SLC6A4 — 138 ClinVar variants
All ClinVar germline SLC6A4 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 47 flagged for review →
1 Likely pathogenic · 2 Conflicting · 7 Benign · 1 Benign/Likely benign · 18 Likely benign · 109 Uncertain significance
Full SLC6A4 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 47
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 41
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
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SLC6A4 p.Val283Leu
Uncertain significance
Multiple submitters
Behavior disorder
- SLC6A4 p.Ala285Val Uncertain significance Single submitter
- SLC6A4 p.Ala331Ser Uncertain significance Single submitter
-
SLC6A4 p.Ala413Val
Uncertain significance
Single submitter
Behavior disorder
- SLC6A4 p.Ala500Thr Uncertain significance Single submitter
-
SLC6A4 p.Ala505Val
Uncertain significance
Single submitter
Behavior disorder
- SLC6A4 p.Arg461His Uncertain significance Single submitter
-
SLC6A4 p.Arg464Trp
Uncertain significance
Single submitter
Behavior disorder
-
SLC6A4 p.Arg60Trp
Uncertain significance
Single submitter
Behavior disorder
-
SLC6A4 p.Asn208Ser
Uncertain significance
Single submitter
Behavior disorder
-
SLC6A4 p.Asn45Ser
Uncertain significance
Single submitter
Behavior disorder
-
SLC6A4 p.Asn569Ser
Uncertain significance
Single submitter
Behavior disorder
- SLC6A4 p.Asp624Tyr Uncertain significance Single submitter
- SLC6A4 p.Cys357Tyr Uncertain significance Single submitter
- SLC6A4 p.Cys588Phe Uncertain significance Single submitter
- SLC6A4 p.Gly250Asp Uncertain significance Single submitter
- SLC6A4 p.Gly250Ser Uncertain significance Single submitter
-
SLC6A4 p.Gly25Arg
Uncertain significance
Single submitter
Behavior disorder
- SLC6A4 p.Gly498Ala Uncertain significance Single submitter
- SLC6A4 p.His456Asn Uncertain significance Single submitter
- SLC6A4 p.His456Tyr Uncertain significance Single submitter
-
SLC6A4 p.Ile157Val
Uncertain significance
Single submitter
Behavior disorder
- SLC6A4 p.Ile290Val Uncertain significance Single submitter
-
SLC6A4 p.Ile425Val
Uncertain significance
Single submitter
Behavior disorder
- SLC6A4 p.Ile575Asn Uncertain significance Single submitter
- SLC6A4 p.Leu563Ile Uncertain significance Single submitter
- SLC6A4 p.Phe127Ser Uncertain significance Single submitter
- SLC6A4 p.Phe422Ser Uncertain significance Single submitter
- SLC6A4 p.Pro131Leu Uncertain significance Single submitter
- SLC6A4 p.Pro315Thr Uncertain significance Single submitter
- SLC6A4 p.Ser189Phe Uncertain significance Single submitter
- SLC6A4 p.Ser214Phe Uncertain significance Single submitter
-
SLC6A4 p.Ser293Phe
Uncertain significance
Single submitter
Behavior disorder
- SLC6A4 p.Ser611Thr Uncertain significance Single submitter
-
SLC6A4 p.Thr225Met
Uncertain significance
Single submitter
Behavior disorder
- SLC6A4 p.Thr3Met Uncertain significance Single submitter
- SLC6A4 p.Thr472Asn Uncertain significance Single submitter
- SLC6A4 p.Thr600Ile Uncertain significance Single submitter
- SLC6A4 p.Tyr516Cys Uncertain significance Single submitter
- SLC6A4 p.Val102Ile Uncertain significance Single submitter
- SLC6A4 p.Val466Met Uncertain significance Single submitter
Predictors split 6
The independent predictors disagree with each other — read with care.
