SLC19A3 (Thiamine transporter 2) variants and mutations
SLC19A3 (also known as Thiamine transporter 2) is a human protein-coding gene encoding a thiamine transporter 2 protein. A high-affinity thiamine transporter that helps supply vitamin B1 to cells, including the brain. Variants can cause biotin-thiamine-responsive basal ganglia disease. This analysis covers 939 SLC19A3 variants and mutations. Of these, 99% have computational variant effect predictions. Disease context includes biotin-responsive basal ganglia disease, hereditary disease, and Leigh syndrome. Example SLC19A3 variants include M1L, D2N, and C3F.
Variant analysis overview
- Gene: SLC19A3
- Protein: Thiamine transporter 2
- UniProt accession: Q9BZV2
- Organism: Homo sapiens
- Variants analyzed: 939
- Variant scope: all variants
- Completed: 2026-10-09
Variant and mutation evidence
- Variant composition: 766 unspecified-consequence records; 2 stop lost; 1 stop retained variant; 79 synonymous variants; 98 missense variants; 3 stop-gained variants; 4 splice-region variants; 12 frameshift variants; 1 in-frame insertions; 1 in-frame deletions; 3 substitution
- Prediction scores: 934 variants have prediction scores (99% of the analyzed set).
Clinical, disease, and population context
- Disease context: 25 disease associations are represented. Top associations: biotin-responsive basal ganglia disease, hereditary disease, Leigh syndrome, dystonic disorder, infantile spams-psychomotor retardation-progressive brain atrophy-basal ganglia, neurodegenerative disease, peritonitis, Spastic paraplegia, biliary tract disorder, nephronophthisis, familial idiopathic steroid-resistant nephrotic syndrome, liver inflammatory myofibroblastic tumor.
Protein structure and variant hotspots
- Protein features: 12 transmembrane segments; 2 post-translational modification sites.
- Structural context: 501 variants have structural context.
- PTM context: 2 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, MaveDB, LitVar.
Diseases linked to SLC19A3
Notable SLC19A3 variants
Examples include M1L, D2N, C3F, Y4*, Y4N, R5T, T6A, T6N. Listed records include available protein-change notation, database identifiers, clinical classifications, computational predictions, population evidence, experimental measurements, and disease context.
- M1L (p.Met1Leu), rs2470581081, ClinGen CA350878164, ClinVar RCV003502762, ESM-1b 1.00, AlphaMissense 0.20, Likely pathogenic, Biotin-responsive basal ganglia disease
- D2N (p.Asp2Asn), rs747378211, ClinGen CA2149420, ClinVar RCV000805176, ClinVar RCV006250871, REVEL 0.22, ESM-1b 0.00, Uncertain significance, Biotin-responsive basal ganglia disease; not provided
- C3F (p.Cys3Phe), Ensembl rs984355953, REVEL 0.32, ESM-1b 0.00
- Y4* (p.Tyr4Ter), rs2470581058, ClinGen CA350878136, ClinVar RCV003503177, CADD 33.00, Pathogenic
- Y4N (p.Tyr4Asn), rs1319391961, ClinGen CA350878143, ClinVar RCV001889165, TOPMed rs1319391961, REVEL 0.26, ESM-1b 0.00, Uncertain significance, Biotin-responsive basal ganglia disease
- R5T (p.Arg5Thr), gnomAD rs1461540875, REVEL 0.34, ESM-1b 0.49
- T6A (p.Thr6Ala), ESP rs368949246, TOPMed rs368949246, gnomAD rs368949246, REVEL 0.17, ESM-1b 0.00
- T6N (p.Thr6Asn), rs773766196, ClinGen CA2149419, ClinVar RCV000817072, ExAC rs773766196, REVEL 0.11, ESM-1b 0.00, Uncertain significance, Biotin-responsive basal ganglia disease
- T6S (p.Thr6Ser), rs773766196, ClinGen CA350878126, ClinVar RCV003002123, ESM-1b 0.00, AlphaMissense 0.07, Uncertain significance, Biotin-responsive basal ganglia disease
- S7* (p.Ser7Ter), rs713993048, ClinGen CA273053, ClinVar RCV000149551, ClinVar RCV001310776, CADD 34.00, Pathogenic
- L8P (p.Leu8Pro), cosmic curated COSV51451, gnomAD rs1472451485, REVEL 0.38, ESM-1b 0.00
- S9N (p.Ser9Asn), rs1373557684, ClinGen CA350878110, ClinVar RCV001211359, TOPMed rs1373557684, REVEL 0.20, ESM-1b 0.00, Uncertain significance, Biotin-responsive basal ganglia disease
- S9R (p.Ser9Arg), NCI-TCGA Cosmic COSV5145, cosmic curated COSV51454, ESM-1b 0.00, AlphaMissense 0.13, Variant assessed as somatic; moderate impact.
