Sugi Variant

Sugi Variant/HYCC1

HYCC1 — 392 ClinVar variants

All ClinVar germline HYCC1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 127 flagged for review →

7 Pathogenic · 5 Pathogenic/Likely pathogenic · 11 Likely pathogenic · 16 Conflicting · 36 Benign · 9 Benign/Likely benign · 116 Likely benign · 192 Uncertain significance

Full HYCC1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 127

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 92

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

Predictors split 28

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

All HYCC1 variants

Pathogenic 7

  • c.414+1G>A Single submitter leukodystrophy, hypomyelinating, 5
  • c.415-1G>A Single submitter
  • c.51+1G>A Single submitter leukodystrophy, hypomyelinating, 5
  • p.Arg217Ter Single submitter leukodystrophy, hypomyelinating, 5
  • p.Asp261fs Single submitter leukodystrophy, hypomyelinating, 5
  • c.627-439_831+348del No assertion criteria leukodystrophy, hypomyelinating, 5
  • p.Leu53Pro No assertion criteria leukodystrophy, hypomyelinating, 5

Pathogenic/Likely pathogenic 5

  • c.414+1G>T Multiple submitters leukodystrophy, hypomyelinating, 5
  • p.Cys213fs Multiple submitters leukodystrophy, hypomyelinating, 5
  • p.Glu51fs Multiple submitters leukodystrophy, hypomyelinating, 5
  • p.Leu241Ter Multiple submitters leukodystrophy, hypomyelinating, 5
  • p.Tyr42Ter Multiple submitters leukodystrophy, hypomyelinating, 5

Likely pathogenic 11

  • p.Gln49Ter Multiple submitters leukodystrophy, hypomyelinating, 5
  • c.154-1G>T Single submitter leukodystrophy, hypomyelinating, 5
  • c.831+1G>T Single submitter leukodystrophy, hypomyelinating, 5
  • c.832-2A>T Single submitter leukodystrophy, hypomyelinating, 5
  • p.Gln117Ter Single submitter leukodystrophy, hypomyelinating, 5
  • p.Gln59fs Single submitter tooth agenesis, selective, X-linked, 1
  • p.Gln77Ter Single submitter leukodystrophy, hypomyelinating, 5
  • p.Glu393fs Single submitter leukodystrophy, hypomyelinating, 5
  • p.Leu286Ter Single submitter FAM126A-related disorders
  • p.Lys34fs Single submitter leukodystrophy, hypomyelinating, 5
  • p.Ser227fs Single submitter FAM126A-related disorders

Conflicting classifications of pathogenicity 16

  • c.52-9T>A Single submitter leukodystrophy, hypomyelinating, 5
  • c.626+5A>G Single submitter Inborn genetic diseases
  • c.831+10T>C Single submitter leukodystrophy, hypomyelinating, 5
  • p.Arg407Gln Single submitter leukodystrophy, hypomyelinating, 5 ⚠
  • p.Asn94Ser Single submitter leukodystrophy, hypomyelinating, 5 ⚠
  • p.Asp348= Single submitter leukodystrophy, hypomyelinating, 5
  • p.Cys401Arg Single submitter leukodystrophy, hypomyelinating, 5 ⚠
  • p.Cys57Arg Single submitter leukodystrophy, hypomyelinating, 5 ⚠
  • p.Gln505= Single submitter leukodystrophy, hypomyelinating, 5
  • p.Gly324= Single submitter leukodystrophy, hypomyelinating, 5
  • p.Gly507Arg Single submitter Inborn genetic diseases ⚠
  • p.Thr498Ala Single submitter leukodystrophy, hypomyelinating, 5 ⚠
  • p.Tyr194= Single submitter leukodystrophy, hypomyelinating, 5
  • p.Tyr493= Single submitter leukodystrophy, hypomyelinating, 5
  • p.Tyr64Cys Single submitter leukodystrophy, hypomyelinating, 5 ⚠
  • p.Val494Ile Single submitter Inborn genetic diseases ⚠

Benign 36

Benign/Likely benign 9

  • c.414+19C>T Multiple submitters leukodystrophy, hypomyelinating, 5
  • c.530+12G>A Multiple submitters leukodystrophy, hypomyelinating, 5
  • c.743+20C>T Multiple submitters leukodystrophy, hypomyelinating, 5
  • c.991+11C>T Multiple submitters leukodystrophy, hypomyelinating, 5
  • p.Arg217Gln Multiple submitters leukodystrophy, hypomyelinating, 5
  • p.Gly391Arg Multiple submitters leukodystrophy, hypomyelinating, 5
  • p.Ser144= Multiple submitters leukodystrophy, hypomyelinating, 5
  • p.Ser208= Multiple submitters leukodystrophy, hypomyelinating, 5
  • p.Val212= Multiple submitters leukodystrophy, hypomyelinating, 5

