HKDC1 — 197 ClinVar variants
All ClinVar germline HKDC1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 170 flagged for review →
8 Likely pathogenic · 1 Conflicting · 3 Benign · 15 Likely benign · 170 Uncertain significance
Full HKDC1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 170
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 2
ClinVar calls these pathogenic, but the computational predictors lean tolerated — the highest-value review flag.
-
HKDC1 p.Thr58Met
Likely pathogenic
Multiple submitters
retinitis pigmentosa 92
-
HKDC1 p.Arg337Trp
Likely pathogenic
No assertion criteria
Short stature
Predictors agree, ClinVar conflicts 1
ClinVar submitters conflict, but the independent predictors unanimously agree — a QC review flag, not a reclassification.
-
HKDC1 p.His420Tyr
Conflicting
Single submitter
retinitis pigmentosa 92
Predictors lean, ClinVar uncertain 119
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
-
HKDC1 p.Phe528Ser
Uncertain significance
Multiple submitters
retinitis pigmentosa 92
- HKDC1 p.Val371Ile Uncertain significance Multiple submitters
- HKDC1 p.Ala389Gly Uncertain significance Single submitter
- HKDC1 p.Ala391Val Uncertain significance Single submitter
- HKDC1 p.Ala458Thr Uncertain significance Single submitter
- HKDC1 p.Ala45Val Uncertain significance Single submitter
- HKDC1 p.Ala493Val Uncertain significance Single submitter
- HKDC1 p.Ala582Ser Uncertain significance Single submitter
- HKDC1 p.Ala652Thr Uncertain significance Single submitter
- HKDC1 p.Ala829Val Uncertain significance Single submitter
- HKDC1 p.Ala98Thr Uncertain significance Single submitter
- HKDC1 p.Arg120Cys Uncertain significance Single submitter
- HKDC1 p.Arg120His Uncertain significance Single submitter
- HKDC1 p.Arg178Gln Uncertain significance Single submitter
- HKDC1 p.Arg194Gly Uncertain significance Single submitter
- HKDC1 p.Arg30Trp Uncertain significance Single submitter
- HKDC1 p.Arg337Gln Uncertain significance Single submitter
- HKDC1 p.Arg381His Uncertain significance Single submitter
- HKDC1 p.Arg42Trp Uncertain significance Single submitter
- HKDC1 p.Arg462Pro Uncertain significance Single submitter
- HKDC1 p.Arg467Gln Uncertain significance Single submitter
- HKDC1 p.Arg481Gly Uncertain significance Single submitter
- HKDC1 p.Arg549Gln Uncertain significance Single submitter
- HKDC1 p.Arg774Cys Uncertain significance Single submitter
- HKDC1 p.Arg774Ser Uncertain significance Single submitter
- HKDC1 p.Arg776Gln Uncertain significance Single submitter
- HKDC1 p.Arg828Gln Uncertain significance Single submitter
- HKDC1 p.Asn208Asp Uncertain significance Single submitter
- HKDC1 p.Asn244Asp Uncertain significance Single submitter
- HKDC1 p.Asn655Ser Uncertain significance Single submitter
- HKDC1 p.Asp184Tyr Uncertain significance Single submitter
- HKDC1 p.Asp202Asn Uncertain significance Single submitter
- HKDC1 p.Asp220Glu Uncertain significance Single submitter
- HKDC1 p.Asp267Asn Uncertain significance Single submitter
