SLC6A3 — 550 ClinVar variants

All ClinVar germline SLC6A3 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 153 flagged for review →

9 Pathogenic · 11 Likely pathogenic · 12 Conflicting · 71 Benign · 12 Benign/Likely benign · 268 Likely benign · 167 Uncertain significance

Full SLC6A3 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 153

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 agree, ClinVar conflicts 7

ClinVar submitters conflict, but the independent predictors unanimously agree — a QC review flag, not a reclassification.

Predictors lean, ClinVar uncertain 122

ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.

Predictors split 24

The independent predictors disagree with each other — read with care.

All SLC6A3 variants

Pathogenic 9

  • c.1269+1G>A Multiple submitters parkinsonism-dystonia, infantile
  • p.Arg588Ter Single submitter parkinsonism-dystonia, infantile
  • p.Cys463Ter Single submitter
  • p.Cys523_Phe531delinsTer Single submitter classic dopamine transporter deficiency syndrome
  • p.Phe114fs Single submitter parkinsonism-dystonia, infantile
  • p.Tyr297_Leu298insTer Single submitter parkinsonism-dystonia, infantile
  • p.Leu224Pro No assertion criteria classic dopamine transporter deficiency syndrome
  • p.Leu368Gln No assertion criteria classic dopamine transporter deficiency syndrome
  • p.Pro395Leu No assertion criteria classic dopamine transporter deficiency syndrome

Likely pathogenic 11

  • c.1031+1G>A Single submitter parkinsonism-dystonia, infantile
  • c.1032-1G>C Single submitter parkinsonism-dystonia, infantile
  • c.1398+5G>A Single submitter classic dopamine transporter deficiency syndrome
  • c.1767+2T>C Single submitter parkinsonism-dystonia, infantile
  • p.Ala314Val Single submitter SLC6A3-related disorder
  • p.Ala570fs Single submitter classic dopamine transporter deficiency syndrome
  • p.Arg85Trp Single submitter
  • p.Gly386Arg Single submitter parkinsonism-dystonia, infantile
  • p.His547fs Single submitter
  • p.Trp63Ter Single submitter SLC6A3-related disorder
  • c.1767+2_1767+3del No assertion criteria SLC6A3-related disorder

Conflicting classifications of pathogenicity 12

  • c.1157-15C>T Single submitter parkinsonism-dystonia, infantile
  • p.Ala480= Single submitter parkinsonism-dystonia, infantile
  • p.Ala559Val Single submitter parkinsonism-dystonia, infantile ⚠
  • p.Arg521Trp Single submitter parkinsonism-dystonia, infantile ⚠
  • p.Arg60Trp Single submitter parkinsonism-dystonia, infantile ⚠
  • p.Asp385= Single submitter Inborn genetic diseases
  • p.Gln373Arg Single submitter parkinsonism-dystonia, infantile ⚠
  • p.Gly110= Single submitter parkinsonism-dystonia, infantile
  • p.Leu167Phe Single submitter parkinsonism-dystonia, infantile ⚠
  • p.Lys619Asn Single submitter parkinsonism-dystonia, infantile ⚠
  • p.Pro26Leu Single submitter parkinsonism-dystonia, infantile ⚠
  • p.Ser505= Single submitter parkinsonism-dystonia, infantile

Benign 71

Benign/Likely benign 12

  • c.1399-11del Multiple submitters parkinsonism-dystonia, infantile
  • c.1767+13A>G Multiple submitters classic dopamine transporter deficiency syndrome
  • c.653+13C>T Multiple submitters parkinsonism-dystonia, infantile
  • p.Asn182= Multiple submitters parkinsonism-dystonia, infantile
  • p.Asn466= Multiple submitters parkinsonism-dystonia, infantile
  • p.Glu20= Multiple submitters parkinsonism-dystonia, infantile
  • p.Ile452= Multiple submitters parkinsonism-dystonia, infantile
  • p.Ile490= Multiple submitters classic dopamine transporter deficiency syndrome
  • p.Ile564= Multiple submitters parkinsonism-dystonia, infantile
  • p.Phe362= Multiple submitters parkinsonism-dystonia, infantile
  • p.Val464Ile Multiple submitters parkinsonism-dystonia, infantile
  • p.Val471= Multiple submitters parkinsonism-dystonia, infantile

