HAL — 196 ClinVar variants
All ClinVar germline HAL variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 114 flagged for review →
1 Likely pathogenic · 6 Conflicting · 12 Benign · 1 Benign/Likely benign · 17 Likely benign · 159 Uncertain significance
Full HAL gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 114
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.
-
HAL p.Arg133His
Conflicting
Single submitter
histidinemia
Predictors lean, ClinVar uncertain 83
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
-
HAL p.Asn476Lys
Uncertain significance
Multiple submitters
histidinemia
-
HAL p.Glu472Lys
Uncertain significance
Multiple submitters
histidinemia
-
HAL p.Leu242Met
Uncertain significance
Multiple submitters
histidinemia
-
HAL p.Phe485Leu
Uncertain significance
Multiple submitters
histidinemia
-
HAL p.Thr123Met
Uncertain significance
Multiple submitters
histidinemia
- HAL p.Ala20Thr Uncertain significance Single submitter
-
HAL p.Ala281Thr
Uncertain significance
Single submitter
histidinemia
- HAL p.Ala325Thr Uncertain significance Single submitter
- HAL p.Ala334Gly Uncertain significance Single submitter
- HAL p.Ala503Thr Uncertain significance Single submitter
- HAL p.Ala505Thr Uncertain significance Single submitter
- HAL p.Ala559Pro Uncertain significance Single submitter
- HAL p.Arg192Cys Uncertain significance Single submitter
- HAL p.Arg208Trp Uncertain significance Single submitter
-
HAL p.Arg29Gln
Uncertain significance
Single submitter
histidinemia
- HAL p.Arg328Gln Uncertain significance Single submitter
- HAL p.Arg359Cys Uncertain significance Single submitter
-
HAL p.Arg359His
Uncertain significance
Single submitter
histidinemia
- HAL p.Arg390Cys Uncertain significance Single submitter
- HAL p.Arg568Cys Uncertain significance Single submitter
- HAL p.Arg56Ser Uncertain significance Single submitter
- HAL p.Arg584Cys Uncertain significance Single submitter
- HAL p.Arg594His Uncertain significance Single submitter
- HAL p.Arg69Gln Uncertain significance Single submitter
- HAL p.Asn428Thr Uncertain significance Single submitter
-
HAL p.Asn443Lys
Uncertain significance
Single submitter
histidinemia
- HAL p.Asn66Ile Uncertain significance Single submitter
- HAL p.Asp119Gly Uncertain significance Single submitter
- HAL p.Asp41Tyr Uncertain significance Single submitter
- HAL p.Asp427Asn Uncertain significance Single submitter
- HAL p.Asp92Asn Uncertain significance Single submitter
-
HAL p.Cys388Tyr
Uncertain significance
Single submitter
histidinemia
- HAL p.Cys475Arg Uncertain significance Single submitter
- HAL p.Gln562His Uncertain significance Single submitter
- HAL p.Glu109Asp Uncertain significance Single submitter
-
HAL p.Glu601Lys
Uncertain significance
Single submitter
histidinemia
- HAL p.Glu75Lys Uncertain significance Single submitter
-
HAL p.Gly197Ala
Uncertain significance
Single submitter
histidinemia
- HAL p.Gly197Asp Uncertain significance Single submitter
- HAL p.Gly308Arg Uncertain significance Single submitter
- HAL p.Gly442Glu Uncertain significance Single submitter
-
HAL p.Gly491Val
Uncertain significance
Single submitter
histidinemia
- HAL p.Gly60Ser Uncertain significance Single submitter
- HAL p.His376Arg Uncertain significance Single submitter
- HAL p.His404Arg Uncertain significance Single submitter
-
HAL p.His645Tyr
Uncertain significance
Single submitter
histidinemia
- HAL p.Ile157Arg Uncertain significance Single submitter
- HAL p.Ile157Met Uncertain significance Single submitter
- HAL p.Ile166Val Uncertain significance Single submitter
- HAL p.Ile234Leu Uncertain significance Single submitter
- HAL p.Ile362Thr Uncertain significance Single submitter
