CLHC1 — 101 ClinVar variants

All ClinVar germline CLHC1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 94 flagged for review →

1 Likely pathogenic · 6 Likely benign · 94 Uncertain significance

Full CLHC1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 94

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 vs ClinVar 1

ClinVar calls these pathogenic, but the computational predictors lean tolerated — the highest-value review flag.

CLHC1 p.Arg382Gln Likely pathogenic No assertion criteria
Marked Hypotonia

Predictors lean, ClinVar uncertain 56

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

Predictors split 37

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

All CLHC1 variants

Likely pathogenic 1

p.Arg382Gln No assertion criteria Marked Hypotonia ⚠

Likely benign 6

p.Ala577Thr Single submitter
p.Arg286His Single submitter
p.Gln488Pro Single submitter
p.Lys229Arg Single submitter
p.Thr116Ile Single submitter
p.Thr559Met Single submitter

Uncertain significance 94

p.Ala121Thr Single submitter ⚠
p.Ala196Val Single submitter ⚠
p.Ala336Gly Single submitter ⚠
p.Ala367Val Single submitter ⚠
p.Ala567Thr Single submitter ⚠
p.Arg206Gly Single submitter ⚠
p.Arg286Cys Single submitter ⚠
p.Arg286Pro Single submitter ⚠
p.Arg326Pro Single submitter ⚠
p.Arg326Ter Single submitter
p.Arg382Trp Single submitter ⚠
p.Arg563Gln Single submitter ⚠
p.Asn175His Single submitter ⚠
p.Asn319Lys Single submitter ⚠
p.Asn530Ser Single submitter ⚠
p.Asp20Val Single submitter ⚠
p.Asp222Tyr Single submitter ⚠
p.Asp273Asn Single submitter ⚠
p.Asp283His Single submitter ⚠
p.Asp284Glu Single submitter ⚠
p.Asp384Glu Single submitter ⚠
p.Asp47Asn Single submitter ⚠
p.Asp552Gly Single submitter ⚠
p.Asp79Ala Single submitter ⚠
p.Cys363Phe Single submitter ⚠
p.Cys479Phe Single submitter ⚠
p.Cys546Trp Single submitter ⚠
p.Gln136His Single submitter ⚠
p.Gln195Pro Single submitter ⚠
p.Gln232Arg Single submitter ⚠
p.Gln265Lys Single submitter ⚠
p.Gln411Glu Single submitter ⚠
p.Gln424His Single submitter ⚠
p.Gln5His Single submitter ⚠
p.Glu127Asp Single submitter ⚠
p.Glu146Gly Single submitter ⚠
p.Glu172Asp Single submitter ⚠
p.Glu22Gly Single submitter ⚠
p.Glu282Asp Single submitter ⚠
p.Glu290Lys Single submitter ⚠
p.Glu399Ala Single submitter ⚠
p.Gly409Ala Single submitter ⚠
p.Gly44Ala Single submitter ⚠
p.Gly509Asp Single submitter ⚠
p.Gly519Cys Single submitter ⚠
p.His139Arg Single submitter ⚠
p.His359Arg Single submitter ⚠
p.Ile117Met Single submitter ⚠
p.Ile125Asn Single submitter ⚠
p.Ile126Val Single submitter ⚠
p.Ile298Val Single submitter ⚠
p.Ile305Met Single submitter ⚠
p.Ile536Val Single submitter ⚠
p.Ile561Val Single submitter ⚠
p.Ile571Val Single submitter ⚠
p.Ile6Lys Single submitter ⚠
p.Leu176Val Single submitter ⚠
p.Leu348Pro Single submitter ⚠
p.Leu349Ile Single submitter ⚠
p.Leu354Arg Single submitter ⚠
p.Leu354Phe Single submitter ⚠
p.Leu383Ile Single submitter ⚠
p.Lys153Thr Single submitter ⚠
p.Lys207Asn Single submitter ⚠
p.Lys457Met Single submitter ⚠
p.Lys482Glu Single submitter ⚠
p.Lys506Arg Single submitter ⚠
p.Lys75Glu Single submitter ⚠
p.Lys86Gln Single submitter ⚠
p.Met123Val Single submitter ⚠
p.Met168Val Single submitter ⚠
p.Met183Thr Single submitter ⚠
p.Met253Ile Single submitter ⚠
p.Phe551Cys Single submitter ⚠
p.Phe81Leu Single submitter ⚠
p.Pro161Thr Single submitter ⚠
p.Pro164Leu Single submitter ⚠
p.Pro321Thr Single submitter ⚠
p.Pro344Ser Single submitter ⚠
p.Pro346Leu Single submitter ⚠
p.Pro364Thr Single submitter ⚠
p.Ser131Leu Single submitter ⚠
p.Ser246Asn Single submitter ⚠
p.Ser306Leu Single submitter ⚠
p.Ser490Tyr Single submitter ⚠
p.Thr357Ile Single submitter ⚠
p.Thr35Ala Single submitter ⚠
p.Thr446Ser Single submitter ⚠
p.Trp389Cys Single submitter ⚠
p.Tyr147Cys Single submitter ⚠
p.Tyr452His Single submitter ⚠
p.Val110Ile Single submitter ⚠
p.Val261Met Single submitter ⚠
p.Val524Ala Single submitter ⚠