- HKDC1 p.Asp278Asn Uncertain significance Single submitter
- HKDC1 p.Asp471Asn Uncertain significance Single submitter
- HKDC1 p.Asp532Asn Uncertain significance Single submitter
- HKDC1 p.Asp611Asn Uncertain significance Single submitter
- HKDC1 p.Asp656Asn Uncertain significance Single submitter
- HKDC1 p.Asp725Asn Uncertain significance Single submitter
- HKDC1 p.Asp759Asn Uncertain significance Single submitter
-
HKDC1 p.Cys217Tyr
Uncertain significance
Single submitter
retinitis pigmentosa 92
- HKDC1 p.Cys703Arg Uncertain significance Single submitter
- HKDC1 p.Gln110Glu Uncertain significance Single submitter
- HKDC1 p.Gln805Glu Uncertain significance Single submitter
- HKDC1 p.Gln805Lys Uncertain significance Single submitter
- HKDC1 p.Gln831Lys Uncertain significance Single submitter
- HKDC1 p.Gln911Arg Uncertain significance Single submitter
- HKDC1 p.Glu108Asp Uncertain significance Single submitter
- HKDC1 p.Glu496Lys Uncertain significance Single submitter
- HKDC1 p.Glu693Lys Uncertain significance Single submitter
- HKDC1 p.Gly101Arg Uncertain significance Single submitter
-
HKDC1 p.Gly121Arg
Uncertain significance
Single submitter
retinitis pigmentosa 92
- HKDC1 p.Gly166Asp Uncertain significance Single submitter
- HKDC1 p.Gly227Val Uncertain significance Single submitter
-
HKDC1 p.Gly284Ser
Uncertain significance
Single submitter
keratoconus 1
- HKDC1 p.Gly414Ser Uncertain significance Single submitter
- HKDC1 p.Gly452Arg Uncertain significance Single submitter
- HKDC1 p.Gly505Arg Uncertain significance Single submitter
- HKDC1 p.Gly50Ser Uncertain significance Single submitter
- HKDC1 p.Gly535Val Uncertain significance Single submitter
- HKDC1 p.Gly617Ala Uncertain significance Single submitter
- HKDC1 p.Gly665Ala Uncertain significance Single submitter
- HKDC1 p.Gly698Arg Uncertain significance Single submitter
- HKDC1 p.Gly834Ser Uncertain significance Single submitter
- HKDC1 p.Gly861Ser Uncertain significance Single submitter
-
HKDC1 p.Gly86Arg
Uncertain significance
Single submitter
retinitis pigmentosa 92
- HKDC1 p.His420Gln Uncertain significance Single submitter
- HKDC1 p.Ile419Thr Uncertain significance Single submitter
- HKDC1 p.Ile673Thr Uncertain significance Single submitter
- HKDC1 p.Ile717Thr Uncertain significance Single submitter
- HKDC1 p.Ile717Val Uncertain significance Single submitter
- HKDC1 p.Ile840Met Uncertain significance Single submitter
- HKDC1 p.Leu302Met Uncertain significance Single submitter
- HKDC1 p.Leu385Val Uncertain significance Single submitter
- HKDC1 p.Leu563Met Uncertain significance Single submitter
- HKDC1 p.Leu648Pro Uncertain significance Single submitter
- HKDC1 p.Leu733Val Uncertain significance Single submitter
- HKDC1 p.Leu765Phe Uncertain significance Single submitter
- HKDC1 p.Lys315Asn Uncertain significance Single submitter
- HKDC1 p.Lys468Glu Uncertain significance Single submitter
- HKDC1 p.Lys527Asn Uncertain significance Single submitter
- HKDC1 p.Lys557Asn Uncertain significance Single submitter