- S10N (p.Ser10Asn), cosmic curated COSV51454, ExAC rs748439898, TOPMed rs748439898, gnomAD rs748439898, REVEL 0.20, ESM-1b 0.00
- S11F (p.Ser11Phe), gnomAD rs1264662505, ESM-1b 1.00, AlphaMissense 0.20
- W12C (p.Trp12Cys), ExAC rs778816786, gnomAD rs778816786, REVEL 0.91, ESM-1b 1.00, Pathogenic
- I13M (p.Ile13Met), rs2106332726, ClinGen CA350878079, ClinVar RCV001763821, Ensembl rs2106332726, ESM-1b 0.00, AlphaMissense 0.09, Uncertain significance, not provided
- I13T (p.Ile13Thr), Ensembl rs2106332731, REVEL 0.31, ESM-1b 0.42
- Y14C (p.Tyr14Cys), gnomAD rs1247672714, REVEL 0.49, ESM-1b 1.00
- Y14D (p.Tyr14Asp), Ensembl rs1695728316, ESM-1b 1.00, AlphaMissense 0.32
- T16I (p.Thr16Ile), NCI-TCGA Cosmic COSV5145, cosmic curated COSV51451, REVEL 0.84, ESM-1b 1.00, Variant assessed as somatic; moderate impact.
- V17M (p.Val17Met), cosmic curated COSV11321, ESM-1b 0.17, AlphaMissense 0.10
- I18V (p.Ile18Val), rs1574565534, ClinGen CA350878051, ClinVar RCV000811563, Ensembl rs1574565534, ESM-1b 0.00, AlphaMissense 0.08, Uncertain significance, Biotin-responsive basal ganglia disease
- L19P (p.Leu19Pro), ESP rs142553867, ExAC rs142553867, TOPMed rs142553867, gnomAD rs142553867, REVEL 0.93, ESM-1b 1.00
- C20S (p.Cys20Ser), rs1287862643, ClinGen CA350878039, ClinVar RCV003329918, gnomAD rs1287862643, REVEL 0.72, ESM-1b 0.86, Uncertain significance, not provided
- C20Y (p.Cys20Tyr), rs1695727249, ClinGen CA350878037, ClinVar RCV001363632, TOPMed rs1695727249, REVEL 0.74, ESM-1b 1.00, Uncertain significance, Biotin-responsive basal ganglia disease
- L21S (p.Leu21Ser), TOPMed rs976521434, REVEL 0.50, ESM-1b 1.00
- F22L (p.Phe22Leu), TOPMed rs1695727018, ESM-1b 1.00, AlphaMissense 0.87
- G23D (p.Gly23Asp), ExAC rs121917882, TOPMed rs121917882, gnomAD rs121917882, REVEL 0.96, ESM-1b 1.00, Pathogenic, in BTBGD
- G23R (p.Gly23Arg), rs1209312070, ClinGen CA350878018, ClinVar RCV002909524, gnomAD rs1209312070, REVEL 0.82, ESM-1b 1.00, Likely pathogenic, Biotin-responsive basal ganglia disease
- G23V (p.Gly23Val), rs121917882, ClinGen CA253226, cosmic curated COSV51452, ClinVar RCV000004824, REVEL 0.91, ESM-1b 1.00, Pathogenic/Likely pathogenic, SLC19A3-related disorder; Inborn genetic diseases; not provided
- F24I (p.Phe24Ile), gnomAD rs1272375245, REVEL 0.80, ESM-1b 1.00
- F25S (p.Phe25Ser), Ensembl rs1574565470, REVEL 0.87, ESM-1b 1.00
- S26F (p.Ser26Phe), cosmic curated COSV51452, ESM-1b 1.00, AlphaMissense 0.23
- M27T (p.Met27Thr), TOPMed rs1695726256, gnomAD rs1695726256, REVEL 0.20, ESM-1b 0.92
- M28I (p.Met28Ile), rs1296450224, ClinGen CA350877975, ClinVar RCV003026705, TOPMed rs1296450224, REVEL 0.33, ESM-1b 0.00, Uncertain significance, Biotin-responsive basal ganglia disease
- M28fsX, rs775835429, Pathogenic
- R29I (p.Arg29Ile), cosmic curated COSV99296, REVEL 0.69, ESM-1b 1.00
- R29K (p.Arg29Lys), cosmic curated COSV11321, ExAC rs751334362, gnomAD rs751334362, REVEL 0.32, ESM-1b 0.00
- R29S (p.Arg29Ser), gnomAD rs1351230521, REVEL 0.74, ESM-1b 1.00
