REVEL 0.25, CADD 24.40
- T20M (p.Thr20Met), rs773699589, ClinGen CA637786, NCI-TCGA Cosmic COSV5869, cosmic curated COSV58697, REVEL 0.13, CADD 17.50, Uncertain significance, Inborn genetic diseases; Kufor-Rakeb syndrome; Autosomal recessive spastic parap
- T20P (p.Thr20Pro), rs2524479587, ClinGen CA338265522, ClinVar RCV002652990, Uncertain significance, Autosomal recessive spastic paraplegia type 78; Kufor-Rakeb syndrome
- I21V (p.Ile21Val), TOPMed rs2077533553
- G22E (p.Gly22Glu), gnomAD rs1439673688, REVEL 0.32, CADD 12.50, Uncertain significance, not provided
- T23R (p.Thr23Arg), NCI-TCGA Cosmic COSV1004, cosmic curated COSV10045, Variant assessed as somatic; moderate impact.
- T23S (p.Thr23Ser), TOPMed rs934435975, gnomAD rs934435975, REVEL 0.12, CADD 22.20
- I25V (p.Ile25Val), rs762253735, ClinGen CA637784, ClinVar RCV002938128, ExAC rs762253735, REVEL 0.29, CADD 7.27, Uncertain significance, Autosomal recessive spastic paraplegia type 78; Kufor-Rakeb syndrome
- D26N (p.Asp26Asn), ExAC rs777060631, gnomAD rs777060631, REVEL 0.15, CADD 23.80
- P27L (p.Pro27Leu), ExAC rs768964549, gnomAD rs768964549, REVEL 0.36, CADD 26.30
- S30Y (p.Ser30Tyr), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- V32I (p.Val32Ile), TOPMed rs1158449120, gnomAD rs1158449120, REVEL 0.28, CADD 19.50
- V32L (p.Val32Leu), TOPMed rs1158449120, gnomAD rs1158449120, REVEL 0.28, CADD 19.60
- S33* (p.Ser33Ter), NCI-TCGA TCGA novel, gnomAD rs1418201460, CADD 37.00, PolyPhen-2 0.30, Variant assessed as somatic; high impact.
- S33T (p.Ser33Thr), TOPMed rs1205052411, gnomAD rs1205052411, REVEL 0.25, CADD 22.70
- V35A (p.Val35Ala), TOPMed rs2077532054, gnomAD rs2077532054, REVEL 0.11, CADD 25.70
- V35M (p.Val35Met), rs1283092397, ClinGen CA338265314, ClinVar RCV003783227, TOPMed rs1283092397, REVEL 0.13, CADD 16.60, Uncertain significance, Autosomal recessive spastic paraplegia type 78; Kufor-Rakeb syndrome
- R36T (p.Arg36Thr), Ensembl rs924432726
- S38G (p.Ser38Gly), rs780883238, ClinGen CA637754, ClinVar RCV001770694, ClinVar RCV002540278, REVEL 0.08, CADD 21.40, Uncertain significance, Kufor-Rakeb syndrome; Autosomal recessive spastic paraplegia type 78; not provid
- S38N (p.Ser38Asn), Ensembl rs2077524042, REVEL 0.07, CADD 19.80
- G39A (p.Gly39Ala), gnomAD rs1168556655, REVEL 0.23, CADD 25.00
- G39D (p.Gly39Asp), gnomAD rs1168556655, REVEL 0.40, CADD 25.80
- G39S (p.Gly39Ser), gnomAD rs1432026507, REVEL 0.33, CADD 25.80, Uncertain significance, not provided; Inborn genetic diseases
- Y40* (p.Tyr40Ter), ExAC rs751082709, gnomAD rs751082709, CADD 38.00, PolyPhen-2 0.83
- C41F (p.Cys41Phe), gnomAD rs1418430423, REVEL 0.13, CADD 22.30
- P44L (p.Pro44Leu), TOPMed rs2077523348
- W45L (p.Trp45Leu), NCI-TCGA Cosmic COSV1004, cosmic curated COSV10045, Variant assessed as somatic; moderate impact.