-
SLC6A4 p.Lys605Asn
Likely benign
Multiple submitters
Behavior disorder
- SLC6A4 p.Gln254His Uncertain significance Single submitter
- SLC6A4 p.Ile168Thr Uncertain significance Single submitter
- SLC6A4 p.Lys279Arg Uncertain significance Single submitter
- SLC6A4 p.Phe440Tyr Uncertain significance Single submitter
-
SLC6A4 p.Phe465Leu
Likely benign
Single submitter
Behavior disorder
All SLC6A4 variants
Likely pathogenic 1
- p.Thr583fs Single submitter obsessive-compulsive disorder
Conflicting classifications of pathogenicity 2
Benign 7
- c.*2160G>T Multiple submitters Behavior disorder
- c.*2353A>G Multiple submitters Behavior disorder
- c.*2389A>G Multiple submitters Behavior disorder
- c.*2957C>T Multiple submitters Behavior disorder
- p.Thr439= Multiple submitters Behavior disorder
- c.-149C>A Single submitter Behavior disorder
- c.*2388C>T Single submitter Behavior disorder
Benign/Likely benign 1
- p.Asn101= Multiple submitters Behavior disorder
Likely benign 18
- c.*328A>G Multiple submitters Behavior disorder
- c.*3448G>C Multiple submitters Behavior disorder
- p.Lys605Asn Multiple submitters Behavior disorder ⚠
- p.Phe465= Multiple submitters Behavior disorder
- c.-173C>G Single submitter Behavior disorder
- c.-185C>A Single submitter
- c.*1748C>A Single submitter
- c.*2703A>G Single submitter Behavior disorder
- c.*3047A>G Single submitter Behavior disorder
- c.*463T>G Single submitter
- c.*597C>T Single submitter Behavior disorder
- c.*670T>G Single submitter
- p.His456= Single submitter Behavior disorder
- p.Ile587Val Single submitter
- p.Phe465Leu Single submitter Behavior disorder ⚠
- c.1818+4C>T No assertion criteria SLC6A4-related disorder
- p.Ala55= No assertion criteria SLC6A4-related disorder
- p.Thr433= No assertion criteria SLC6A4-related disorder
Uncertain significance 109
- c.*1727C>T Multiple submitters Behavior disorder
- p.Val283Leu Multiple submitters Behavior disorder ⚠
- c.1205-9C>T Single submitter Behavior disorder
- c.1318-11G>A Single submitter Behavior disorder
- c.698+11G>A Single submitter
- c.837+2T>C Single submitter obsessive-compulsive disorder
- c.837+4A>T Single submitter Behavior disorder
- c.-218C>A Single submitter Behavior disorder
- c.-269C>A Single submitter Behavior disorder
- c.-49A>G Single submitter Behavior disorder
- c.*1029C>T Single submitter Behavior disorder
- c.*1060G>A Single submitter Behavior disorder
- c.*1123G>A Single submitter Behavior disorder
- c.*1127T>C Single submitter Behavior disorder
- c.*1178C>T Single submitter Behavior disorder
- c.*1179G>A Single submitter Behavior disorder
- c.*11G>A Single submitter Behavior disorder
- c.*1211G>A Single submitter Behavior disorder
- c.*1262A>C Single submitter Behavior disorder
- c.*130G>A Single submitter Behavior disorder
- c.*1329G>A Single submitter Behavior disorder
- c.*162C>T Single submitter Behavior disorder
- c.*1642C>G Single submitter Behavior disorder
- c.*1658T>C Single submitter Behavior disorder
- c.*1767G>C Single submitter
- c.*186C>T Single submitter Behavior disorder
- c.*1900T>C Single submitter Behavior disorder
- c.*1933T>C Single submitter Behavior disorder
- c.*2019C>T Single submitter Behavior disorder
- c.*2085A>C Single submitter Behavior disorder