- P30L (p.Pro30Leu), gnomAD rs1321093527, REVEL 0.76, ESM-1b 1.00
- P30T (p.Pro30Thr), rs2106332649, ClinGen CA350877968, ClinVar RCV001360312, Ensembl rs2106332649, ESM-1b 1.00, AlphaMissense 0.64, Uncertain significance, Biotin-responsive basal ganglia disease
- S31L (p.Ser31Leu), gnomAD rs1404181786, REVEL 0.48, ESM-1b 1.00
- E32K (p.Glu32Lys), cosmic curated COSV99295, TOPMed rs1695725329, ESM-1b 1.00, AlphaMissense 0.74
- P33L (p.Pro33Leu), rs2106332628, ClinGen CA350877943, ClinVar RCV001952655, Ensembl rs2106332628, ESM-1b 1.00, AlphaMissense 0.60, Uncertain significance, Biotin-responsive basal ganglia disease
- P33S (p.Pro33Ser), gnomAD rs1559252781, REVEL 0.64, ESM-1b 1.00
- F34V (p.Phe34Val), rs201603239, ClinGen CA2149410, ClinVar RCV000818608, ExAC rs201603239, REVEL 0.92, ESM-1b 1.00, Uncertain significance, Biotin-responsive basal ganglia disease
- L35F (p.Leu35Phe), rs376764604, ClinGen CA2149409, cosmic curated COSV51454, ClinVar RCV002908588, REVEL 0.53, ESM-1b 1.00, Uncertain significance, not provided; Biotin-responsive basal ganglia disease
- I36N (p.Ile36Asn), cosmic curated COSV99296, ESM-1b 1.00, AlphaMissense 0.31
- I36T (p.Ile36Thr), TOPMed rs1241452578, gnomAD rs1241452578, ESM-1b 0.00, AlphaMissense 0.20
- I36V (p.Ile36Val), rs372637185, ClinGen CA2149408, ClinVar RCV000730839, ClinVar RCV001046655, REVEL 0.09, ESM-1b 0.00, Conflicting interpretations, not provided; Biotin-responsive basal ganglia disease
- P37L (p.Pro37Leu), rs759094678, cosmic curated COSV10509, ClinGen CA350877920, ClinVar RCV003115479, REVEL 0.54, ESM-1b 1.00, Uncertain significance, Biotin-responsive basal ganglia disease
- P37R (p.Pro37Arg), ExAC rs759094678, TOPMed rs759094678, gnomAD rs759094678, REVEL 0.60, ESM-1b 1.00, Uncertain significance
- P37S (p.Pro37Ser), cosmic curated COSV51454, REVEL 0.60, ESM-1b 1.00
- Y38C (p.Tyr38Cys), rs766975844, ClinGen CA2149405, ClinVar RCV001769223, ExAC rs766975844, REVEL 0.78, ESM-1b 1.00, Uncertain significance, not provided
- Y38F (p.Tyr38Phe), ExAC rs766975844, gnomAD rs766975844, REVEL 0.56, ESM-1b 0.00, Uncertain significance
- Y38H (p.Tyr38His), ESP rs368305641, ExAC rs368305641, TOPMed rs368305641, gnomAD rs368305641, REVEL 0.82, ESM-1b 1.00
- L39S (p.Leu39Ser), Ensembl rs1695723600, ESM-1b 1.00, AlphaMissense 0.89
- L39V (p.Leu39Val), gnomAD rs1275760674, REVEL 0.81, ESM-1b 1.00
- S40A (p.Ser40Ala), ExAC rs761309307, gnomAD rs761309307, REVEL 0.15, ESM-1b 0.00
- S40F (p.Ser40Phe), cosmic curated COSV51454, ESM-1b 0.48, AlphaMissense 0.16
- G41A (p.Gly41Ala), rs778816786, ClinGen CA350878086, ClinVar RCV001941887, NCI-TCGA TCGA novel, AlphaMissense 0.77, MetaLR 0.91, Pathogenic
- G41E (p.Gly41Glu), gnomAD rs1695723186, REVEL 0.62, ESM-1b 1.00
- G41R (p.Gly41Arg), Ensembl rs1695723282, ESM-1b 1.00, AlphaMissense 0.20
- G41V (p.Gly41Val), NCI-TCGA Cosmic COSV5145, cosmic curated COSV51452, REVEL 0.74, ESM-1b 1.00, Variant assessed as somatic; moderate impact.