Likely benign 268

  • c.1032-111C>T Multiple submitters
  • c.1032-138C>T Multiple submitters
  • c.1399-262G>A Multiple submitters
  • c.1599+12C>G Multiple submitters parkinsonism-dystonia, infantile
  • c.1768-76G>T Multiple submitters
  • c.1839+185G>A Multiple submitters
  • c.1840-7_1840-3dup Multiple submitters parkinsonism-dystonia, infantile
  • c.418+9C>T Multiple submitters parkinsonism-dystonia, infantile
  • c.419-109T>G Multiple submitters
  • c.419-5G>T Multiple submitters parkinsonism-dystonia, infantile
  • c.*190C>T Multiple submitters
  • p.Ala346= Multiple submitters parkinsonism-dystonia, infantile
  • p.Ala559= Multiple submitters parkinsonism-dystonia, infantile
  • p.Asn157= Multiple submitters parkinsonism-dystonia, infantile
  • p.Asn205= Multiple submitters parkinsonism-dystonia, infantile
  • p.Asp381= Multiple submitters parkinsonism-dystonia, infantile
  • p.Glu602= Multiple submitters parkinsonism-dystonia, infantile
  • p.Gly258= Multiple submitters parkinsonism-dystonia, infantile
  • p.His165= Multiple submitters parkinsonism-dystonia, infantile
  • p.Ile493= Multiple submitters parkinsonism-dystonia, infantile
  • p.Leu277= Multiple submitters parkinsonism-dystonia, infantile
  • p.Phe543= Multiple submitters parkinsonism-dystonia, infantile
  • p.Pro26= Multiple submitters parkinsonism-dystonia, infantile
  • p.Ser360= Multiple submitters parkinsonism-dystonia, infantile
  • p.Ser422= Multiple submitters parkinsonism-dystonia, infantile
  • p.Thr432= Multiple submitters parkinsonism-dystonia, infantile
  • p.Thr512= Multiple submitters parkinsonism-dystonia, infantile
  • p.Tyr166= Multiple submitters parkinsonism-dystonia, infantile
  • p.Val152= Multiple submitters parkinsonism-dystonia, infantile
  • p.Val363= Multiple submitters parkinsonism-dystonia, infantile
  • c.1031+17G>A Single submitter parkinsonism-dystonia, infantile
  • c.1032-14T>C Single submitter parkinsonism-dystonia, infantile
  • c.1032-17G>A Single submitter parkinsonism-dystonia, infantile
  • c.1032-20G>A Single submitter parkinsonism-dystonia, infantile
  • c.1032-20G>C Single submitter parkinsonism-dystonia, infantile
  • c.1032-242G>A Single submitter
  • c.1032-5T>C Single submitter parkinsonism-dystonia, infantile
  • c.1156+200_1156+237del Single submitter
  • c.1156+229C>T Single submitter
  • c.1156+238C>A Single submitter
  • c.1156+270G>T Single submitter
  • c.1156+276C>A Single submitter
  • c.1156+299T>C Single submitter
  • c.1156+9C>T Single submitter parkinsonism-dystonia, infantile
  • c.1157-17G>A Single submitter parkinsonism-dystonia, infantile
  • c.1157-20C>G Single submitter parkinsonism-dystonia, infantile
  • c.1269+11C>T Single submitter parkinsonism-dystonia, infantile
  • c.1269+12G>T Single submitter parkinsonism-dystonia, infantile
  • c.1269+16C>T Single submitter parkinsonism-dystonia, infantile
  • c.1269+20C>T Single submitter parkinsonism-dystonia, infantile
  • c.1270-10C>T Single submitter parkinsonism-dystonia, infantile
  • c.1270-12C>T Single submitter parkinsonism-dystonia, infantile
  • c.1270-19C>T Single submitter parkinsonism-dystonia, infantile
  • c.1270-4G>A Single submitter parkinsonism-dystonia, infantile
