SLC19A1 — 236 ClinVar variants
All ClinVar germline SLC19A1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 115 flagged for review →
1 Pathogenic · 18 Benign · 2 Benign/Likely benign · 86 Likely benign · 129 Uncertain significance
Full SLC19A1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 115
Variants where the independent computational evidence doesn't line up with the clinical picture — a QC signal for a second look, not a reclassification.
Predictors lean, ClinVar uncertain 96
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
- SLC19A1 p.Ala469Ser Uncertain significance Multiple submitters
- SLC19A1 p.Arg148His Uncertain significance Multiple submitters
- SLC19A1 p.Arg422Gln Uncertain significance Multiple submitters
- SLC19A1 p.Asp584Asn Uncertain significance Multiple submitters
- SLC19A1 p.Glu505Gly Uncertain significance Multiple submitters
- SLC19A1 p.Glu62Lys Uncertain significance Multiple submitters
- SLC19A1 p.Gly585Cys Uncertain significance Multiple submitters
- SLC19A1 p.Leu101Phe Uncertain significance Multiple submitters
- SLC19A1 p.Pro427Leu Uncertain significance Multiple submitters
- SLC19A1 p.Pro529Leu Uncertain significance Multiple submitters
- SLC19A1 p.Ser225Trp Uncertain significance Multiple submitters
- SLC19A1 p.Ser389Thr Uncertain significance Multiple submitters
-
SLC19A1 p.Ser46Cys
Uncertain significance
Multiple submitters
megaloblastic anemia, folate-responsive
- SLC19A1 p.Thr356Met Uncertain significance Multiple submitters
- SLC19A1 p.Ala158Thr Uncertain significance Single submitter
- SLC19A1 p.Ala200Thr Uncertain significance Single submitter
- SLC19A1 p.Ala279Thr Uncertain significance Single submitter
- SLC19A1 p.Ala302Val Uncertain significance Single submitter
- SLC19A1 p.Ala309Val Uncertain significance Single submitter
- SLC19A1 p.Ala340Val Uncertain significance Single submitter
- SLC19A1 p.Ala39Val Uncertain significance Single submitter
- SLC19A1 p.Ala483Val Uncertain significance Single submitter
- SLC19A1 p.Ala551Thr Uncertain significance Single submitter
- SLC19A1 p.Ala7Val Uncertain significance Single submitter
- SLC19A1 p.Arg148Leu Uncertain significance Single submitter
- SLC19A1 p.Arg229Ser Uncertain significance Single submitter
- SLC19A1 p.Arg23Trp Uncertain significance Single submitter
- SLC19A1 p.Arg256Gln Uncertain significance Single submitter
- SLC19A1 p.Arg256Trp Uncertain significance Single submitter
- SLC19A1 p.Arg263Gln Uncertain significance Single submitter
- SLC19A1 p.Arg264Trp Uncertain significance Single submitter
- SLC19A1 p.Arg303Gln Uncertain significance Single submitter
- SLC19A1 p.Arg303Trp Uncertain significance Single submitter
- SLC19A1 p.Arg333Cys Uncertain significance Single submitter
- SLC19A1 p.Arg429His Uncertain significance Single submitter
- SLC19A1 p.Arg456Gln Uncertain significance Single submitter
- SLC19A1 p.Arg456Trp Uncertain significance Single submitter
- SLC19A1 p.Arg460Trp Uncertain significance Single submitter
- SLC19A1 p.Arg465Trp Uncertain significance Single submitter
- SLC19A1 p.Asn277Ser Uncertain significance Single submitter
- SLC19A1 p.Asp506Val Uncertain significance Single submitter
- SLC19A1 p.Asp56Asn Uncertain significance Single submitter
- SLC19A1 p.Gln11Glu Uncertain significance Single submitter
- SLC19A1 p.Gln266His Uncertain significance Single submitter