- P42L (p.Pro42Leu), cosmic curated COSV51453, REVEL 0.68, ESM-1b 1.00
- D43N (p.Asp43Asn), rs773678018, ClinGen CA2149403, ClinVar RCV001870188, ExAC rs773678018, REVEL 0.36, ESM-1b 1.00, Uncertain significance, Biotin-responsive basal ganglia disease
- K44* (p.Lys44Ter), rs2470580726, ClinGen CA2739278490, ClinVar RCV003612849, Pathogenic
- K44E (p.Lys44Glu), rs137852957, ClinGen CA253228, ClinVar RCV000004827, gnomAD rs137852957, REVEL 0.79, ESM-1b 1.00, Pathogenic, Biotin-responsive basal ganglia disease
- N45H (p.Asn45His), cosmic curated COSV51451, ESM-1b 1.00, AlphaMissense 0.21
- L46M (p.Leu46Met), ExAC rs772514747, gnomAD rs772514747, REVEL 0.60, ESM-1b 0.00
- L46P (p.Leu46Pro), rs2470580712, ClinGen CA350877866, ClinVar RCV003989081, ESM-1b 1.00, AlphaMissense 0.87, Uncertain significance, Biotin-responsive basal ganglia disease
- T47A (p.Thr47Ala), cosmic curated COSV10438, ESM-1b 1.00, AlphaMissense 0.14
- T47I (p.Thr47Ile), gnomAD rs1272646707, REVEL 0.83, ESM-1b 1.00
- S48G (p.Ser48Gly), Ensembl rs1574565267, ESM-1b 0.00, AlphaMissense 0.08
- S48I (p.Ser48Ile), ExAC rs768551143, TOPMed rs768551143, gnomAD rs768551143, REVEL 0.17, ESM-1b 0.00
- S48R (p.Ser48Arg), Ensembl rs1695721832, ESM-1b 0.33, AlphaMissense 0.18
- E50* (p.Glu50Ter), rs1131691902, ClinGen CA350877842, ClinVar RCV000494363, gnomAD rs1131691902, CADD 32.00, Likely pathogenic
- E50A (p.Glu50Ala), ExAC rs749364879, gnomAD rs749364879, REVEL 0.47, ESM-1b 1.00
- E50K (p.Glu50Lys), gnomAD rs1131691902, REVEL 0.36, ESM-1b 1.00, Likely pathogenic
- I51V (p.Ile51Val), rs764398318, ClinGen CA2149363, ClinVar RCV000640708, ClinVar RCV003318614, REVEL 0.17, ESM-1b 0.00, Uncertain significance, not provided; Biotin-responsive basal ganglia disease
- N53K (p.Asn53Lys), gnomAD rs1412270295, REVEL 0.45, ESM-1b 1.00
- N53T (p.Asn53Thr), rs2106329724, ClinGen CA350877812, ClinVar RCV001884589, Ensembl rs2106329724, ESM-1b 1.00, AlphaMissense 0.13, Uncertain significance, Biotin-responsive basal ganglia disease
- N53N (p.Asn53Asn), gnomAD 2-227686162-A-G, CADD 3.79
- N53S (p.Asn53Ser), rs2106315871, gnomAD 2-227686163-T-C, REVEL 0.10, ESM-1b 1.00
- E54* (p.Glu54Ter), rs1695594361, ClinGen CA350877807, ClinVar RCV002852519, CADD 7.12, Pathogenic
- E54K (p.Glu54Lys), cosmic curated COSV51452, Ensembl rs1695594361, REVEL 0.46, ESM-1b 1.00, Pathogenic
- I55V (p.Ile55Val), 1000Genomes rs183021027, ExAC rs183021027, TOPMed rs183021027, gnomAD rs183021027, REVEL 0.20, ESM-1b 0.00