Likely benign 116

  • c.743+19G>A Multiple submitters leukodystrophy, hypomyelinating, 5
  • p.Ala355Val Multiple submitters Inborn genetic diseases
  • p.Ala447Thr Multiple submitters leukodystrophy, hypomyelinating, 5
  • p.Arg407= Multiple submitters leukodystrophy, hypomyelinating, 5
  • p.Cys472Tyr Multiple submitters leukodystrophy, hypomyelinating, 5
  • p.Glu488= Multiple submitters leukodystrophy, hypomyelinating, 5
  • p.Gly473= Multiple submitters leukodystrophy, hypomyelinating, 5
  • p.Leu106= Multiple submitters leukodystrophy, hypomyelinating, 5
  • p.Phe454= Multiple submitters leukodystrophy, hypomyelinating, 5
  • p.Ser321= Multiple submitters leukodystrophy, hypomyelinating, 5
  • p.Val56= Multiple submitters leukodystrophy, hypomyelinating, 5
  • c.333+11A>C Single submitter leukodystrophy, hypomyelinating, 5
  • c.333+15G>A Single submitter leukodystrophy, hypomyelinating, 5
  • c.334-20A>G Single submitter leukodystrophy, hypomyelinating, 5
  • c.334-3dup Single submitter leukodystrophy, hypomyelinating, 5
  • c.334-4A>G Single submitter
  • c.334-5T>C Single submitter
  • c.51+13G>T Single submitter leukodystrophy, hypomyelinating, 5
  • c.51+20T>A Single submitter leukodystrophy, hypomyelinating, 5
  • c.51+77T>A Single submitter
  • c.51+9del Single submitter leukodystrophy, hypomyelinating, 5
  • c.52-11A>C Single submitter leukodystrophy, hypomyelinating, 5
  • c.52-13T>A Single submitter leukodystrophy, hypomyelinating, 5
  • c.52-17T>C Single submitter leukodystrophy, hypomyelinating, 5
  • c.52-20A>T Single submitter leukodystrophy, hypomyelinating, 5
  • c.52-299_52-295del Single submitter
  • c.52-4T>A Single submitter leukodystrophy, hypomyelinating, 5
  • c.52-4T>G Single submitter leukodystrophy, hypomyelinating, 5
  • c.530+25dup Single submitter
  • c.530+28C>G Single submitter
  • c.531-16T>G Single submitter leukodystrophy, hypomyelinating, 5
  • c.531-191A>C Single submitter
  • c.627-10G>T Single submitter leukodystrophy, hypomyelinating, 5
  • c.744-7T>G Single submitter leukodystrophy, hypomyelinating, 5
  • c.831+11G>A Single submitter
  • c.831+14T>G Single submitter leukodystrophy, hypomyelinating, 5
  • c.832-10T>G Single submitter leukodystrophy, hypomyelinating, 5
  • c.832-13T>C Single submitter leukodystrophy, hypomyelinating, 5
  • c.832-18T>G Single submitter leukodystrophy, hypomyelinating, 5
  • c.991+10dup Single submitter leukodystrophy, hypomyelinating, 5
  • c.991+13T>C Single submitter leukodystrophy, hypomyelinating, 5
  • c.992-15C>T Single submitter leukodystrophy, hypomyelinating, 5
  • c.992-6G>T Single submitter leukodystrophy, hypomyelinating, 5
  • c.992-901A>G Single submitter
  • c.992-934A>G Single submitter
  • c.*2198A>G Single submitter leukodystrophy, hypomyelinating, 5
  • c.*3106G>A Single submitter leukodystrophy, hypomyelinating, 5
  • c.*372G>C Single submitter leukodystrophy, hypomyelinating, 5
  • c.*3753C>T Single submitter leukodystrophy, hypomyelinating, 5
  • c.*4221G>C Single submitter leukodystrophy, hypomyelinating, 5
  • c.*583A>G Single submitter leukodystrophy, hypomyelinating, 5
  • c.*798C>G Single submitter leukodystrophy, hypomyelinating, 5
  • c.*8C>T Single submitter
  • p.Ala151= Single submitter leukodystrophy, hypomyelinating, 5
  • p.Ala174= Single submitter leukodystrophy, hypomyelinating, 5
  • p.Ala267= Single submitter leukodystrophy, hypomyelinating, 5
  • p.Ala316= Single submitter leukodystrophy, hypomyelinating, 5
  • p.Ala356= Single submitter leukodystrophy, hypomyelinating, 5
  • p.Ala447= Single submitter leukodystrophy, hypomyelinating, 5