- SLC19A1 p.Gln482Glu Uncertain significance Single submitter
- SLC19A1 p.Gln518His Uncertain significance Single submitter
- SLC19A1 p.Gln520Arg Uncertain significance Single submitter
- SLC19A1 p.Gln587Pro Uncertain significance Single submitter
- SLC19A1 p.Gly154Ser Uncertain significance Single submitter
- SLC19A1 p.Gly17Glu Uncertain significance Single submitter
- SLC19A1 p.Gly236Arg Uncertain significance Single submitter
- SLC19A1 p.Gly572Arg Uncertain significance Single submitter
- SLC19A1 p.Gly585Ser Uncertain significance Single submitter
- SLC19A1 p.His569Tyr Uncertain significance Single submitter
- SLC19A1 p.Ile362Val Uncertain significance Single submitter
- SLC19A1 p.Ile382Asn Uncertain significance Single submitter
- SLC19A1 p.Ile445Met Uncertain significance Single submitter
- SLC19A1 p.Leu161Pro Uncertain significance Single submitter
- SLC19A1 p.Leu227Gln Uncertain significance Single submitter
- SLC19A1 p.Leu22Phe Uncertain significance Single submitter
- SLC19A1 p.Leu255Pro Uncertain significance Single submitter
- SLC19A1 p.Leu472Pro Uncertain significance Single submitter
- SLC19A1 p.Lys336Gln Uncertain significance Single submitter
- SLC19A1 p.Pro18Arg Uncertain significance Single submitter
- SLC19A1 p.Pro234Arg Uncertain significance Single submitter
- SLC19A1 p.Pro359Leu Uncertain significance Single submitter
- SLC19A1 p.Pro464Leu Uncertain significance Single submitter
- SLC19A1 p.Pro468Leu Uncertain significance Single submitter
- SLC19A1 p.Pro500Leu Uncertain significance Single submitter
- SLC19A1 p.Pro501Arg Uncertain significance Single submitter
- SLC19A1 p.Pro501Leu Uncertain significance Single submitter
- SLC19A1 p.Pro501Ser Uncertain significance Single submitter
- SLC19A1 p.Pro539Ser Uncertain significance Single submitter
- SLC19A1 p.Pro545Ser Uncertain significance Single submitter
- SLC19A1 p.Pro556Arg Uncertain significance Single submitter
- SLC19A1 p.Pro94Leu Uncertain significance Single submitter
- SLC19A1 p.Ser225Leu Uncertain significance Single submitter
- SLC19A1 p.Ser375Phe Uncertain significance Single submitter
- SLC19A1 p.Ser499Asn Uncertain significance Single submitter
- SLC19A1 p.Ser515Cys Uncertain significance Single submitter
- SLC19A1 p.Ser515Phe Uncertain significance Single submitter
- SLC19A1 p.Ser544Phe Uncertain significance Single submitter
- SLC19A1 p.Ser550Pro Uncertain significance Single submitter
- SLC19A1 p.Thr222Ile Uncertain significance Single submitter
- SLC19A1 p.Thr345Ala Uncertain significance Single submitter
- SLC19A1 p.Thr69Met Uncertain significance Single submitter
- SLC19A1 p.Tyr187His Uncertain significance Single submitter
- SLC19A1 p.Tyr435Cys Uncertain significance Single submitter
- SLC19A1 p.Tyr74Asn Uncertain significance Single submitter
- SLC19A1 p.Val104Glu Uncertain significance Single submitter
- SLC19A1 p.Val14Leu Uncertain significance Single submitter
- SLC19A1 p.Val197Ala Uncertain significance Single submitter
- SLC19A1 p.Val342Phe Uncertain significance Single submitter
- SLC19A1 p.Val437Leu Uncertain significance Single submitter
- SLC19A1 p.Val437Met Uncertain significance Single submitter
- SLC19A1 p.Val83Leu Uncertain significance Single submitter
Predictors split 19
The independent predictors disagree with each other — read with care.