- F56L (p.Phe56Leu), rs769102876, ClinGen CA2149361, ClinVar RCV001068683, ExAC rs769102876, REVEL 0.32, ESM-1b 1.00, Uncertain significance, Biotin-responsive basal ganglia disease
- P57H (p.Pro57His), cosmic curated COSV10457, ESM-1b 1.00, AlphaMissense 0.70
- P57T (p.Pro57Thr), rs1695593996, ClinGen CA350877784, ClinVar RCV001218486, Ensembl rs1695593996, ESM-1b 1.00, AlphaMissense 0.41, Uncertain significance, Biotin-responsive basal ganglia disease
- V58F (p.Val58Phe), rs200412423, ClinGen CA2149359, ClinVar RCV001061337, 1000Genomes rs200412423, REVEL 0.55, ESM-1b 0.00, Uncertain significance, Biotin-responsive basal ganglia disease
- V58I (p.Val58Ile), rs200412423, ClinGen CA2149358, NCI-TCGA Cosmic COSV5145, cosmic curated COSV51453, REVEL 0.23, ESM-1b 1.00, Uncertain significance, Biotin-responsive basal ganglia disease; Inborn genetic diseases
- W59* (p.Trp59Ter), rs2470575306, ClinGen CA350877770, ClinVar RCV003613167, Pathogenic
- W59R (p.Trp59Arg), rs1695593561, ClinGen CA350877775, ClinVar RCV003107769, ClinVar RCV005240693, ESM-1b 1.00, AlphaMissense 0.96, Uncertain significance, Biotin-responsive basal ganglia disease; not specified
- T60A (p.Thr60Ala), gnomAD rs1177722977, REVEL 0.83, ESM-1b 1.00
- Y61* (p.Tyr61Ter), TOPMed rs1695592894, CADD 36.00, Likely benign
- Y61S (p.Tyr61Ser), Ensembl rs1574560910, REVEL 0.93, ESM-1b 1.00
- S62C (p.Ser62Cys), TOPMed rs1266097365, gnomAD rs1266097365, REVEL 0.87, ESM-1b 1.00, Uncertain significance
- S62F (p.Ser62Phe), rs1266097365, ClinGen CA350877748, ClinVar RCV001900944, TOPMed rs1266097365, REVEL 0.88, ESM-1b 1.00, Uncertain significance, Biotin-responsive basal ganglia disease
- Y63* (p.Tyr63Ter), rs1559250774, ClinGen CA350877742, ClinVar RCV000760653, ClinVar RCV001387186, Pathogenic
- Y63H (p.Tyr63His), rs144817990, ClinGen CA206291, ClinVar RCV000193057, ClinVar RCV000806997, REVEL 0.79, ESM-1b 1.00, Uncertain significance, Biotin-responsive basal ganglia disease; not specified; not provided
- Y63N (p.Tyr63Asn), 1000Genomes rs144817990, ESP rs144817990, ExAC rs144817990, TOPMed rs144817990, ESM-1b 1.00, AlphaMissense 0.20, Likely benign
- Y63S (p.Tyr63Ser), Ensembl rs1574560880, ESM-1b 1.00, AlphaMissense 0.18
- L64Q (p.Leu64Gln), TOPMed rs1484028218, gnomAD rs1484028218, REVEL 0.91, ESM-1b 1.00
- V65A (p.Val65Ala), TOPMed rs1695591205, REVEL 0.32, ESM-1b 0.00
- V65E (p.Val65Glu), TOPMed rs1695591205, REVEL 0.60, ESM-1b 1.00
- V65L (p.Val65Leu), rs1695591331, ClinGen CA350877734, ClinVar RCV001216545, TOPMed rs1695591331, REVEL 0.21, ESM-1b 0.00, Uncertain significance, Biotin-responsive basal ganglia disease
