SLC44A1 — 114 ClinVar variants

All ClinVar germline SLC44A1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 82 flagged for review →

5 Pathogenic · 3 Likely pathogenic · 1 Conflicting · 7 Benign · 12 Likely benign · 86 Uncertain significance

Full SLC44A1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 82

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 1

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

SLC44A1 p.Ser8Thr Conflicting Single submitter

Predictors lean, ClinVar uncertain 69

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

Predictors split 12

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

All SLC44A1 variants

Pathogenic 5

p.Ser196fs Single submitter neurodegeneration, childhood-onset, with ataxia, tremor, optic atrophy, and cognitive decline
p.Tyr351Ter Single submitter
c.126+5161_270-2343del No assertion criteria neurodegeneration, childhood-onset, with ataxia, tremor, optic atrophy, and cognitive decline
p.Asp517fs No assertion criteria neurodegeneration, childhood-onset, with ataxia, tremor, optic atrophy, and cognitive decline
p.Ser126fs No assertion criteria neurodegeneration, childhood-onset, with ataxia, tremor, optic atrophy, and cognitive decline

Likely pathogenic 3

c.36+2T>C Single submitter SLC44A1-related disorder
p.Gln337Ter Single submitter neurodevelopmental disorder
p.Glu213Ter Single submitter SLC44A1-related disorder

Conflicting classifications of pathogenicity 1

p.Ser8Thr Single submitter ⚠

Benign 7

p.Ser644Ala Single submitter
p.Thr193Ala Single submitter
c.1951-9T>C No assertion criteria SLC44A1-related disorder
c.670+9T>C No assertion criteria SLC44A1-related disorder
c.*862G>A No assertion criteria SLC44A1-related disorder
p.Ile318= No assertion criteria SLC44A1-related disorder
p.Val567= No assertion criteria SLC44A1-related disorder

Likely benign 12

p.Ala518= Multiple submitters
p.Ala7= Multiple submitters
c.760+16_760+19del Single submitter
p.Ala166= Single submitter
p.Arg268Lys Single submitter
p.Asn507= Single submitter
p.His322= Single submitter
p.Leu400= Single submitter
p.Pro365Ala Single submitter
p.Thr531Ala Single submitter
p.Val110= Single submitter
p.Leu225= No assertion criteria SLC44A1-related disorder

Uncertain significance 86

p.Arg287Trp Multiple submitters ⚠
p.Ser126Asn Multiple submitters ⚠
p.Ala116Thr Single submitter ⚠
p.Ala116Val Single submitter ⚠
p.Ala166Val Single submitter ⚠
p.Ala315Ser Single submitter ⚠
p.Ala315Thr Single submitter ⚠
p.Ala408Val Single submitter ⚠
p.Ala430Val Single submitter ⚠
p.Ala500Val Single submitter ⚠
p.Ala55Thr Single submitter ⚠
p.Ala602Gly Single submitter ⚠
p.Ala642Thr Single submitter ⚠
p.Ala654Gly Single submitter ⚠
p.Ala7Val Single submitter ⚠
p.Arg234Gly Single submitter ⚠
p.Arg311His Single submitter
p.Arg311Leu Single submitter ⚠
p.Arg313Cys Single submitter ⚠
p.Arg437Cys Single submitter ⚠
p.Arg476Ter Single submitter
p.Arg89Gln Single submitter ⚠
p.Arg89Trp Single submitter ⚠
p.Asn560Ser Single submitter ⚠
p.Asn608Ser Single submitter
p.Asn99Ser Single submitter ⚠
p.Asp419Val Single submitter ⚠
p.Asp96Asn Single submitter ⚠
p.Cys402Arg Single submitter ⚠
p.Cys46Tyr Single submitter ⚠
p.Cys477Arg Single submitter ⚠
p.Cys477Ser Single submitter ⚠
p.Cys492Tyr Single submitter ⚠
p.Gln129Arg Single submitter ⚠
p.Gln278Lys Single submitter ⚠
p.Gln367Arg Single submitter ⚠
p.Glu133Lys Single submitter ⚠
p.Gly255Ala Single submitter ⚠
p.Ile246Val Single submitter ⚠
p.Ile393Met Single submitter ⚠
p.Ile436Val Single submitter ⚠
p.Ile455Leu Single submitter ⚠
p.Ile547Thr Single submitter
p.Ile574Val Single submitter ⚠
p.Ile589Met Single submitter ⚠
p.Ile603Thr Single submitter ⚠
p.Leu356Phe Single submitter ⚠
p.Leu452Ser Single submitter ⚠
p.Leu558Val Single submitter ⚠
p.Lys123Arg Single submitter ⚠
p.Lys161Arg Single submitter ⚠
p.Lys75Glu Single submitter ⚠
p.Met307Thr Single submitter
p.Met592Thr Single submitter ⚠
p.Met84Val Single submitter ⚠
p.Phe342Ser Single submitter ⚠
p.Pro146Ser Single submitter ⚠
p.Pro365Ser Single submitter ⚠
p.Pro456Leu Single submitter ⚠
p.Pro80Ser Single submitter ⚠
p.Pro97Ala Single submitter ⚠
p.Ser152Pro Single submitter ⚠
p.Ser155Pro Single submitter ⚠
p.Ser237Thr Single submitter ⚠
p.Ser396Arg Single submitter ⚠
p.Ser465Arg Single submitter ⚠
p.Ser5Gly Single submitter ⚠
p.Ser652Leu Single submitter ⚠
p.Ser655Asn Single submitter ⚠
p.Ser8Phe Single submitter ⚠
p.Thr151Ala Single submitter ⚠
p.Thr210Ala Single submitter ⚠
p.Thr256Ser Single submitter ⚠
p.Thr275Ser Single submitter ⚠
p.Thr361Ser Single submitter ⚠
p.Thr52Ala Single submitter ⚠
p.Thr87Asn Single submitter ⚠
p.Trp394Cys Single submitter ⚠
p.Tyr149Cys Single submitter ⚠
p.Tyr184Cys Single submitter ⚠
p.Tyr590Phe Single submitter ⚠
p.Val298Ala Single submitter ⚠
p.Val389Glu Single submitter ⚠
p.Val596Leu Single submitter ⚠
p.Val641Ile Single submitter ⚠
p.Val92Ala Single submitter ⚠