- HAL p.Ile651Val Uncertain significance Single submitter
- HAL p.Leu218Ser Uncertain significance Single submitter
- HAL p.Leu22Phe Uncertain significance Single submitter
- HAL p.Leu257Ile Uncertain significance Single submitter
- HAL p.Leu513Pro Uncertain significance Single submitter
- HAL p.Leu657Phe Uncertain significance Single submitter
- HAL p.Leu70Phe Uncertain significance Single submitter
- HAL p.Lys277Thr Uncertain significance Single submitter
- HAL p.Lys511Asn Uncertain significance Single submitter
- HAL p.Lys571Gln Uncertain significance Single submitter
- HAL p.Lys650Glu Uncertain significance Single submitter
- HAL p.Phe93Val Uncertain significance Single submitter
- HAL p.Ser149Tyr Uncertain significance Single submitter
- HAL p.Ser203Asn Uncertain significance Single submitter
- HAL p.Ser314Pro Uncertain significance Single submitter
- HAL p.Ser517Leu Uncertain significance Single submitter
- HAL p.Ser525Gly Uncertain significance Single submitter
-
HAL p.Ser96Phe
Uncertain significance
Single submitter
histidinemia
-
HAL p.Thr141Ala
Uncertain significance
Single submitter
histidinemia
- HAL p.Thr350Ser Uncertain significance Single submitter
- HAL p.Thr410Ile Uncertain significance Single submitter
-
HAL p.Thr426Arg
Uncertain significance
Single submitter
histidinemia
- HAL p.Thr46Pro Uncertain significance Single submitter
- HAL p.Thr502Met Uncertain significance Single submitter
-
HAL p.Trp537Arg
Uncertain significance
Single submitter
histidinemia
- HAL p.Val268Ala Uncertain significance Single submitter
- HAL p.Val32Met Uncertain significance Single submitter
-
HAL p.Val340Met
Uncertain significance
Single submitter
histidinemia
-
HAL p.Val364Ile
Uncertain significance
Single submitter
histidinemia
- HAL p.Val414Leu Uncertain significance Single submitter
-
HAL p.Val549Met
Uncertain significance
Single submitter
histidinemia
- HAL p.Val8Ile Uncertain significance Single submitter
Predictors split 30
The independent predictors disagree with each other — read with care.
-
HAL p.Arg9Cys
Uncertain significance
Multiple submitters
histidinemia
-
HAL p.Gly165Ser
Uncertain significance
Multiple submitters
histidinemia
- HAL p.Ile458Thr Uncertain significance Multiple submitters
- HAL p.Ala334Thr Uncertain significance Single submitter
- HAL p.Ala425Thr Uncertain significance Single submitter
- HAL p.Ala452Ser Uncertain significance Single submitter
- HAL p.Ala512Pro Uncertain significance Single submitter
-
HAL p.Arg208Gln
Uncertain significance
Single submitter
histidinemia
-
HAL p.Arg369Gln
Conflicting
Single submitter
histidinemia
-
HAL p.Arg390His
Uncertain significance
Single submitter
histidinemia
- HAL p.Arg9His Uncertain significance Single submitter
- HAL p.Asn238Ser Uncertain significance Single submitter
- HAL p.Asp68Glu Uncertain significance Single submitter
- HAL p.Cys561Ser Uncertain significance Single submitter
- HAL p.Gly343Cys Uncertain significance Single submitter
- HAL p.His377Gln Uncertain significance Single submitter
- HAL p.Ile136Thr Uncertain significance Single submitter
- HAL p.Ile471Asn Uncertain significance Single submitter
- HAL p.Ile600Val Uncertain significance Single submitter
- HAL p.Lys248Thr Uncertain significance Single submitter
- HAL p.Pro276Leu Uncertain significance Single submitter
- HAL p.Pro276Ser Uncertain significance Single submitter
-
HAL p.Pro575Leu
Uncertain significance
Single submitter
histidinemia
-
HAL p.Pro598Leu
Uncertain significance
Single submitter
histidinemia
-
HAL p.Ser585Cys
Uncertain significance
Single submitter
histidinemia
-
HAL p.Thr229Ile
Uncertain significance
Single submitter
histidinemia