  • c.1398+12C>T Single submitter parkinsonism-dystonia, infantile
  • c.1398+13G>A Single submitter parkinsonism-dystonia, infantile
  • c.1398+13G>T Single submitter parkinsonism-dystonia, infantile
  • c.1398+16G>A Single submitter parkinsonism-dystonia, infantile
  • c.1398+5_1398+6dup Single submitter parkinsonism-dystonia, infantile
  • c.1399-11C>T Single submitter parkinsonism-dystonia, infantile
  • c.1399-18G>C Single submitter parkinsonism-dystonia, infantile
  • c.1399-19A>C Single submitter parkinsonism-dystonia, infantile
  • c.1399-19A>G Single submitter parkinsonism-dystonia, infantile
  • c.1498+10G>T Single submitter parkinsonism-dystonia, infantile
  • c.1498+14_1498+15insG Single submitter
  • c.1498+8C>T Single submitter parkinsonism-dystonia, infantile
  • c.1498+9G>A Single submitter
  • c.1499-12C>G Single submitter parkinsonism-dystonia, infantile
  • c.1499-14C>T Single submitter parkinsonism-dystonia, infantile
  • c.1499-185C>T Single submitter
  • c.1499-239C>T Single submitter
  • c.1599+13G>A Single submitter parkinsonism-dystonia, infantile
  • c.1599+9C>A Single submitter parkinsonism-dystonia, infantile
  • c.1600-137G>T Single submitter
  • c.1600-17G>A Single submitter parkinsonism-dystonia, infantile
  • c.1600-18C>T Single submitter parkinsonism-dystonia, infantile
  • c.1600-9_1600-8delinsCT Single submitter parkinsonism-dystonia, infantile
  • c.1767+14C>T Single submitter parkinsonism-dystonia, infantile
  • c.1767+15G>A Single submitter parkinsonism-dystonia, infantile
  • c.1767+16G>A Single submitter parkinsonism-dystonia, infantile
  • c.1767+19C>T Single submitter parkinsonism-dystonia, infantile
  • c.1767+20G>C Single submitter parkinsonism-dystonia, infantile
  • c.1767+280C>G Single submitter
  • c.1768-12T>C Single submitter parkinsonism-dystonia, infantile
  • c.1768-7C>T Single submitter parkinsonism-dystonia, infantile
  • c.1839+15C>T Single submitter parkinsonism-dystonia, infantile
  • c.1839+26TC[2] Single submitter
  • c.1839+8C>T Single submitter parkinsonism-dystonia, infantile
  • c.1839+9_1839+14del Single submitter parkinsonism-dystonia, infantile
  • c.1840-240G>A Single submitter
  • c.1840-68_1840-49del Single submitter
  • c.1840-8C>A Single submitter parkinsonism-dystonia, infantile
  • c.286+10A>T Single submitter parkinsonism-dystonia, infantile
  • c.286+16G>C Single submitter parkinsonism-dystonia, infantile
  • c.286+18C>T Single submitter parkinsonism-dystonia, infantile
  • c.286+8C>T Single submitter parkinsonism-dystonia, infantile
  • c.287-106G>A Single submitter
  • c.287-119G>A Single submitter
  • c.287-13T>C Single submitter parkinsonism-dystonia, infantile
  • c.287-16C>A Single submitter parkinsonism-dystonia, infantile
  • c.287-20G>C Single submitter parkinsonism-dystonia, infantile
  • c.287-5C>G Single submitter parkinsonism-dystonia, infantile
  • c.287-5C>T Single submitter parkinsonism-dystonia, infantile
  • c.287-6C>T Single submitter parkinsonism-dystonia, infantile
  • c.418+10G>A Single submitter parkinsonism-dystonia, infantile
  • c.418+14G>T Single submitter
  • c.418+16C>A Single submitter parkinsonism-dystonia, infantile
  • c.418+18C>T Single submitter parkinsonism-dystonia, infantile