- HKDC1 p.Lys843Asn Uncertain significance Single submitter
- HKDC1 p.Lys843Thr Uncertain significance Single submitter
- HKDC1 p.Lys89Asn Uncertain significance Single submitter
- HKDC1 p.Lys94Thr Uncertain significance Single submitter
- HKDC1 p.Met138Arg Uncertain significance Single submitter
- HKDC1 p.Met215Thr Uncertain significance Single submitter
- HKDC1 p.Met255Leu Uncertain significance Single submitter
- HKDC1 p.Met296Thr Uncertain significance Single submitter
- HKDC1 p.Met412Leu Uncertain significance Single submitter
-
HKDC1 p.Met412Val
Uncertain significance
Single submitter
retinitis pigmentosa 92
- HKDC1 p.Phe538Leu Uncertain significance Single submitter
- HKDC1 p.Phe711Tyr Uncertain significance Single submitter
- HKDC1 p.Phe785Tyr Uncertain significance Single submitter
- HKDC1 p.Pro520Leu Uncertain significance Single submitter
- HKDC1 p.Pro868Ser Uncertain significance Single submitter
- HKDC1 p.Ser109Asn Uncertain significance Single submitter
- HKDC1 p.Ser382Leu Uncertain significance Single submitter
- HKDC1 p.Ser445Leu Uncertain significance Single submitter
- HKDC1 p.Ser449Asn Uncertain significance Single submitter
- HKDC1 p.Ser602Leu Uncertain significance Single submitter
- HKDC1 p.Ser609Gly Uncertain significance Single submitter
- HKDC1 p.Ser787Thr Uncertain significance Single submitter
- HKDC1 p.Thr330Ala Uncertain significance Single submitter
- HKDC1 p.Thr679Ile Uncertain significance Single submitter
- HKDC1 p.Thr888Ile Uncertain significance Single submitter
- HKDC1 p.Tyr301His Uncertain significance Single submitter
- HKDC1 p.Tyr515His Uncertain significance Single submitter
- HKDC1 p.Tyr740Asn Uncertain significance Single submitter
- HKDC1 p.Tyr740Cys Uncertain significance Single submitter
- HKDC1 p.Tyr748Ser Uncertain significance Single submitter
- HKDC1 p.Val463Met Uncertain significance Single submitter
- HKDC1 p.Val487Met Uncertain significance Single submitter
- HKDC1 p.Val578Met Uncertain significance Single submitter
- HKDC1 p.Val632Met Uncertain significance Single submitter
- HKDC1 p.Val651Phe Uncertain significance Single submitter
- HKDC1 p.Val654Met Uncertain significance Single submitter
Predictors split 48
The independent predictors disagree with each other — read with care.
- HKDC1 p.Ala460Thr Uncertain significance Single submitter
- HKDC1 p.Ala882Val Uncertain significance Single submitter
- HKDC1 p.Arg195Thr Uncertain significance Single submitter
- HKDC1 p.Arg274Cys Uncertain significance Single submitter
- HKDC1 p.Arg274His Uncertain significance Single submitter
- HKDC1 p.Arg274Ser Uncertain significance Single submitter
- HKDC1 p.Arg398Gly Uncertain significance Single submitter
- HKDC1 p.Arg398Trp Uncertain significance Single submitter
- HKDC1 p.Arg405Trp Uncertain significance Single submitter
- HKDC1 p.Arg426Cys Likely benign Single submitter
- HKDC1 p.Arg426His Uncertain significance Single submitter
- HKDC1 p.Arg44Trp Uncertain significance Single submitter
- HKDC1 p.Arg492Trp Uncertain significance Single submitter