- W45R (p.Trp45Arg), ExAC rs757858388, gnomAD rs757858388, REVEL 0.28, CADD 26.70
- R46G (p.Arg46Gly), TOPMed rs2077523047, gnomAD rs2077523047, REVEL 0.20, CADD 26.30
- R46K (p.Arg46Lys), TOPMed rs1234361943, gnomAD rs1234361943, REVEL 0.16, CADD 20.40
- I48V (p.Ile48Val), ExAC rs764367853, gnomAD rs764367853, REVEL 0.08, CADD 8.98
- G49R (p.Gly49Arg), 1000Genomes rs56379718, ESP rs56379718, ExAC rs56379718, TOPMed rs56379718, Benign
- G49S (p.Gly49Ser), rs56379718, ClinGen CA637746, cosmic curated COSV10882, ClinVar RCV000874010, REVEL 0.04, CADD 24.60, Benign/Likely benign, Inborn genetic diseases; Kufor-Rakeb syndrome; Autosomal recessive spastic parap
- G49V (p.Gly49Val), rs372254666, ClinGen CA637745, ClinVar RCV001048775, ClinVar RCV001509026, REVEL 0.11, CADD 20.30, Uncertain significance, Kufor-Rakeb syndrome; Autosomal recessive spastic paraplegia type 78; not provid
- Y50C (p.Tyr50Cys), TOPMed rs916488046
- Y50H (p.Tyr50His), rs2101123287, ClinGen CA338264918, ClinVar RCV001983568, Ensembl rs2101123287, REVEL 0.16, CADD 23.70, Uncertain significance, Kufor-Rakeb syndrome; Autosomal recessive spastic paraplegia type 78
- V52A (p.Val52Ala), Ensembl rs1570895967
- V52F (p.Val52Phe), ExAC rs766408337, TOPMed rs766408337, gnomAD rs766408337, REVEL 0.20, CADD 8.58
- V52I (p.Val52Ile), cosmic curated COSV58702, ExAC rs766408337, TOPMed rs766408337, gnomAD rs766408337, REVEL 0.07, CADD 3.77, Likely benign, Inborn genetic diseases
- V53M (p.Val53Met), rs142699829, ClinGen CA637740, cosmic curated COSV58697, ClinVar RCV001224405, REVEL 0.02, CADD 14.50, Uncertain significance, Autosomal recessive spastic paraplegia type 78; Kufor-Rakeb syndrome; Inborn gen
- V54I (p.Val54Ile), TOPMed rs2077521634
- W55C (p.Trp55Cys), rs1399740972, ClinGen CA338264788, ClinVar RCV002988737, TOPMed rs1399740972, REVEL 0.07, CADD 24.40, Uncertain significance, Autosomal recessive spastic paraplegia type 78; Kufor-Rakeb syndrome
- M56V (p.Met56Val), gnomAD rs1329426374, REVEL 0.08, CADD 12.80
- A58G (p.Ala58Gly), TOPMed rs2077521263, gnomAD rs2077521263, REVEL 0.11, CADD 22.60
- A58V (p.Ala58Val), NCI-TCGA Cosmic COSV5869, cosmic curated COSV58699, Variant assessed as somatic; moderate impact.
