EFHC2 — 97 ClinVar variants
All ClinVar germline EFHC2 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 86 flagged for review →
3 Conflicting · 1 Benign · 13 Likely benign · 80 Uncertain significance
Full EFHC2 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 86
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 2
ClinVar submitters conflict, but the independent predictors unanimously agree — a QC review flag, not a reclassification.
-
EFHC2 p.Cys57Tyr
Conflicting
Single submitter
ornithine carbamoyltransferase deficiency
- EFHC2 p.Ile470Met Conflicting Single submitter
Predictors lean, ClinVar uncertain 39
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
- EFHC2 p.Ala697Ser Uncertain significance Single submitter
- EFHC2 p.Arg133His Uncertain significance Single submitter
- EFHC2 p.Arg301Gln Uncertain significance Single submitter
- EFHC2 p.Arg405Cys Uncertain significance Single submitter
- EFHC2 p.Arg405His Uncertain significance Single submitter
- EFHC2 p.Arg522His Uncertain significance Single submitter
- EFHC2 p.Arg608Cys Uncertain significance Single submitter
- EFHC2 p.Arg608His Uncertain significance Single submitter
- EFHC2 p.Arg608Leu Uncertain significance Single submitter
- EFHC2 p.Asn12His Uncertain significance Single submitter
- EFHC2 p.Asn305Ser Uncertain significance Single submitter
- EFHC2 p.Asn525Ile Uncertain significance Single submitter
- EFHC2 p.Asn525Ser Uncertain significance Single submitter
- EFHC2 p.Asp616Asn Uncertain significance Single submitter
- EFHC2 p.Asp742Glu Uncertain significance Single submitter
- EFHC2 p.Cys29Arg Uncertain significance Single submitter
- EFHC2 p.Gln688Arg Uncertain significance Single submitter
- EFHC2 p.Glu747Asp Uncertain significance Single submitter
- EFHC2 p.Gly296Asp Uncertain significance Single submitter
- EFHC2 p.Gly317Ser Uncertain significance Single submitter
- EFHC2 p.Gly479Arg Uncertain significance Single submitter
- EFHC2 p.Ile464Met Uncertain significance Single submitter
- EFHC2 p.Ile59Met Uncertain significance Single submitter
- EFHC2 p.Leu319Val Uncertain significance Single submitter
- EFHC2 p.Leu90Phe Uncertain significance Single submitter
- EFHC2 p.Lys411Arg Uncertain significance Single submitter
- EFHC2 p.Met480Ile Uncertain significance Single submitter
- EFHC2 p.Pro710Leu Uncertain significance Single submitter
- EFHC2 p.Ser339Cys Uncertain significance Single submitter
- EFHC2 p.Ser377Leu Uncertain significance Single submitter
- EFHC2 p.Ser500Phe Uncertain significance Single submitter
- EFHC2 p.Ser572Thr Uncertain significance Single submitter
- EFHC2 p.Ser66Arg Uncertain significance Single submitter
- EFHC2 p.Ser66Asn Uncertain significance Single submitter
- EFHC2 p.Thr360Met Uncertain significance Single submitter
- EFHC2 p.Thr413Ile Uncertain significance Single submitter
- EFHC2 p.Tyr307Cys Uncertain significance Single submitter
- EFHC2 p.Tyr457His Uncertain significance Single submitter
- EFHC2 p.Val207Ile Uncertain significance Single submitter
Predictors split 45
The independent predictors disagree with each other — read with care.