- SLC19A1 p.Val380Ala Uncertain significance Multiple submitters
- SLC19A1 p.Ala368Val Uncertain significance Single submitter
- SLC19A1 p.Arg208Gly Uncertain significance Single submitter
- SLC19A1 p.Arg263Trp Uncertain significance Single submitter
- SLC19A1 p.Arg61Trp Uncertain significance Single submitter
- SLC19A1 p.Cys458Gly Benign Single submitter
- SLC19A1 p.Gln386Arg Uncertain significance Single submitter
- SLC19A1 p.Gly178Ser Likely benign Single submitter
- SLC19A1 p.Leu426Phe Uncertain significance Single submitter
- SLC19A1 p.Leu455Pro Uncertain significance Single submitter
- SLC19A1 p.Phe103Leu Uncertain significance Single submitter
- SLC19A1 p.Phe212Leu Uncertain significance Single submitter
- SLC19A1 p.Ser156Leu Uncertain significance Single submitter
- SLC19A1 p.Thr404Met Uncertain significance Single submitter
- SLC19A1 p.Trp270Cys Uncertain significance Single submitter
- SLC19A1 p.Tyr136Phe Uncertain significance Single submitter
- SLC19A1 p.Val295Gly Uncertain significance Single submitter
- SLC19A1 p.Val71Ala Uncertain significance Single submitter
- SLC19A1 p.Val83Ala Uncertain significance Single submitter
All SLC19A1 variants
Pathogenic 1
- p.Gly348Arg No assertion criteria immunodeficiency 114, folate-responsive
Benign 18
- c.-43C>T Multiple submitters
- p.Ala324= Multiple submitters
- p.Ala469Val Multiple submitters
- p.Ile414= Multiple submitters
- p.Ile417Thr Multiple submitters
- p.Leu338Phe Multiple submitters
- p.Pro232= Multiple submitters
- p.Val116= Multiple submitters
- c.189+14G>A Single submitter
- c.949+20del Single submitter
- c.950-14C>T Single submitter
- c.*640C>T Single submitter
- p.Ala279= Single submitter
- p.Asn588= Single submitter
- p.Cys458Gly Single submitter ⚠
- p.Leu97= Single submitter
- p.Phe141= Single submitter
- p.Thr87= Single submitter
Benign/Likely benign 2
- c.1151+8C>A Multiple submitters
- p.Asp56His Multiple submitters
Likely benign 86
- p.Ala131= Multiple submitters
- p.Gly512= Multiple submitters
- p.His569= Multiple submitters
- p.Phe406= Multiple submitters
- p.Pro464= Multiple submitters
- c.1151+16G>T Single submitter
- c.1152-6G>A Single submitter
- c.1294-23_1294-15dup Single submitter
- c.189+13C>T Single submitter
- c.189+16G>C Single submitter
- c.949+17C>T Single submitter
- c.949+19C>T Single submitter
- c.950-5C>A Single submitter
- c.950-9C>T Single submitter
- p.Ala200= Single submitter
- p.Ala224= Single submitter
- p.Ala252= Single submitter
- p.Ala252Val Single submitter
- p.Ala302= Single submitter
- p.Ala312= Single submitter
- p.Ala332Val Single submitter
- p.Ala367= Single submitter
- p.Ala39= Single submitter
- p.Ala7= Single submitter
- p.Arg148= Single submitter
- p.Arg373= Single submitter
- p.Arg422= Single submitter
- p.Arg460Gln Single submitter
- p.Asn293= Single submitter
- p.Asn306= Single submitter
- p.Asp420= Single submitter
- p.Asp506= Single submitter
- p.Asp522Asn Single submitter
- p.Cys220= Single submitter