  • c.418+213G>T Single submitter
  • c.418+7T>A Single submitter parkinsonism-dystonia, infantile
  • c.419-12C>G Single submitter parkinsonism-dystonia, infantile
  • c.419-16del Single submitter parkinsonism-dystonia, infantile
  • c.419-260A>G Single submitter
  • c.419-5G>A Single submitter parkinsonism-dystonia, infantile
  • c.419-6C>T Single submitter parkinsonism-dystonia, infantile
  • c.653+11G>A Single submitter parkinsonism-dystonia, infantile
  • c.653+12T>C Single submitter parkinsonism-dystonia, infantile
  • c.653+14G>A Single submitter parkinsonism-dystonia, infantile
  • c.653+17T>A Single submitter parkinsonism-dystonia, infantile
  • c.653+39C>A Single submitter
  • c.654-14A>G Single submitter parkinsonism-dystonia, infantile
  • c.654-17C>A Single submitter parkinsonism-dystonia, infantile
  • c.654-18G>A Single submitter parkinsonism-dystonia, infantile
  • c.654-60G>A Single submitter
  • c.654-75C>T Single submitter
  • c.654-8C>T Single submitter parkinsonism-dystonia, infantile
  • c.792+10G>A Single submitter parkinsonism-dystonia, infantile
  • c.792+12G>A Single submitter parkinsonism-dystonia, infantile
  • c.792+13G>A Single submitter parkinsonism-dystonia, infantile
  • c.792+18C>T Single submitter parkinsonism-dystonia, infantile
  • c.792+223C>A Single submitter
  • c.792+7C>T Single submitter parkinsonism-dystonia, infantile
  • c.792+9C>T Single submitter parkinsonism-dystonia, infantile
  • c.793-16C>G Single submitter parkinsonism-dystonia, infantile
  • c.793-7C>T Single submitter parkinsonism-dystonia, infantile
  • c.927+110G>C Single submitter
  • c.927+11T>A Single submitter parkinsonism-dystonia, infantile
  • c.927+8_927+9del Single submitter parkinsonism-dystonia, infantile
  • c.928-12C>G Single submitter parkinsonism-dystonia, infantile
  • c.928-16C>T Single submitter parkinsonism-dystonia, infantile
  • c.928-18C>T Single submitter parkinsonism-dystonia, infantile
  • c.928-19C>T Single submitter parkinsonism-dystonia, infantile
  • c.-45-101G>A Single submitter
  • c.-45-145C>T Single submitter
  • c.*235G>A Single submitter
  • c.*314TGCTCCC[1] Single submitter
  • p.Ala128= Single submitter parkinsonism-dystonia, infantile
  • p.Ala129Thr Single submitter parkinsonism-dystonia, infantile
  • p.Ala16= Single submitter parkinsonism-dystonia, infantile
  • p.Ala214= Single submitter parkinsonism-dystonia, infantile
  • p.Ala23= Single submitter parkinsonism-dystonia, infantile
  • p.Ala270= Single submitter parkinsonism-dystonia, infantile
  • p.Ala279= Single submitter parkinsonism-dystonia, infantile
  • p.Ala290= Single submitter parkinsonism-dystonia, infantile
  • p.Ala308= Single submitter parkinsonism-dystonia, infantile
  • p.Ala314= Single submitter parkinsonism-dystonia, infantile
  • p.Ala346Thr Single submitter parkinsonism-dystonia, infantile ⚠
  • p.Ala399= Single submitter parkinsonism-dystonia, infantile
  • p.Ala408= Single submitter
  • p.Ala455= Single submitter parkinsonism-dystonia, infantile
  • p.Ala576= Single submitter parkinsonism-dystonia, infantile
  • p.Ala592= Single submitter parkinsonism-dystonia, infantile
  • p.Ala77= Single submitter parkinsonism-dystonia, infantile