- HKDC1 p.Arg768Gln Uncertain significance Single submitter
- HKDC1 p.Arg776Trp Uncertain significance Single submitter
- HKDC1 p.Arg793Gln Uncertain significance Single submitter
- HKDC1 p.Arg91Gln Uncertain significance Single submitter
- HKDC1 p.Asn208Ser Uncertain significance Single submitter
- HKDC1 p.Asp220Gly Uncertain significance Single submitter
- HKDC1 p.Asp251Glu Uncertain significance Single submitter
- HKDC1 p.Gln160His Uncertain significance Single submitter
- HKDC1 p.Gln798His Uncertain significance Single submitter
- HKDC1 p.Glu876Lys Uncertain significance Single submitter
- HKDC1 p.Gly268Arg Uncertain significance Single submitter
- HKDC1 p.Gly697Arg Uncertain significance Single submitter
- HKDC1 p.Gly697Glu Uncertain significance Single submitter
- HKDC1 p.Gly710Glu Uncertain significance Single submitter
- HKDC1 p.Gly807Arg Uncertain significance Single submitter
- HKDC1 p.Gly807Ser Uncertain significance Single submitter
- HKDC1 p.Ile355Phe Uncertain significance Single submitter
- HKDC1 p.Ile752Met Uncertain significance Single submitter
- HKDC1 p.Ile789Val Uncertain significance Single submitter
- HKDC1 p.Lys290Glu Uncertain significance Single submitter
- HKDC1 p.Lys401Asn Uncertain significance Single submitter
- HKDC1 p.Met47Thr Uncertain significance Single submitter
- HKDC1 p.Met554Ile Uncertain significance Single submitter
- HKDC1 p.Met686Val Uncertain significance Single submitter
- HKDC1 p.Pro222Leu Uncertain significance Single submitter
- HKDC1 p.Pro363Leu Uncertain significance Single submitter
- HKDC1 p.Pro735Leu Uncertain significance Single submitter
- HKDC1 p.Ser170Leu Uncertain significance Single submitter
- HKDC1 p.Thr376Ile Uncertain significance Single submitter
- HKDC1 p.Thr811Ala Uncertain significance Single submitter
- HKDC1 p.Thr811Met Uncertain significance Single submitter
- HKDC1 p.Thr856Ser Uncertain significance Single submitter
- HKDC1 p.Val516Ile Uncertain significance Single submitter
- HKDC1 p.Val654Leu Uncertain significance Single submitter
- HKDC1 p.Val68Ile Uncertain significance Single submitter
All HKDC1 variants
Likely pathogenic 8
- p.Thr58Met Multiple submitters retinitis pigmentosa 92 ⚠
- c.1265+2T>C Single submitter retinitis pigmentosa 92
- p.Asp84Asn Single submitter retinitis pigmentosa 92
- p.Ile616fs Single submitter retinitis pigmentosa 92
- p.Tyr417Cys Single submitter retinitis pigmentosa 92
- p.Arg337Trp No assertion criteria Short stature ⚠
- p.Arg768Ter No assertion criteria Nonsyndromic cleft lip palate
- p.Gly101Trp No assertion criteria Short stature
Conflicting classifications of pathogenicity 1
- p.His420Tyr Single submitter retinitis pigmentosa 92 ⚠
Benign 3
- p.Ala824= Multiple submitters
- p.Thr66Ile Multiple submitters
- p.Val859= Single submitter
Likely benign 15
- c.592-15C>T Single submitter
- c.875+13C>T Single submitter
- p.Arg188His Single submitter
- p.Arg42= Single submitter
- p.Arg426Cys Single submitter ⚠
- p.Arg723Gln Single submitter
- p.Asp631= Single submitter