- G59A (p.Gly59Ala), TOPMed rs2077520961
- G59W (p.Gly59Trp), gnomAD rs1463031705, REVEL 0.48, CADD 27.30
- L64F (p.Leu64Phe), rs769534201, ClinGen CA637738, ClinVar RCV002710242, ExAC rs769534201, REVEL 0.05, CADD 23.40, Uncertain significance, Autosomal recessive spastic paraplegia type 78; Kufor-Rakeb syndrome
- L64H (p.Leu64His), TOPMed rs2077520497
- F65L (p.Phe65Leu), 1000Genomes rs201564843, ExAC rs201564843, TOPMed rs201564843, gnomAD rs201564843
- R66C (p.Arg66Cys), rs768327980, ClinGen CA338264536, NCI-TCGA Cosmic COSV1004, cosmic curated COSV10045, REVEL 0.21, CADD 28.40, Uncertain significance, not provided; Autosomal recessive spastic paraplegia type 78; Kufor-Rakeb syndro
- R66G (p.Arg66Gly), rs768327980, ClinGen CA637735, ClinVar RCV003060924, ExAC rs768327980, REVEL 0.19, CADD 22.70, Uncertain significance, Autosomal recessive spastic paraplegia type 78; Kufor-Rakeb syndrome
- R66H (p.Arg66His), rs367745335, ClinGen CA637734, cosmic curated COSV99045, ClinVar RCV000431349, REVEL 0.07, CADD 20.60, Conflicting interpretations, Inborn genetic diseases; Kufor-Rakeb syndrome; Autosomal recessive spastic parap
- R66L (p.Arg66Leu), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- K68E (p.Lys68Glu), ExAC rs779739052
- L70R (p.Leu70Arg), gnomAD rs1235924841, REVEL 0.09, CADD 2.26
- W71* (p.Trp71Ter), rs1468568465, rs373607247, NCI-TCGA Cosmic COSV1004, cosmic curated COSV10045, CADD 36.00, PolyPhen-2 0.00, Pathogenic
- W71C (p.Trp71Cys), gnomAD rs1468568465, REVEL 0.28, CADD 26.70
- W71L (p.Trp71Leu), rs373607247, ClinGen CA637730, cosmic curated COSV10045, ClinVar RCV000804051, REVEL 0.13, CADD 22.20, Uncertain significance, Kufor-Rakeb syndrome; Autosomal recessive spastic paraplegia type 78
- W71S (p.Trp71Ser), rs373607247, ClinGen CA637731, ClinVar RCV001350251, ClinVar RCV005432682, REVEL 0.23, CADD 27.30, Uncertain significance, not specified; Autosomal recessive spastic paraplegia type 78; Kufor-Rakeb syndr
- G72R (p.Gly72Arg), TOPMed rs1450164817
- V73A (p.Val73Ala), rs756478512, ClinGen CA637729, ClinVar RCV002619916, ExAC rs756478512, REVEL 0.24, CADD 26.20, Uncertain significance, Kufor-Rakeb syndrome; Autosomal recessive spastic paraplegia type 78
- V73G (p.Val73Gly), ExAC rs756478512, TOPMed rs756478512, REVEL 0.35, CADD 28.00, Uncertain significance
- V73L (p.Val73Leu), gnomAD rs1264349572, REVEL 0.12, CADD 24.80
- V73M (p.Val73Met), gnomAD rs1264349572, REVEL 0.20, CADD 25.60
- R74L (p.Arg74Leu), NCI-TCGA Cosmic COSV5870, cosmic curated COSV58701, Variant assessed as somatic; moderate impact.