  • p.Arg125= Single submitter parkinsonism-dystonia, infantile
  • p.Arg237Gln Single submitter parkinsonism-dystonia, infantile
  • p.Arg445= Single submitter parkinsonism-dystonia, infantile
  • p.Arg60= Single submitter parkinsonism-dystonia, infantile
  • p.Arg601His Single submitter Inborn genetic diseases
  • p.Arg615His Single submitter parkinsonism-dystonia, infantile
  • p.Asn49= Single submitter parkinsonism-dystonia, infantile
  • p.Asn558= Single submitter parkinsonism-dystonia, infantile
  • p.Asn82= Single submitter parkinsonism-dystonia, infantile
  • p.Asp231= Single submitter parkinsonism-dystonia, infantile
  • p.Asp292= Single submitter parkinsonism-dystonia, infantile
  • p.Asp313= Single submitter parkinsonism-dystonia, infantile
  • p.Asp600Glu Single submitter Inborn genetic diseases
  • p.Cys306= Single submitter parkinsonism-dystonia, infantile
  • p.Gln226= Single submitter parkinsonism-dystonia, infantile
  • p.Glu28= Single submitter parkinsonism-dystonia, infantile
  • p.Glu56= Single submitter parkinsonism-dystonia, infantile
  • p.Glu598= Single submitter parkinsonism-dystonia, infantile
  • p.Gly220= Single submitter parkinsonism-dystonia, infantile
  • p.Gly323= Single submitter parkinsonism-dystonia, infantile
  • p.Gly325= Single submitter parkinsonism-dystonia, infantile
  • p.Gly361= Single submitter parkinsonism-dystonia, infantile
  • p.Gly369= Single submitter parkinsonism-dystonia, infantile
  • p.Gly380= Single submitter parkinsonism-dystonia, infantile
  • p.Gly39= Single submitter parkinsonism-dystonia, infantile
  • p.Gly433= Single submitter parkinsonism-dystonia, infantile
  • p.Gly481= Single submitter parkinsonism-dystonia, infantile
  • p.Gly95= Single submitter parkinsonism-dystonia, infantile
  • p.His444= Single submitter
  • p.Ile148= Single submitter parkinsonism-dystonia, infantile
  • p.Ile160= Single submitter parkinsonism-dystonia, infantile
  • p.Ile248= Single submitter parkinsonism-dystonia, infantile
  • p.Ile330= Single submitter parkinsonism-dystonia, infantile
  • p.Ile398= Single submitter
  • p.Ile420= Single submitter parkinsonism-dystonia, infantile
  • p.Ile431= Single submitter parkinsonism-dystonia, infantile
  • p.Ile435= Single submitter parkinsonism-dystonia, infantile
  • p.Ile67= Single submitter parkinsonism-dystonia, infantile
  • p.Leu120= Single submitter parkinsonism-dystonia, infantile
  • p.Leu150= Single submitter parkinsonism-dystonia, infantile
  • p.Leu244= Single submitter parkinsonism-dystonia, infantile
  • p.Leu255= Single submitter
  • p.Leu298= Single submitter parkinsonism-dystonia, infantile
  • p.Leu305= Single submitter parkinsonism-dystonia, infantile
  • p.Leu368= Single submitter parkinsonism-dystonia, infantile
  • p.Leu416= Single submitter parkinsonism-dystonia, infantile
  • p.Leu434= Single submitter parkinsonism-dystonia, infantile
  • p.Leu450= Single submitter parkinsonism-dystonia, infantile
  • p.Leu485= Single submitter
  • p.Leu518= Single submitter parkinsonism-dystonia, infantile
  • p.Leu532= Single submitter parkinsonism-dystonia, infantile
  • p.Leu583= Single submitter
  • p.Leu591= Single submitter parkinsonism-dystonia, infantile