- p.Asp886= Single submitter
- p.Gly698Asp Single submitter
- p.Ser892Pro Single submitter
- p.Thr210= Single submitter
- p.Thr457= Single submitter
- p.Trp721Ter Single submitter
- p.Val632= Single submitter
- p.Ile334Asn No assertion criteria long QT syndrome
Uncertain significance 170
- p.His145fs Multiple submitters retinitis pigmentosa 92
- p.Phe528Ser Multiple submitters retinitis pigmentosa 92 ⚠
- p.Val371Ile Multiple submitters ⚠
- p.Ala389Gly Single submitter ⚠
- p.Ala391Val Single submitter ⚠
- p.Ala458Thr Single submitter ⚠
- p.Ala45Val Single submitter ⚠
- p.Ala460Thr Single submitter ⚠
- p.Ala493Val Single submitter ⚠
- p.Ala582Ser Single submitter ⚠
- p.Ala652Thr Single submitter ⚠
- p.Ala829Val Single submitter ⚠
- p.Ala882Val Single submitter ⚠
- p.Ala98Thr Single submitter ⚠
- p.Arg120Cys Single submitter ⚠
- p.Arg120His Single submitter ⚠
- p.Arg178Gln Single submitter ⚠
- p.Arg194Gly Single submitter ⚠
- p.Arg195Thr Single submitter ⚠
- p.Arg274Cys Single submitter ⚠
- p.Arg274His Single submitter ⚠
- p.Arg274Ser Single submitter ⚠
- p.Arg30Trp Single submitter ⚠
- p.Arg337Gln Single submitter ⚠
- p.Arg381His Single submitter ⚠
- p.Arg398Gly Single submitter ⚠
- p.Arg398Trp Single submitter ⚠
- p.Arg405Trp Single submitter ⚠
- p.Arg426His Single submitter ⚠
- p.Arg42Trp Single submitter ⚠
- p.Arg44Trp Single submitter ⚠
- p.Arg462Pro Single submitter ⚠
- p.Arg467Gln Single submitter ⚠
- p.Arg481Gly Single submitter ⚠
- p.Arg492Trp Single submitter ⚠
- p.Arg549Gln Single submitter ⚠
- p.Arg768Gln Single submitter ⚠
- p.Arg774Cys Single submitter ⚠
- p.Arg774Ser Single submitter ⚠
- p.Arg776Gln Single submitter ⚠
- p.Arg776Trp Single submitter ⚠
- p.Arg793Gln Single submitter ⚠
- p.Arg828Gln Single submitter ⚠
- p.Arg91Gln Single submitter ⚠
- p.Asn208Asp Single submitter ⚠
- p.Asn208Ser Single submitter ⚠
- p.Asn244Asp Single submitter ⚠
- p.Asn655Ser Single submitter ⚠
- p.Asp184Tyr Single submitter ⚠
- p.Asp202Asn Single submitter ⚠
- p.Asp220Glu Single submitter ⚠
- p.Asp220Gly Single submitter ⚠
- p.Asp251Glu Single submitter ⚠
- p.Asp267Asn Single submitter ⚠
- p.Asp278Asn Single submitter ⚠
- p.Asp471Asn Single submitter ⚠
- p.Asp532Asn Single submitter ⚠
- p.Asp611Asn Single submitter ⚠
- p.Asp656Asn Single submitter ⚠
- p.Asp725Asn Single submitter ⚠
- p.Asp759Asn Single submitter ⚠
- p.Cys217Tyr Single submitter retinitis pigmentosa 92 ⚠
- p.Cys703Arg Single submitter ⚠
- p.Gln110Glu Single submitter ⚠
- p.Gln160His Single submitter ⚠
- p.Gln763Pro Single submitter
- p.Gln798His Single submitter ⚠
- p.Gln805Glu Single submitter ⚠
- p.Gln805Lys Single submitter ⚠
- p.Gln831Lys Single submitter ⚠
- p.Gln911Arg Single submitter ⚠
- p.Glu108Asp Single submitter ⚠
- p.Glu496Lys Single submitter ⚠
- p.Glu693Lys Single submitter ⚠
- p.Glu876Lys Single submitter ⚠
- p.Gly101Arg Single submitter ⚠
- p.Gly121Arg Single submitter retinitis pigmentosa 92 ⚠
- p.Gly166Asp Single submitter ⚠
- p.Gly227Val Single submitter ⚠
- p.Gly268Arg Single submitter ⚠