- HAL p.Trp26Arg Uncertain significance Single submitter
- HAL p.Val487Met Uncertain significance Single submitter
-
HAL p.Val532Ile
Uncertain significance
Single submitter
histidinemia
- HAL p.Val80Met Uncertain significance Single submitter
All HAL variants
Likely pathogenic 1
- c.1520-5_1538del Single submitter histidinemia
Conflicting classifications of pathogenicity 6
- c.1763+9A>C Single submitter histidinemia
- c.715+9A>G Single submitter histidinemia
- c.855+9C>T Single submitter histidinemia
- p.Arg133His Single submitter histidinemia ⚠
- p.Arg369Gln Single submitter histidinemia ⚠
- p.Thr528= Single submitter histidinemia
Benign 12
- c.1353+13A>G Multiple submitters histidinemia
- c.485-5T>C Multiple submitters histidinemia
- c.-127C>A Multiple submitters histidinemia
- c.*110C>A Multiple submitters histidinemia
- c.*1241A>C Multiple submitters histidinemia
- c.*1312C>T Multiple submitters histidinemia
- c.*1499A>G Multiple submitters histidinemia
- p.Asn307= Multiple submitters histidinemia
- p.Ile460Leu Multiple submitters
- p.Pro259= Multiple submitters histidinemia
- p.Thr141= Multiple submitters histidinemia
- p.Val439Ile Multiple submitters histidinemia
Benign/Likely benign 1
- p.Tyr164= Multiple submitters histidinemia
Likely benign 17
- c.-216A>C Multiple submitters histidinemia
- c.-38C>T Multiple submitters histidinemia
- c.*191C>T Multiple submitters histidinemia
- c.*530T>G Multiple submitters histidinemia
- c.*617G>A Multiple submitters histidinemia
- c.-322T>C Single submitter histidinemia
- c.*836C>T Single submitter histidinemia
- c.*914T>C Single submitter histidinemia
- p.Ala239= Single submitter
- p.Glu115= Single submitter histidinemia
- p.His531= Single submitter
- p.Ile157Val Single submitter
- c.248-5T>C No assertion criteria HAL-related disorder
- p.Ala526= No assertion criteria HAL-related disorder
- p.Ile600= No assertion criteria HAL-related disorder
- p.Pro652= No assertion criteria HAL-related disorder
- p.Pro95= No assertion criteria HAL-related disorder
Uncertain significance 159
- c.*392C>T Multiple submitters histidinemia
- p.Arg9Cys Multiple submitters histidinemia ⚠
- p.Asn476Lys Multiple submitters histidinemia ⚠
- p.Glu472Lys Multiple submitters histidinemia ⚠
- p.Gly165Ser Multiple submitters histidinemia ⚠
- p.Ile458Thr Multiple submitters ⚠
- p.Leu242Met Multiple submitters histidinemia ⚠
- p.Phe485Leu Multiple submitters histidinemia ⚠
- p.Thr123Met Multiple submitters histidinemia ⚠
- c.1764-4G>T Single submitter histidinemia
- c.1764-5T>C Single submitter histidinemia
- c.308+14C>T Single submitter histidinemia
- c.309-2A>G Single submitter histidinemia
- c.904-5G>A Single submitter histidinemia
- c.-108C>T Single submitter histidinemia
- c.-120C>T Single submitter histidinemia
- c.-139C>A Single submitter histidinemia
- c.-5G>A Single submitter histidinemia
- c.-68G>A Single submitter histidinemia
- c.-7C>T Single submitter histidinemia
- c.*1161C>T Single submitter histidinemia
- c.*1169G>T Single submitter histidinemia
- c.*1283T>C Single submitter histidinemia
- c.*1300T>G Single submitter histidinemia
- c.*132C>T Single submitter histidinemia
- c.*1359C>A Single submitter histidinemia
- c.*1409G>A Single submitter histidinemia
- c.*1489A>C Single submitter histidinemia
- c.*1518C>T Single submitter histidinemia
- c.*1548G>A Single submitter histidinemia
- c.*227A>C Single submitter histidinemia
- c.*428C>G Single submitter histidinemia
- c.*4G>A Single submitter histidinemia
- c.*509A>T Single submitter histidinemia
- c.*547G>T Single submitter histidinemia
- c.*555G>A Single submitter histidinemia
- c.*603A>G Single submitter histidinemia