- R74Q (p.Arg74Gln), rs767725094, ClinGen CA637727, cosmic curated COSV58704, ClinVar RCV002050812, REVEL 0.09, CADD 21.90, Uncertain significance, Kufor-Rakeb syndrome; Autosomal recessive spastic paraplegia type 78
- R74W (p.Arg74Trp), rs753087058, ClinGen CA637728, ClinVar RCV000710708, ClinVar RCV001861951, REVEL 0.06, CADD 22.90, Uncertain significance, Kufor-Rakeb syndrome; Autosomal recessive spastic paraplegia type 78; Inborn gen
- R76G (p.Arg76Gly), ExAC rs751715295, TOPMed rs751715295, gnomAD rs751715295, REVEL 0.22, CADD 27.30, Uncertain significance
- R76Q (p.Arg76Gln), rs536805463, ClinGen CA637724, ClinVar RCV002292730, ClinVar RCV003097817, REVEL 0.09, CADD 23.80, Uncertain significance, not provided; Kufor-Rakeb syndrome; Autosomal recessive spastic paraplegia type
- R76W (p.Arg76Trp), rs751715295, ClinGen CA637726, ClinVar RCV001925311, ExAC rs751715295, REVEL 0.16, CADD 30.00, Uncertain significance, Kufor-Rakeb syndrome; Autosomal recessive spastic paraplegia type 78
- L77F (p.Leu77Phe), rs763004392, ClinGen CA637723, ClinVar RCV000417817, ClinVar RCV001865371, REVEL 0.09, CADD 19.50, Uncertain significance, Kufor-Rakeb syndrome; Autosomal recessive spastic paraplegia type 78; not provid
- R78Q (p.Arg78Gln), rs773087322, ClinGen CA637722, NCI-TCGA Cosmic COSV5870, cosmic curated COSV58701, REVEL 0.07, CADD 8.61, Conflicting interpretations, Kufor-Rakeb syndrome; Autosomal recessive spastic paraplegia type 78; Inborn gen
- R78W (p.Arg78Trp), rs1443334892, NCI-TCGA Cosmic COSV5870, cosmic curated COSV58701, TOPMed rs1443334892, REVEL 0.12, CADD 24.60, Variant assessed as somatic; moderate impact.
- P79L (p.Pro79Leu), gnomAD rs1293000670, REVEL 0.14, CADD 23.60
- P79R (p.Pro79Arg), gnomAD rs1293000670, REVEL 0.16, CADD 20.30
- C80Y (p.Cys80Tyr), Ensembl rs1005612211, REVEL 0.52, CADD 26.00
- N81S (p.Asn81Ser), TOPMed rs1570895086, REVEL 0.06, CADD 2.27
- L82V (p.Leu82Val), ExAC rs761558105, TOPMed rs761558105, gnomAD rs761558105, REVEL 0.19, CADD 22.90, Likely benign
- A83T (p.Ala83Thr), gnomAD rs1346827451, REVEL 0.11, CADD 22.00
- H84Q (p.His84Gln), ExAC rs554944790, TOPMed rs554944790, gnomAD rs554944790, REVEL 0.05, CADD 18.40, Likely benign
- H84Y (p.His84Tyr), TOPMed rs1225584212, REVEL 0.03, CADD 14.70
- A85S (p.Ala85Ser), Ensembl rs1553172504
- A85T (p.Ala85Thr), Ensembl rs1553172504, REVEL 0.34, CADD 26.00
- E86D (p.Glu86Asp), rs775223241, ClinGen CA338264217, ClinVar RCV003042571, Uncertain significance, Kufor-Rakeb syndrome; Autosomal recessive spastic paraplegia type 78
- E86K (p.Glu86Lys), rs1557715739, ClinGen CA338264231, ClinVar RCV002612433, ClinVar RCV005425063, REVEL 0.19, CADD 24.20, Uncertain significance, not provided; Kufor-Rakeb syndrome; Autosomal recessive spastic paraplegia type
- T87I (p.Thr87Ile), Ensembl rs2077515685