- p.Gly284Ser Single submitter keratoconus 1 ⚠
- p.Gly414Ser Single submitter ⚠
- p.Gly452Arg Single submitter ⚠
- p.Gly505Arg Single submitter ⚠
- p.Gly50Ser Single submitter ⚠
- p.Gly535Val Single submitter ⚠
- p.Gly617Ala Single submitter ⚠
- p.Gly665Ala Single submitter ⚠
- p.Gly697Arg Single submitter ⚠
- p.Gly697Glu Single submitter ⚠
- p.Gly698Arg Single submitter ⚠
- p.Gly710Glu Single submitter ⚠
- p.Gly807Arg Single submitter ⚠
- p.Gly807Ser Single submitter ⚠
- p.Gly834Ser Single submitter ⚠
- p.Gly861Ser Single submitter ⚠
- p.Gly86Arg Single submitter retinitis pigmentosa 92 ⚠
- p.His420Gln Single submitter ⚠
- p.Ile355Phe Single submitter ⚠
- p.Ile419Thr Single submitter ⚠
- p.Ile558Val Single submitter
- p.Ile673Thr Single submitter ⚠
- p.Ile717Thr Single submitter ⚠
- p.Ile717Val Single submitter ⚠
- p.Ile752Met Single submitter ⚠
- p.Ile789Val Single submitter ⚠
- p.Ile840Met Single submitter ⚠
- p.Leu302Met Single submitter ⚠
- p.Leu385Val Single submitter ⚠
- p.Leu563Met Single submitter ⚠
- p.Leu648Pro Single submitter ⚠
- p.Leu733Val Single submitter ⚠
- p.Leu765Phe Single submitter ⚠
- p.Lys290Glu Single submitter ⚠
- p.Lys315Asn Single submitter ⚠
- p.Lys401Asn Single submitter ⚠
- p.Lys468Glu Single submitter ⚠
- p.Lys527Asn Single submitter ⚠
- p.Lys557Asn Single submitter ⚠
- p.Lys843Asn Single submitter ⚠
- p.Lys843Thr Single submitter ⚠
- p.Lys89Asn Single submitter ⚠
- p.Lys94Thr Single submitter ⚠
- p.Met138Arg Single submitter ⚠
- p.Met215Thr Single submitter ⚠
- p.Met255Leu Single submitter ⚠
- p.Met296Thr Single submitter ⚠
- p.Met412Leu Single submitter ⚠
- p.Met412Val Single submitter retinitis pigmentosa 92 ⚠
- p.Met47Thr Single submitter ⚠
- p.Met554Ile Single submitter ⚠
- p.Met686Val Single submitter ⚠
- p.Phe538Leu Single submitter ⚠
- p.Phe711Tyr Single submitter ⚠
- p.Phe785Tyr Single submitter ⚠
- p.Pro222Leu Single submitter ⚠
- p.Pro363Leu Single submitter ⚠
- p.Pro520Leu Single submitter ⚠
- p.Pro735Leu Single submitter ⚠
- p.Pro868Ser Single submitter ⚠
- p.Ser109Asn Single submitter ⚠
- p.Ser170Leu Single submitter ⚠
- p.Ser382Leu Single submitter ⚠
- p.Ser445Leu Single submitter ⚠
- p.Ser449Asn Single submitter ⚠
- p.Ser602Leu Single submitter ⚠
- p.Ser609Arg Single submitter
- p.Ser609Gly Single submitter ⚠
- p.Ser787Thr Single submitter ⚠
- p.Thr330Ala Single submitter ⚠
- p.Thr376Ile Single submitter ⚠
- p.Thr679Ile Single submitter ⚠
- p.Thr811Ala Single submitter ⚠
- p.Thr811Met Single submitter ⚠
- p.Thr856Ser Single submitter ⚠
- p.Thr888Ile Single submitter ⚠
- p.Tyr301His Single submitter ⚠
- p.Tyr515His Single submitter ⚠
- p.Tyr740Asn Single submitter ⚠
- p.Tyr740Cys Single submitter ⚠
- p.Tyr748Ser Single submitter ⚠
- p.Val463Met Single submitter ⚠
- p.Val487Met Single submitter ⚠
- p.Val516Ile Single submitter ⚠
- p.Val578Met Single submitter ⚠
- p.Val632Met Single submitter ⚠
- p.Val651Phe Single submitter ⚠
- p.Val654Leu Single submitter ⚠
- p.Val654Met Single submitter ⚠
- p.Val68Ile Single submitter ⚠