  • p.Leu71= Single submitter parkinsonism-dystonia, infantile
  • p.Leu89= Single submitter parkinsonism-dystonia, infantile
  • p.Lys19= Single submitter parkinsonism-dystonia, infantile
  • p.Phe154= Single submitter parkinsonism-dystonia, infantile
  • p.Phe320= Single submitter parkinsonism-dystonia, infantile
  • p.Phe326= Single submitter parkinsonism-dystonia, infantile
  • p.Phe457= Single submitter parkinsonism-dystonia, infantile
  • p.Phe462= Single submitter parkinsonism-dystonia, infantile
  • p.Pro17= Single submitter parkinsonism-dystonia, infantile
  • p.Pro236= Single submitter parkinsonism-dystonia, infantile
  • p.Pro273= Single submitter parkinsonism-dystonia, infantile
  • p.Pro387= Single submitter parkinsonism-dystonia, infantile
  • p.Pro395= Single submitter parkinsonism-dystonia, infantile
  • p.Pro50= Single submitter parkinsonism-dystonia, infantile
  • p.Pro516= Single submitter parkinsonism-dystonia, infantile
  • p.Pro54= Single submitter parkinsonism-dystonia, infantile
  • p.Pro554= Single submitter
  • p.Pro597= Single submitter parkinsonism-dystonia, infantile
  • p.Ser13= Single submitter parkinsonism-dystonia, infantile
  • p.Ser190= Single submitter parkinsonism-dystonia, infantile
  • p.Ser202= Single submitter
  • p.Ser299= Single submitter parkinsonism-dystonia, infantile
  • p.Ser321= Single submitter parkinsonism-dystonia, infantile
  • p.Ser44= Single submitter parkinsonism-dystonia, infantile
  • p.Ser7= Single submitter parkinsonism-dystonia, infantile
  • p.Ser72= Single submitter parkinsonism-dystonia, infantile
  • p.Thr144= Single submitter parkinsonism-dystonia, infantile
  • p.Thr349= Single submitter parkinsonism-dystonia, infantile
  • p.Thr350= Single submitter parkinsonism-dystonia, infantile
  • p.Thr356= Single submitter parkinsonism-dystonia, infantile
  • p.Thr400= Single submitter parkinsonism-dystonia, infantile
  • p.Thr417= Single submitter parkinsonism-dystonia, infantile
  • p.Thr43= Single submitter parkinsonism-dystonia, infantile
  • p.Thr449= Single submitter parkinsonism-dystonia, infantile
  • p.Thr473= Single submitter parkinsonism-dystonia, infantile
  • p.Thr482= Single submitter parkinsonism-dystonia, infantile
  • p.Thr566= Single submitter parkinsonism-dystonia, infantile
  • p.Tyr274= Single submitter parkinsonism-dystonia, infantile
  • p.Tyr370= Single submitter parkinsonism-dystonia, infantile
  • p.Tyr470= Single submitter parkinsonism-dystonia, infantile
  • p.Tyr548= Single submitter parkinsonism-dystonia, infantile
  • p.Tyr551= Single submitter parkinsonism-dystonia, infantile
  • p.Tyr575= Single submitter parkinsonism-dystonia, infantile
  • p.Tyr593= Single submitter parkinsonism-dystonia, infantile
  • p.Val14= Single submitter parkinsonism-dystonia, infantile
  • p.Val24= Single submitter
  • p.Val247= Single submitter parkinsonism-dystonia, infantile
  • p.Val377= Single submitter parkinsonism-dystonia, infantile
  • p.Val453= Single submitter parkinsonism-dystonia, infantile
  • p.Val495= Single submitter parkinsonism-dystonia, infantile
  • p.Val604= Single submitter parkinsonism-dystonia, infantile
  • p.Glu215= No assertion criteria SLC6A3-related disorder

Uncertain significance 167