- L88V (p.Leu88Val), TOPMed rs2077515464, gnomAD rs2077515464, REVEL 0.05, CADD 19.60
- V89I (p.Val89Ile), rs534590083, ClinGen CA637714, ClinVar RCV001331223, ClinVar RCV001531614, REVEL 0.03, CADD 18.50, Uncertain significance, Autosomal recessive spastic paraplegia type 78; Kufor-Rakeb syndrome; Inborn gen
- I90T (p.Ile90Thr), cosmic curated COSV10045, gnomAD rs1487807472, REVEL 0.24, CADD 27.60
- E91* (p.Glu91Ter), ExAC rs778193284, TOPMed rs778193284, gnomAD rs778193284, CADD 44.00, PolyPhen-2 0.00, Uncertain significance
- E91K (p.Glu91Lys), rs778193284, ClinGen CA637713, cosmic curated COSV10439, ClinVar RCV003070526, REVEL 0.11, CADD 24.20, Uncertain significance, Autosomal recessive spastic paraplegia type 78; Kufor-Rakeb syndrome; not provid
- R93T (p.Arg93Thr), TOPMed rs2077514700
- D94N (p.Asp94Asn), gnomAD rs1217958647
- K95Q (p.Lys95Gln), ESP rs375309807, TOPMed rs375309807, gnomAD rs375309807
- K95R (p.Lys95Arg), rs2101118952, ClinGen CA338264081, ClinVar RCV001935175, Ensembl rs2101118952, REVEL 0.04, CADD 21.40, Uncertain significance, Kufor-Rakeb syndrome; Autosomal recessive spastic paraplegia type 78
- E96* (p.Glu96Ter), TOPMed rs2077514344, CADD 48.00, PolyPhen-2 0.00
- E96D (p.Glu96Asp), ExAC rs756666487, gnomAD rs756666487, REVEL 0.07, CADD 34.00
- S99F (p.Ser99Phe), NCI-TCGA Cosmic COSV5869, cosmic curated COSV58699, Variant assessed as somatic; moderate impact.
- W100R (p.Trp100Arg), ExAC rs781539788, TOPMed rs781539788, gnomAD rs781539788, REVEL 0.37, CADD 22.60
- Q101K (p.Gln101Lys), TOPMed rs1570892631, REVEL 0.13, CADD 18.30
- L102F (p.Leu102Phe), ExAC rs769073401, gnomAD rs769073401, REVEL 0.10, CADD 23.40
- F103L (p.Phe103Leu), TOPMed rs1247483235
- V105A (p.Val105Ala), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- V105I (p.Val105Ile), gnomAD rs1190667301, REVEL 0.08, CADD 21.70
- Q106* (p.Gln106Ter), Ensembl rs1570892513
- A111T (p.Ala111Thr), Ensembl rs2077499962, Uncertain significance, Inborn genetic diseases
- I112V (p.Ile112Val), rs747340052, ClinGen CA637688, ClinVar RCV001920142, ExAC rs747340052, REVEL 0.03, CADD 9.81, Uncertain significance, Kufor-Rakeb syndrome; Autosomal recessive spastic paraplegia type 78
- G113C (p.Gly113Cys), ExAC rs750571443, TOPMed rs750571443, gnomAD rs750571443
- G113S (p.Gly113Ser), ExAC rs750571443, TOPMed rs750571443, gnomAD rs750571443, REVEL 0.04, CADD 3.47
- E114G (p.Glu114Gly), NCI-TCGA TCGA novel, Variant assessed as somatic; high impact.
- E114K (p.Glu114Lys), rs757224113, ClinGen CA637683, cosmic curated COSV10882, ClinVar RCV002031042, REVEL 0.07, CADD 16.80, Uncertain significance, Autosomal recessive spastic paraplegia type 78; Kufor-Rakeb syndrome
- E114V (p.Glu114Val), Ensembl rs2101109641
- G115C (p.Gly115Cys), NCI-TCGA Cosmic COSV1004, cosmic curated COSV10045, Variant assessed as somatic; moderate impact.