- V65M (p.Val65Met), TOPMed rs1695591331, gnomAD rs1695591331, REVEL 0.36, ESM-1b 1.00, Uncertain significance
- L66P (p.Leu66Pro), rs1553571813, ClinGen CA350877726, ClinVar RCV000656115, Ensembl rs1553571813, ESM-1b 1.00, AlphaMissense 0.77, Pathogenic, Biotin-responsive basal ganglia disease
- L66V (p.Leu66Val), TOPMed rs1390228508, gnomAD rs1390228508, REVEL 0.25, ESM-1b 0.00
- L68M (p.Leu68Met), TOPMed rs1431161790, ESM-1b 1.00, AlphaMissense 0.14, Uncertain significance
- L68P (p.Leu68Pro), cosmic curated COSV51455, REVEL 0.51, ESM-1b 1.00, Uncertain significance, not provided
- L68V (p.Leu68Val), rs1431161790, ClinGen CA350877718, ClinVar RCV002838485, ESM-1b 0.00, AlphaMissense 0.14, Uncertain significance, Biotin-responsive basal ganglia disease
- P69L (p.Pro69Leu), ExAC rs774152328, REVEL 0.58, ESM-1b 1.00
- V70L (p.Val70Leu), cosmic curated COSV10959, ExAC rs768590734, gnomAD rs768590734, REVEL 0.61, ESM-1b 1.00
- V72A (p.Val72Ala), ExAC rs748889067, TOPMed rs748889067, gnomAD rs748889067, REVEL 0.64, ESM-1b 0.90
- V72F (p.Val72Phe), Ensembl rs1695590000, ESM-1b 0.00, AlphaMissense 0.16
- L73F (p.Leu73Phe), rs373943165, ClinGen CA2149351, ClinVar RCV001774442, ClinVar RCV002540479, REVEL 0.69, ESM-1b 0.00, Uncertain significance, not provided; Inborn genetic diseases
- T74I (p.Thr74Ile), 1000Genomes rs568987417, ExAC rs568987417, gnomAD rs568987417, REVEL 0.90, ESM-1b 1.00
- T74P (p.Thr74Pro), Ensembl rs1574560781, ESM-1b 1.00, AlphaMissense 0.86
- D75E (p.Asp75Glu), cosmic curated COSV10457, ESM-1b 1.00, AlphaMissense 0.91
- D75G (p.Asp75Gly), Ensembl rs1695589066, REVEL 0.89, ESM-1b 1.00
- D75N (p.Asp75Asn), rs980641322, ClinGen CA66660892, NCI-TCGA Cosmic COSV9929, cosmic curated COSV99295, REVEL 0.73, ESM-1b 1.00, Conflicting interpretations, not provided; Biotin-responsive basal ganglia disease
- R78C (p.Arg78Cys), rs1329744665, ClinGen CA350877658, cosmic curated COSV51451, ClinVar RCV001359775, REVEL 0.58, ESM-1b 1.00, Uncertain significance, Biotin-responsive basal ganglia disease
- R78H (p.Arg78His), rs757743169, ClinGen CA2149348, ClinVar RCV002725645, ExAC rs757743169, REVEL 0.75, ESM-1b 1.00, Uncertain significance, Biotin-responsive basal ganglia disease
- R78L (p.Arg78Leu), ExAC rs757743169, TOPMed rs757743169, gnomAD rs757743169, REVEL 0.70, ESM-1b 1.00, Uncertain significance
- Y79* (p.Tyr79Ter), Ensembl rs1574560714
- K80N (p.Lys80Asn), NCI-TCGA Cosmic COSV9929, cosmic curated COSV99295, ESM-1b 1.00, AlphaMissense 0.96, Variant assessed as somatic; moderate impact.