- EFHC2 p.Glu506Lys Likely benign Multiple submitters
- EFHC2 p.Glu507Gln Benign Multiple submitters
- EFHC2 p.Ala549Gly Uncertain significance Single submitter
-
EFHC2 p.Arg135Gln
Conflicting
Single submitter
X-linked intellectual disability
- EFHC2 p.Arg135Trp Uncertain significance Single submitter
- EFHC2 p.Arg163Gln Uncertain significance Single submitter
- EFHC2 p.Arg163Trp Uncertain significance Single submitter
- EFHC2 p.Arg200Gln Uncertain significance Single submitter
- EFHC2 p.Arg211His Uncertain significance Single submitter
- EFHC2 p.Arg280Gln Likely benign Single submitter
- EFHC2 p.Arg436Cys Uncertain significance Single submitter
- EFHC2 p.Arg605Cys Uncertain significance Single submitter
- EFHC2 p.Asn116Asp Uncertain significance Single submitter
- EFHC2 p.Asn345Ser Uncertain significance Single submitter
- EFHC2 p.Asp142Gly Uncertain significance Single submitter
- EFHC2 p.Asp144Gly Uncertain significance Single submitter
- EFHC2 p.Asp258Asn Uncertain significance Single submitter
- EFHC2 p.Asp462Tyr Uncertain significance Single submitter
- EFHC2 p.Glu46Asp Uncertain significance Single submitter
- EFHC2 p.Gly155Ser Uncertain significance Single submitter
- EFHC2 p.Gly271Asp Uncertain significance Single submitter
- EFHC2 p.Gly296Ser Uncertain significance Single submitter
- EFHC2 p.Gly369Arg Uncertain significance Single submitter
- EFHC2 p.Gly44Asp Uncertain significance Single submitter
- EFHC2 p.His134Arg Uncertain significance Single submitter
- EFHC2 p.Ile464Phe Uncertain significance Single submitter
- EFHC2 p.Ile464Val Uncertain significance Single submitter
- EFHC2 p.Leu265Phe Uncertain significance Single submitter
- EFHC2 p.Lys103Glu Uncertain significance Single submitter
- EFHC2 p.Met242Thr Uncertain significance Single submitter
- EFHC2 p.Pro140Ala Uncertain significance Single submitter
- EFHC2 p.Pro192Thr Uncertain significance Single submitter
- EFHC2 p.Pro209Ala Uncertain significance Single submitter
- EFHC2 p.Pro380Ser Uncertain significance Single submitter
- EFHC2 p.Pro383Leu Uncertain significance Single submitter
- EFHC2 p.Pro393Ser Uncertain significance Single submitter
- EFHC2 p.Pro412Leu Uncertain significance Single submitter
- EFHC2 p.Ser336Arg Uncertain significance Single submitter
- EFHC2 p.Ser642Phe Uncertain significance Single submitter
- EFHC2 p.Thr513Met Uncertain significance Single submitter
- EFHC2 p.Tyr102Cys Uncertain significance Single submitter
- EFHC2 p.Tyr102His Uncertain significance Single submitter
- EFHC2 p.Tyr225Cys Uncertain significance Single submitter
- EFHC2 p.Tyr541His Uncertain significance Single submitter
- EFHC2 p.Pro209Ser Uncertain significance No assertion criteria
All EFHC2 variants
Conflicting classifications of pathogenicity 3
- p.Arg135Gln Single submitter X-linked intellectual disability ⚠
- p.Cys57Tyr Single submitter ornithine carbamoyltransferase deficiency ⚠
- p.Ile470Met Single submitter ⚠
Benign 1
- p.Glu507Gln Multiple submitters ⚠
Likely benign 13
- p.Glu506Lys Multiple submitters ⚠