- p.Glu221Gly Single submitter
- p.Glu228Asp Single submitter
- p.Gly178Ser Single submitter ⚠
- p.Gly247= Single submitter
- p.Gly341= Single submitter
- p.Gly471= Single submitter
- p.His114= Single submitter
- p.Ile134= Single submitter
- p.Ile444= Single submitter
- p.Leu162= Single submitter
- p.Leu203= Single submitter
- p.Leu258= Single submitter
- p.Leu262= Single submitter
- p.Leu269= Single submitter
- p.Leu291= Single submitter
- p.Leu379= Single submitter
- p.Leu395= Single submitter
- p.Leu452= Single submitter
- p.Leu491= Single submitter
- p.Leu525= Single submitter
- p.Leu566= Single submitter
- p.Phe195= Single submitter
- p.Phe322= Single submitter
- p.Phe369= Single submitter
- p.Phe372= Single submitter
- p.Phe400= Single submitter
- p.Pro13= Single submitter
- p.Pro146= Single submitter
- p.Pro265= Single submitter
- p.Pro500= Single submitter
- p.Pro529= Single submitter
- p.Pro55= Single submitter
- p.Pro82= Single submitter
- p.Pro94= Single submitter
- p.Ser127= Single submitter
- p.Ser168= Single submitter
- p.Ser278= Single submitter
- p.Ser419= Single submitter
- p.Ser499= Single submitter
- p.Ser550= Single submitter
- p.Ser73= Single submitter
- p.Thr166= Single submitter
- p.Thr404= Single submitter
- p.Tyr126= Single submitter
- p.Tyr282= Single submitter
- p.Val160= Single submitter
- p.Val342= Single submitter
- p.Val511Leu Single submitter
- p.Val540= Single submitter
- c.*497del No assertion criteria SLC19A1-related disorder
- c.*538G>C No assertion criteria SLC19A1-related disorder
- p.Arg42= No assertion criteria SLC19A1-related disorder
Uncertain significance 129
- p.Ala469Ser Multiple submitters ⚠
- p.Arg148His Multiple submitters ⚠
- p.Arg422Gln Multiple submitters ⚠
- p.Asp584Asn Multiple submitters ⚠
- p.Glu505Gly Multiple submitters ⚠
- p.Glu62Lys Multiple submitters ⚠
- p.Gly317fs Multiple submitters
- p.Gly585Cys Multiple submitters ⚠
- p.Leu101Phe Multiple submitters ⚠
- p.Phe212del Multiple submitters megaloblastic anemia, folate-responsive
- p.Pro427Leu Multiple submitters ⚠
- p.Pro529Leu Multiple submitters ⚠
- p.Ser225Trp Multiple submitters ⚠
- p.Ser389Thr Multiple submitters ⚠
- p.Ser46Cys Multiple submitters megaloblastic anemia, folate-responsive ⚠
- p.Thr356Met Multiple submitters ⚠
- p.Val380Ala Multiple submitters ⚠
- c.1293+5G>C Single submitter
- c.190-2431C>T Single submitter
- p.Ala158Thr Single submitter ⚠
- p.Ala200Thr Single submitter ⚠
- p.Ala279Thr Single submitter ⚠
- p.Ala279Val Single submitter
- p.Ala302Val Single submitter ⚠
- p.Ala309Val Single submitter ⚠
- p.Ala324Val Single submitter
- p.Ala340Val Single submitter ⚠
- p.Ala368Val Single submitter ⚠
- p.Ala39Val Single submitter ⚠
- p.Ala483Val Single submitter ⚠
- p.Ala551Thr Single submitter ⚠
- p.Ala7Val Single submitter ⚠
- p.Arg148Leu Single submitter ⚠
- p.Arg208Gly Single submitter ⚠
- p.Arg229Ser Single submitter ⚠
- p.Arg23Trp Single submitter ⚠
- p.Arg256Gln Single submitter ⚠
- p.Arg256Trp Single submitter ⚠