- P81L (p.Pro81Leu), rs752029795, ClinGen CA2149346, ClinVar RCV000818153, ClinVar RCV002535464, REVEL 0.82, ESM-1b 1.00, Uncertain significance, Inborn genetic diseases; Biotin-responsive basal ganglia disease
- P81S (p.Pro81Ser), gnomAD rs1307893537, REVEL 0.86, ESM-1b 1.00
- I84M (p.Ile84Met), TOPMed rs1464287492, gnomAD rs1464287492, REVEL 0.42, ESM-1b 1.00
- I84V (p.Ile84Val), gnomAD rs1301426956, REVEL 0.11, ESM-1b 0.00
- L85S (p.Leu85Ser), ExAC rs758769189, gnomAD rs758769189, REVEL 0.55, ESM-1b 1.00
- G87D (p.Gly87Asp), ESP rs370463398, ExAC rs370463398, gnomAD rs370463398, REVEL 0.31, ESM-1b 1.00
- G87G (p.Gly87Gly), rs1695006537, gnomAD 2-227686168-G-A, CADD 3.01
- G87V (p.Gly87Val), gnomAD 2-227686169-C-A, REVEL 0.29, ESM-1b 1.00
- S89G (p.Ser89Gly), ExAC rs759807393, gnomAD rs759807393, REVEL 0.27, ESM-1b 1.00, Likely pathogenic
- S89N (p.Ser89Asn), rs1181303768, NCI-TCGA Cosmic COSV5145, cosmic curated COSV51451, gnomAD rs1181303768, REVEL 0.42, ESM-1b 1.00, Variant assessed as somatic; moderate impact.
- S89R (p.Ser89Arg), rs759807393, ClinGen CA2149341, ClinVar RCV000656114, ClinVar RCV004782411, REVEL 0.60, ESM-1b 1.00, Conflicting interpretations, Biotin-responsive basal ganglia disease; not specified
- S89T (p.Ser89Thr), gnomAD rs1181303768, REVEL 0.18, ESM-1b 1.00
- I91F (p.Ile91Phe), Ensembl rs1695586986, REVEL 0.29, ESM-1b 1.00, Uncertain significance
- I91V (p.Ile91Val), rs1695586986, ClinVar RCV004588782, REVEL 0.17, ESM-1b 0.00, Uncertain significance, not provided
- I92T (p.Ile92Thr), rs537995579, ClinGen CA2149339, ClinVar RCV000697435, ClinVar RCV004777840, REVEL 0.24, ESM-1b 0.00, Uncertain significance, Biotin-responsive basal ganglia disease; not provided
- I92V (p.Ile92Val), ExAC rs776737721, TOPMed rs776737721, gnomAD rs776737721, REVEL 0.14, ESM-1b 0.00
- T93C (p.Thr93Cys), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- T93P (p.Thr93Pro), NCI-TCGA Cosmic COSV9929, cosmic curated COSV99296, ESM-1b 1.00, AlphaMissense 0.42, Variant assessed as somatic; moderate impact.
- T93S (p.Thr93Ser), ExAC rs761757947, gnomAD rs761757947, REVEL 0.19, ESM-1b 0.00
- W94R (p.Trp94Arg), rs1695586409, ClinGen CA350877554, ClinVar RCV001093254, ClinVar RCV001873462, REVEL 0.61, ESM-1b 1.00, Pathogenic/Likely pathogenic, not provided; Biotin-responsive basal ganglia disease
- W94* (p.Trp94Ter), rs2106315874, gnomAD 2-227686166-C-T, CADD 3.22
- L97P (p.Leu97Pro), gnomAD rs1483082721, REVEL 0.93, ESM-1b 1.00
- G100R (p.Gly100Arg), gnomAD rs1252280462, REVEL 0.58, ESM-1b 1.00
- G102E (p.Gly102Glu), ExAC rs768496977, gnomAD rs768496977, REVEL 0.55, ESM-1b 1.00
- V103E (p.Val103Glu), ExAC rs749088473, TOPMed rs749088473, gnomAD rs749088473, REVEL 0.78, ESM-1b 1.00
- V103L (p.Val103Leu), gnomAD rs1327117771, REVEL 0.33, ESM-1b 0.00, Uncertain significance
- V103M (p.Val103Met), rs1327117771, ClinGen CA350877497, ClinVar RCV003481684, gnomAD rs1327117771, REVEL 0.52, ESM-1b 1.00, Uncertain significance, not provided
- K104N (p.Lys104Asn), rs1342774605, ClinGen CA350877485, cosmic curated COSV11321, NCI-TCGA Cosmic COSV9929, REVEL 0.09, ESM-1b 0.57, Uncertain significance, Biotin-responsive basal ganglia disease
- T105I (p.Thr105Ile), TOPMed rs1695585278, REVEL 0.27, ESM-1b 1.00
- T105S (p.Thr105Ser), gnomAD rs1311096123, REVEL 0.13, ESM-1b 0.00
- M106I (p.Met106Ile), NCI-TCGA Cosmic COSV5145, cosmic curated COSV51453, REVEL 0.44, ESM-1b 1.00, Variant assessed as somatic; moderate impact.