- p.Ala477Thr Single submitter
- p.Ala743Val Single submitter
- p.Arg280Gln Single submitter ⚠
- p.Asp720= Single submitter
- p.Ile229Val Single submitter
- p.Ile470Val Single submitter
- p.Ile510Val Single submitter
- p.Lys692Glu Single submitter
- p.Phe320= Single submitter
- p.Pro139= Single submitter
- p.Thr513= Single submitter
- p.Val705Met Single submitter
Uncertain significance 80
- p.Ala549Gly Single submitter ⚠
- p.Ala697Ser Single submitter ⚠
- p.Arg133His Single submitter ⚠
- p.Arg135Trp Single submitter ⚠
- p.Arg163Gln Single submitter ⚠
- p.Arg163Trp Single submitter ⚠
- p.Arg200Gln Single submitter ⚠
- p.Arg211His Single submitter ⚠
- p.Arg301Gln Single submitter ⚠
- p.Arg405Cys Single submitter ⚠
- p.Arg405His Single submitter ⚠
- p.Arg436Cys Single submitter ⚠
- p.Arg522His Single submitter ⚠
- p.Arg605Cys Single submitter ⚠
- p.Arg608Cys Single submitter ⚠
- p.Arg608His Single submitter ⚠
- p.Arg608Leu Single submitter ⚠
- p.Asn116Asp Single submitter ⚠
- p.Asn12His Single submitter ⚠
- p.Asn305Ser Single submitter ⚠
- p.Asn345Ser Single submitter ⚠
- p.Asn525Ile Single submitter ⚠
- p.Asn525Ser Single submitter ⚠
- p.Asp142Gly Single submitter ⚠
- p.Asp144Gly Single submitter ⚠
- p.Asp258Asn Single submitter ⚠
- p.Asp462Tyr Single submitter ⚠
- p.Asp616Asn Single submitter ⚠
- p.Asp742Glu Single submitter ⚠
- p.Cys29Arg Single submitter ⚠
- p.Gln688Arg Single submitter ⚠
- p.Glu46Asp Single submitter ⚠
- p.Glu747Asp Single submitter ⚠
- p.Gly155Ser Single submitter ⚠
- p.Gly271Asp Single submitter ⚠
- p.Gly296Asp Single submitter ⚠
- p.Gly296Ser Single submitter ⚠
- p.Gly317Ser Single submitter ⚠
- p.Gly369Arg Single submitter ⚠
- p.Gly44Asp Single submitter ⚠
- p.Gly479Arg Single submitter ⚠
- p.His134Arg Single submitter ⚠
- p.Ile464Met Single submitter ⚠
- p.Ile464Phe Single submitter ⚠
- p.Ile464Val Single submitter ⚠
- p.Ile59Met Single submitter ⚠
- p.Leu265Phe Single submitter ⚠
- p.Leu319Val Single submitter ⚠
- p.Leu90Phe Single submitter ⚠
- p.Lys103Glu Single submitter ⚠
- p.Lys411Arg Single submitter ⚠
- p.Met242Thr Single submitter ⚠
- p.Met480Ile Single submitter ⚠
- p.Pro140Ala Single submitter ⚠
- p.Pro192Thr Single submitter ⚠
- p.Pro209Ala Single submitter ⚠
- p.Pro380Ser Single submitter ⚠
- p.Pro383Leu Single submitter ⚠
- p.Pro393Ser Single submitter ⚠
- p.Pro412Leu Single submitter ⚠
- p.Pro710Leu Single submitter ⚠
- p.Ser336Arg Single submitter ⚠
- p.Ser339Cys Single submitter ⚠
- p.Ser377Leu Single submitter ⚠
- p.Ser500Phe Single submitter ⚠
- p.Ser572Thr Single submitter ⚠
- p.Ser642Phe Single submitter ⚠
- p.Ser66Arg Single submitter ⚠
- p.Ser66Asn Single submitter ⚠
- p.Thr360Met Single submitter ⚠
- p.Thr413Ile Single submitter ⚠
- p.Thr513Met Single submitter ⚠
- p.Tyr102Cys Single submitter ⚠
- p.Tyr102His Single submitter ⚠
- p.Tyr225Cys Single submitter ⚠
- p.Tyr307Cys Single submitter ⚠
- p.Tyr457His Single submitter ⚠
- p.Tyr541His Single submitter ⚠
- p.Val207Ile Single submitter ⚠
- p.Pro209Ser No assertion criteria ⚠