  • p.Arg323= Single submitter leukodystrophy, hypomyelinating, 5
  • p.Asn280= Single submitter leukodystrophy, hypomyelinating, 5
  • p.Asn479= Single submitter leukodystrophy, hypomyelinating, 5
  • p.Asp262= Single submitter leukodystrophy, hypomyelinating, 5
  • p.Asp33= Single submitter leukodystrophy, hypomyelinating, 5
  • p.Cys371= Single submitter leukodystrophy, hypomyelinating, 5
  • p.Gln205= Single submitter leukodystrophy, hypomyelinating, 5
  • p.Gln239= Single submitter
  • p.Gln361= Single submitter leukodystrophy, hypomyelinating, 5
  • p.Gln508= Single submitter leukodystrophy, hypomyelinating, 5
  • p.Glu343= Single submitter leukodystrophy, hypomyelinating, 5
  • p.Gly107= Single submitter leukodystrophy, hypomyelinating, 5
  • p.Gly471= Single submitter leukodystrophy, hypomyelinating, 5
  • p.Gly67= Single submitter leukodystrophy, hypomyelinating, 5
  • p.Gly7= Single submitter leukodystrophy, hypomyelinating, 5
  • p.Gly7Arg Single submitter leukodystrophy, hypomyelinating, 5
  • p.His325= Single submitter leukodystrophy, hypomyelinating, 5
  • p.Leu123= Single submitter
  • p.Leu147= Single submitter leukodystrophy, hypomyelinating, 5
  • p.Leu157= Single submitter leukodystrophy, hypomyelinating, 5
  • p.Leu172= Single submitter leukodystrophy, hypomyelinating, 5
  • p.Leu186= Single submitter
  • p.Leu260= Single submitter leukodystrophy, hypomyelinating, 5
  • p.Leu276= Single submitter leukodystrophy, hypomyelinating, 5
  • p.Leu286= Single submitter leukodystrophy, hypomyelinating, 5
  • p.Leu423= Single submitter leukodystrophy, hypomyelinating, 5
  • p.Leu434= Single submitter leukodystrophy, hypomyelinating, 5
  • p.Lys132= Single submitter leukodystrophy, hypomyelinating, 5
  • p.Lys222= Single submitter leukodystrophy, hypomyelinating, 5
  • p.Lys379= Single submitter leukodystrophy, hypomyelinating, 5
  • p.Lys392= Single submitter leukodystrophy, hypomyelinating, 5
  • p.Lys436= Single submitter leukodystrophy, hypomyelinating, 5
  • p.Phe183= Single submitter leukodystrophy, hypomyelinating, 5
  • p.Pro128= Single submitter leukodystrophy, hypomyelinating, 5
  • p.Pro466= Single submitter leukodystrophy, hypomyelinating, 5
  • p.Ser199= Single submitter leukodystrophy, hypomyelinating, 5
  • p.Ser310= Single submitter leukodystrophy, hypomyelinating, 5
  • p.Ser362= Single submitter leukodystrophy, hypomyelinating, 5
  • p.Ser438Cys Single submitter Inborn genetic diseases
  • p.Ser467= Single submitter leukodystrophy, hypomyelinating, 5
  • p.Ser482= Single submitter leukodystrophy, hypomyelinating, 5
  • p.Ser66= Single submitter leukodystrophy, hypomyelinating, 5
  • p.Thr126= Single submitter leukodystrophy, hypomyelinating, 5
  • p.Thr445= Single submitter leukodystrophy, hypomyelinating, 5
  • p.Thr448= Single submitter
  • p.Thr75= Single submitter leukodystrophy, hypomyelinating, 5
  • p.Val161= Single submitter leukodystrophy, hypomyelinating, 5
  • p.Val198= Single submitter leukodystrophy, hypomyelinating, 5
  • p.Val449= Single submitter leukodystrophy, hypomyelinating, 5
  • p.Val9= Single submitter leukodystrophy, hypomyelinating, 5
  • c.992-1008C>T No assertion criteria HYCC1-related disorder
  • c.992-898G>A No assertion criteria HYCC1-related disorder
  • c.992-967G>T No assertion criteria HYCC1-related disorder
  • c.992-996C>T No assertion criteria HYCC1-related disorder
  • p.Glu68= No assertion criteria HYCC1-related disorder
  • p.Pro307= No assertion criteria HYCC1-related disorder
  • p.Pro512= No assertion criteria HYCC1-related disorder

Uncertain significance 192