- G115S (p.Gly115Ser), TOPMed rs1367525365
- G115V (p.Gly115Val), rs1321429002, ClinGen CA338263697, ClinVar RCV002659423, TOPMed rs1321429002, REVEL 0.07, CADD 17.70, Uncertain significance, Autosomal recessive spastic paraplegia type 78; Kufor-Rakeb syndrome
- S116R (p.Ser116Arg), rs2077491125, ClinGen CA338263633, ClinVar RCV001314682, Ensembl rs2077491125, REVEL 0.12, CADD 16.60, Uncertain significance, Kufor-Rakeb syndrome; Autosomal recessive spastic paraplegia type 78
- E118* (p.Glu118Ter), ExAC rs756152157, gnomAD rs756152157, CADD 35.00, Pathogenic
- E118K (p.Glu118Lys), rs756152157, ClinGen CA637661, ClinVar RCV003143607, ExAC rs756152157, REVEL 0.06, CADD 15.10, Uncertain significance, not provided
- E118V (p.Glu118Val), gnomAD rs1323581147
- P119A (p.Pro119Ala), Ensembl rs2077490519, REVEL 0.09, CADD 12.80
- P119L (p.Pro119Leu), rs752619582, ClinGen CA637660, cosmic curated COSV10519, ClinVar RCV001036883, REVEL 0.01, CADD 1.44, Conflicting interpretations, Kufor-Rakeb syndrome; Autosomal recessive spastic paraplegia type 78; Inborn gen
- S120P (p.Ser120Pro), TOPMed rs1161855207, gnomAD rs1161855207, REVEL 0.03, CADD 10.50
- S120T (p.Ser120Thr), TOPMed rs1161855207, gnomAD rs1161855207, REVEL 0.02, CADD 7.76
- P121S (p.Pro121Ser), rs1421953227, ClinGen CA338263566, ClinVar RCV001885578, gnomAD rs1421953227, REVEL 0.03, CADD 10.70, Uncertain significance, Autosomal recessive spastic paraplegia type 78; Kufor-Rakeb syndrome
- Q122* (p.Gln122Ter), rs1057519292, ClinGen CA16043960, ClinVar RCV000415546, ClinVar RCV004767251, Pathogenic
- Q122R (p.Gln122Arg), gnomAD rs1381282241, REVEL 0.03, CADD 8.68
- S123A (p.Ser123Ala), Ensembl rs2101103605
- S123F (p.Ser123Phe), NCI-TCGA Cosmic COSV5870, cosmic curated COSV58702, Variant assessed as somatic; moderate impact.
- S123Y (p.Ser123Tyr), ExAC rs745369883, gnomAD rs745369883, REVEL 0.05, CADD 9.20
- A125E (p.Ala125Glu), rs1050244144, ClinGen CA338263486, ClinVar RCV003039936, Uncertain significance, Kufor-Rakeb syndrome; Autosomal recessive spastic paraplegia type 78
- A125G (p.Ala125Gly), rs1050244144, ClinGen CA18646294, ClinVar RCV001940880, ClinVar RCV002561408, REVEL 0.03, CADD 0.47, Uncertain significance, Inborn genetic diseases; Autosomal recessive spastic paraplegia type 78; Kufor-R
- A125P (p.Ala125Pro), rs1248544066, ClinGen CA338263491, ClinVar RCV002349234, ClinVar RCV003094339, REVEL 0.03, CADD 7.08, Uncertain significance, Autosomal recessive spastic paraplegia type 78; Kufor-Rakeb syndrome; Inborn gen
- E126D (p.Glu126Asp), ExAC rs765913972, gnomAD rs765913972, REVEL 0.06, CADD 15.90
- R129Q (p.Arg129Gln), rs762570832, ClinGen CA637655, ClinVar RCV001997137, ExAC rs762570832, REVEL 0.06, CADD 22.30, Uncertain significance, Autosomal recessive spastic paraplegia type 78; Kufor-Rakeb syndrome
- R129W (p.Arg129Trp), rs1318096890, ClinGen CA338263429, ClinVar RCV000702289, TOPMed rs1318096890, REVEL 0.18, CADD 23.10, Uncertain significance, Kufor-Rakeb syndrome; Autosomal recessive spastic paraplegia type 78