- p.Arg263Gln Single submitter ⚠
- p.Arg263Trp Single submitter ⚠
- p.Arg264_Trp270dup Single submitter
- p.Arg264Trp Single submitter ⚠
- p.Arg303Gln Single submitter ⚠
- p.Arg303Trp Single submitter ⚠
- p.Arg333Cys Single submitter ⚠
- p.Arg429His Single submitter ⚠
- p.Arg456Gln Single submitter ⚠
- p.Arg456Trp Single submitter ⚠
- p.Arg460Trp Single submitter ⚠
- p.Arg465Trp Single submitter ⚠
- p.Arg61Trp Single submitter ⚠
- p.Asn277Ser Single submitter ⚠
- p.Asp506Val Single submitter ⚠
- p.Asp56Asn Single submitter ⚠
- p.Cys246fs Single submitter
- p.Gln11Glu Single submitter ⚠
- p.Gln266His Single submitter ⚠
- p.Gln386Arg Single submitter ⚠
- p.Gln482Glu Single submitter ⚠
- p.Gln518His Single submitter ⚠
- p.Gln520Arg Single submitter ⚠
- p.Gln532fs Single submitter
- p.Gln587Pro Single submitter ⚠
- p.Gln591fs Single submitter
- p.Gly154Ser Single submitter ⚠
- p.Gly17Glu Single submitter ⚠
- p.Gly236Arg Single submitter ⚠
- p.Gly572Arg Single submitter ⚠
- p.Gly585Ser Single submitter ⚠
- p.His569Tyr Single submitter ⚠
- p.Ile362Val Single submitter ⚠
- p.Ile382Asn Single submitter ⚠
- p.Ile445Met Single submitter ⚠
- p.Leu161Pro Single submitter ⚠
- p.Leu227Gln Single submitter ⚠
- p.Leu22Phe Single submitter ⚠
- p.Leu255Pro Single submitter ⚠
- p.Leu426Phe Single submitter ⚠
- p.Leu455Pro Single submitter ⚠
- p.Leu472Pro Single submitter ⚠
- p.Lys336Gln Single submitter ⚠
- p.Met122Val Single submitter
- p.Met1Val Single submitter
- p.Phe103Leu Single submitter ⚠
- p.Phe212Leu Single submitter ⚠
- p.Pro18Arg Single submitter ⚠
- p.Pro234Arg Single submitter ⚠
- p.Pro359Leu Single submitter ⚠
- p.Pro464Leu Single submitter ⚠
- p.Pro468Leu Single submitter ⚠
- p.Pro500Leu Single submitter ⚠
- p.Pro501Arg Single submitter ⚠
- p.Pro501Leu Single submitter ⚠
- p.Pro501Ser Single submitter ⚠
- p.Pro539Ser Single submitter ⚠
- p.Pro545Ser Single submitter ⚠
- p.Pro556Arg Single submitter ⚠
- p.Pro94Leu Single submitter ⚠
- p.Ser156Leu Single submitter ⚠
- p.Ser225Leu Single submitter ⚠
- p.Ser375Phe Single submitter ⚠
- p.Ser419Leu Single submitter
- p.Ser499Asn Single submitter ⚠
- p.Ser515Cys Single submitter ⚠
- p.Ser515Phe Single submitter ⚠
- p.Ser544Phe Single submitter ⚠
- p.Ser550Pro Single submitter ⚠
- p.Thr222Ile Single submitter ⚠
- p.Thr345Ala Single submitter ⚠
- p.Thr404Met Single submitter ⚠
- p.Thr69Met Single submitter ⚠
- p.Trp270Cys Single submitter ⚠
- p.Tyr136Phe Single submitter ⚠
- p.Tyr187His Single submitter ⚠
- p.Tyr435Cys Single submitter ⚠
- p.Tyr74Asn Single submitter ⚠
- p.Val104Glu Single submitter ⚠
- p.Val116del Single submitter
- p.Val14Leu Single submitter ⚠
- p.Val164Ala Single submitter
- p.Val197Ala Single submitter ⚠
- p.Val295Gly Single submitter ⚠
- p.Val342Phe Single submitter ⚠
- p.Val370Met Single submitter
- p.Val437Leu Single submitter ⚠
- p.Val437Met Single submitter ⚠
- p.Val71Ala Single submitter ⚠
- p.Val83Ala Single submitter ⚠
- p.Val83Leu Single submitter ⚠