- c.*2091del Single submitter
- c.*2091dup Single submitter
- c.*2094G>A Single submitter Behavior disorder
- c.*2112C>T Single submitter Behavior disorder
- c.*2192G>C Single submitter Behavior disorder
- c.*2412G>C Single submitter Behavior disorder
- c.*242G>A Single submitter Behavior disorder
- c.*2495G>A Single submitter Behavior disorder
- c.*2836C>T Single submitter Behavior disorder
- c.*2970G>A Single submitter Behavior disorder
- c.*3227G>A Single submitter Behavior disorder
- c.*3318T>G Single submitter Behavior disorder
- c.*350G>A Single submitter Behavior disorder
- c.*359T>C Single submitter Behavior disorder
- c.*3831T>C Single submitter Behavior disorder
- c.*3891A>G Single submitter Behavior disorder
- c.*407G>A Single submitter Behavior disorder
- c.*433G>A Single submitter Behavior disorder
- c.*441T>C Single submitter Behavior disorder
- c.*442A>T Single submitter Behavior disorder
- c.*538A>G Single submitter Behavior disorder
- c.*564T>C Single submitter Behavior disorder
- c.*597C>G Single submitter Behavior disorder
- c.*768T>C Single submitter Behavior disorder
- c.*906G>A Single submitter Behavior disorder
- c.*97G>C Single submitter Behavior disorder
- p.Ala228= Single submitter Behavior disorder
- p.Ala285Val Single submitter ⚠
- p.Ala330Gly Single submitter
- p.Ala331Ser Single submitter ⚠
- p.Ala413Val Single submitter Behavior disorder ⚠
- p.Ala419= Single submitter Behavior disorder
- p.Ala500Thr Single submitter ⚠
- p.Ala505Val Single submitter Behavior disorder ⚠
- p.Ala594= Single submitter Behavior disorder
- p.Arg461His Single submitter ⚠
- p.Arg464Trp Single submitter Behavior disorder ⚠
- p.Arg60Trp Single submitter Behavior disorder ⚠
- p.Asn208Ser Single submitter Behavior disorder ⚠
- p.Asn45Ser Single submitter Behavior disorder ⚠
- p.Asn569Ser Single submitter Behavior disorder ⚠
- p.Asp624Tyr Single submitter ⚠
- p.Cys357Tyr Single submitter ⚠
- p.Cys588Phe Single submitter ⚠
- p.Gln254His Single submitter ⚠
- p.Gly244= Single submitter Behavior disorder
- p.Gly250Asp Single submitter ⚠
- p.Gly250Ser Single submitter ⚠
- p.Gly25Arg Single submitter Behavior disorder ⚠
- p.Gly46= Single submitter Behavior disorder
- p.Gly498Ala Single submitter ⚠
- p.His456Asn Single submitter ⚠
- p.His456Tyr Single submitter ⚠
- p.Ile157Val Single submitter Behavior disorder ⚠
- p.Ile168Thr Single submitter ⚠
- p.Ile290Val Single submitter ⚠
- p.Ile425Val Single submitter Behavior disorder ⚠
- p.Ile575Asn Single submitter ⚠
- p.Leu563Ile Single submitter ⚠
- p.Lys279Arg Single submitter ⚠
- p.Phe127Ser Single submitter ⚠
- p.Phe422Ser Single submitter ⚠
- p.Phe440Tyr Single submitter ⚠
- p.Pro131= Single submitter Behavior disorder
- p.Pro131Leu Single submitter ⚠
- p.Pro315Thr Single submitter ⚠
- p.Ser189Phe Single submitter ⚠
- p.Ser214Phe Single submitter ⚠
- p.Ser293Phe Single submitter Behavior disorder ⚠
- p.Ser611Thr Single submitter ⚠
- p.Thr225Met Single submitter Behavior disorder ⚠
- p.Thr3Met Single submitter ⚠
- p.Thr4= Single submitter Behavior disorder
- p.Thr472Asn Single submitter ⚠
- p.Thr600Ile Single submitter ⚠
- p.Thr68= Single submitter Behavior disorder
- p.Tyr516Cys Single submitter ⚠
- p.Val102Ile Single submitter ⚠
- p.Val466Met Single submitter ⚠