- S130R (p.Ser130Arg), gnomAD rs1222487351, REVEL 0.19, CADD 16.70
- A132T (p.Ala132Thr), rs200934541, ClinGen CA637654, ClinVar RCV001046328, ClinVar RCV002372795, REVEL 0.05, CADD 7.20, Uncertain significance, Inborn genetic diseases; Kufor-Rakeb syndrome; Autosomal recessive spastic parap
- A132V (p.Ala132Val), rs764125787, ClinGen CA18646263, ClinVar RCV002016884, 1000Genomes rs764125787, REVEL 0.02, CADD 1.70, Uncertain significance, Autosomal recessive spastic paraplegia type 78; Kufor-Rakeb syndrome
- V134A (p.Val134Ala), rs2101102735, ClinGen CA338263349, ClinVar RCV001980532, Ensembl rs2101102735, Uncertain significance, Kufor-Rakeb syndrome; Autosomal recessive spastic paraplegia type 78
- G135V (p.Gly135Val), TOPMed rs2077487952, REVEL 0.62, CADD 18.70
- A136V (p.Ala136Val), rs562519835, ClinGen CA637652, cosmic curated COSV58701, ClinVar RCV001062022, REVEL 0.17, CADD 7.41, Conflicting interpretations, Kufor-Rakeb syndrome; Autosomal recessive spastic paraplegia type 78; not provid
- V137G (p.Val137Gly), TOPMed rs1482100202, gnomAD rs1482100202, REVEL 0.39, CADD 15.00
- P138A (p.Pro138Ala), gnomAD rs2077487451, REVEL 0.20, CADD 16.50
- E139* (p.Glu139Ter), NCI-TCGA Cosmic COSV1004, cosmic curated COSV10045, NCI-TCGA Cosmic COSV5869, Variant assessed as somatic; high impact.
- E139D (p.Glu139Asp), Ensembl rs2077487362
- G140D (p.Gly140Asp), Ensembl rs2077487056
- G140S (p.Gly140Ser), NCI-TCGA Cosmic COSV5870, cosmic curated COSV58704, gnomAD rs2077487166, REVEL 0.30, CADD 12.90, Variant assessed as somatic; moderate impact.
- A141S (p.Ala141Ser), gnomAD rs1274956152, REVEL 0.16, CADD 1.14
- K143E (p.Lys143Glu), ExAC rs772543354, TOPMed rs772543354, gnomAD rs772543354, REVEL 0.09, CADD 17.30
- D144V (p.Asp144Val), rs145031260, ClinGen CA637649, ClinVar RCV000822972, ClinVar RCV001766749, REVEL 0.24, CADD 27.30, Uncertain significance, Autosomal recessive spastic paraplegia type 78; Kufor-Rakeb syndrome; Inborn gen
- T145M (p.Thr145Met), rs774684946, NCI-TCGA Cosmic COSV1004, cosmic curated COSV10045, ExAC rs774684946, REVEL 0.29, CADD 25.40, Variant assessed as somatic; moderate impact.
- Q147L (p.Gln147Leu), NCI-TCGA Cosmic COSV1004, cosmic curated COSV10045, Variant assessed as somatic; moderate impact.
- H149R (p.His149Arg), ExAC rs778005251, TOPMed rs778005251, gnomAD rs778005251, REVEL 0.08, CADD 9.96
- H149Y (p.His149Tyr), NCI-TCGA Cosmic COSV5870, cosmic curated COSV58703, Variant assessed as somatic; moderate impact.
- K150E (p.Lys150Glu), gnomAD rs1457298892, REVEL 0.03, CADD 1.38
- K150N (p.Lys150Asn), NCI-TCGA Cosmic COSV5869, cosmic curated COSV58698, Variant assessed as somatic; moderate impact.
- E152G (p.Glu152Gly), ExAC rs748158984, gnomAD rs748158984, REVEL 0.33, CADD 21.30
- E152K (p.Glu152Lys), TOPMed rs1173258415, gnomAD rs1173258415, REVEL 0.31, CADD 9.74
Public ATP13A2 analysis runs
- ATP13A2 analysis run — ATP13A2 (1,695 variants) — completed 2026-08-20