- M106V (p.Met106Val), rs769548199, ClinGen CA2149334, cosmic curated COSV51453, ClinVar RCV001980501, REVEL 0.59, ESM-1b 1.00, Uncertain significance, Biotin-responsive basal ganglia disease
- M106T (p.Met106Thr), gnomAD 2-227686157-A-G, REVEL 0.12, ESM-1b 0.17
- Q107K (p.Gln107Lys), ExAC rs745538722, gnomAD rs745538722, REVEL 0.71, ESM-1b 1.00
- V108F (p.Val108Phe), gnomAD rs1320760736, ESM-1b 0.00, AlphaMissense 0.10
- V109I (p.Val109Ile), rs780569649, ClinGen CA2149332, ClinVar RCV000273994, ClinVar RCV000813702, REVEL 0.22, ESM-1b 0.00, Conflicting interpretations, Inborn genetic diseases; not provided; Biotin-responsive basal ganglia disease
- E110* (p.Glu110Ter), NCI-TCGA Cosmic COSV9929, cosmic curated COSV99295, Variant assessed as somatic; high impact.
- E110G (p.Glu110Gly), Ensembl rs1370331656, ESM-1b 1.00, AlphaMissense 0.54
- E110K (p.Glu110Lys), rs2470574690, ClinGen CA350877452, ClinVar RCV003440208, ESM-1b 1.00, AlphaMissense 0.71, Uncertain significance, not provided
- E110Q (p.Glu110Gln), cosmic curated COSV10725, REVEL 0.33, ESM-1b 0.00
- F111L (p.Phe111Leu), ExAC rs770362150, gnomAD rs770362150, REVEL 0.54, ESM-1b 0.00
- F112L (p.Phe112Leu), Ensembl rs2106329430, REVEL 0.32, ESM-1b 0.80, Uncertain significance
- F112S (p.Phe112Ser), rs200971390, ClinGen CA2149330, ClinVar RCV000938104, ClinVar RCV001564416, REVEL 0.56, ESM-1b 1.00, Conflicting interpretations, not provided; Biotin-responsive basal ganglia disease
- F112V (p.Phe112Val), rs1451259233, ClinGen CA350877435, ClinVar RCV002913203, gnomAD rs1451259233, ESM-1b 1.00, AlphaMissense 0.47, Uncertain significance, Biotin-responsive basal ganglia disease
- Y113H (p.Tyr113His), rs145999922, ClinGen CA2149329, ClinVar RCV000408622, ClinVar RCV001546114, REVEL 0.80, ESM-1b 1.00, Conflicting interpretations, SLC19A3-related disorder; Biotin-responsive basal ganglia disease; not provided
- G114A (p.Gly114Ala), TOPMed rs1164678779, gnomAD rs1164678779, REVEL 0.60, ESM-1b 0.43
- G114E (p.Gly114Glu), cosmic curated COSV10509, ESM-1b 1.00, AlphaMissense 0.97
- G114R (p.Gly114Arg), cosmic curated COSV10509, ESM-1b 1.00, AlphaMissense 0.97
- G114V (p.Gly114Val), TOPMed rs1164678779, gnomAD rs1164678779, ESM-1b 1.00, AlphaMissense 0.92
- G114W (p.Gly114Trp), NCI-TCGA Cosmic COSV5145, cosmic curated COSV51452, ESM-1b 1.00, AlphaMissense 0.98, Variant assessed as somatic; moderate impact.
- M115I (p.Met115Ile), ExAC rs753042231, TOPMed rs753042231, gnomAD rs753042231, REVEL 0.12, ESM-1b 0.00
Public SLC19A3 analysis runs
- SLC19A3 analysis run — SLC19A3 (939 variants) — completed 2026-10-09