- c.*673T>C Single submitter histidinemia
- c.*728T>A Single submitter histidinemia
- c.*756C>T Single submitter histidinemia
- c.*789G>A Single submitter histidinemia
- c.*976T>G Single submitter histidinemia
- p.Ala20Thr Single submitter ⚠
- p.Ala281Thr Single submitter histidinemia ⚠
- p.Ala31Thr Single submitter
- p.Ala325Thr Single submitter ⚠
- p.Ala334Gly Single submitter ⚠
- p.Ala334Thr Single submitter ⚠
- p.Ala425Thr Single submitter ⚠
- p.Ala452Ser Single submitter ⚠
- p.Ala503Thr Single submitter ⚠
- p.Ala505Thr Single submitter ⚠
- p.Ala512Pro Single submitter ⚠
- p.Ala559Pro Single submitter ⚠
- p.Arg192Cys Single submitter ⚠
- p.Arg208Gln Single submitter histidinemia ⚠
- p.Arg208Trp Single submitter ⚠
- p.Arg29Gln Single submitter histidinemia ⚠
- p.Arg3= Single submitter histidinemia
- p.Arg328Gln Single submitter ⚠
- p.Arg359Cys Single submitter ⚠
- p.Arg359His Single submitter histidinemia ⚠
- p.Arg390Cys Single submitter ⚠
- p.Arg390His Single submitter histidinemia ⚠
- p.Arg568Cys Single submitter ⚠
- p.Arg56Ser Single submitter ⚠
- p.Arg584Cys Single submitter ⚠
- p.Arg594His Single submitter ⚠
- p.Arg69Gln Single submitter ⚠
- p.Arg9His Single submitter ⚠
- p.Asn238Ser Single submitter ⚠
- p.Asn428Thr Single submitter ⚠
- p.Asn443Lys Single submitter histidinemia ⚠
- p.Asn66Ile Single submitter ⚠
- p.Asp119Gly Single submitter ⚠
- p.Asp41Tyr Single submitter ⚠
- p.Asp427Asn Single submitter ⚠
- p.Asp68Glu Single submitter ⚠
- p.Asp92= Single submitter histidinemia
- p.Asp92Asn Single submitter ⚠
- p.Cys388Tyr Single submitter histidinemia ⚠
- p.Cys475Arg Single submitter ⚠
- p.Cys561Ser Single submitter ⚠
- p.Gln562His Single submitter ⚠
- p.Glu109Asp Single submitter ⚠
- p.Glu11= Single submitter histidinemia
- p.Glu143= Single submitter histidinemia
- p.Glu472= Single submitter histidinemia
- p.Glu601Lys Single submitter histidinemia ⚠
- p.Glu75Lys Single submitter ⚠
- p.Gly197Ala Single submitter histidinemia ⚠
- p.Gly197Asp Single submitter ⚠
- p.Gly308Arg Single submitter ⚠
- p.Gly343Cys Single submitter ⚠
- p.Gly442Glu Single submitter ⚠
- p.Gly491Val Single submitter histidinemia ⚠
- p.Gly60Ser Single submitter ⚠
- p.His376Arg Single submitter ⚠
- p.His377Gln Single submitter ⚠
- p.His404Arg Single submitter ⚠
- p.His645Tyr Single submitter histidinemia ⚠
- p.Ile136Thr Single submitter ⚠
- p.Ile157Arg Single submitter ⚠
- p.Ile157Met Single submitter ⚠
- p.Ile166Val Single submitter ⚠
- p.Ile234Leu Single submitter ⚠
- p.Ile362Thr Single submitter ⚠
- p.Ile471Asn Single submitter ⚠
- p.Ile600Val Single submitter ⚠
- p.Ile651Val Single submitter ⚠
- p.Leu218Ser Single submitter ⚠
- p.Leu22Phe Single submitter ⚠
- p.Leu257Ile Single submitter ⚠
- p.Leu513Pro Single submitter ⚠
- p.Leu608Pro Single submitter histidinemia
- p.Leu61= Single submitter histidinemia
- p.Leu657Phe Single submitter ⚠
- p.Leu70Phe Single submitter ⚠
- p.Lys248Thr Single submitter ⚠
- p.Lys277Thr Single submitter ⚠
- p.Lys511Asn Single submitter ⚠
- p.Lys571Gln Single submitter ⚠
- p.Lys650Glu Single submitter ⚠
- p.Phe93Val Single submitter ⚠
- p.Pro276Leu Single submitter ⚠
- p.Pro276Ser Single submitter ⚠
- p.Pro575Leu Single submitter histidinemia ⚠
- p.Pro598= Single submitter histidinemia
- p.Pro598Leu Single submitter histidinemia ⚠
- p.Ser149Tyr Single submitter ⚠
- p.Ser193Ter Single submitter histidinemia
- p.Ser203Asn Single submitter ⚠
- p.Ser314Pro Single submitter ⚠
- p.Ser517Leu Single submitter ⚠
- p.Ser525Gly Single submitter ⚠
- p.Ser585Cys Single submitter histidinemia ⚠
- p.Ser96Phe Single submitter histidinemia ⚠
- p.Thr141Ala Single submitter histidinemia ⚠
- p.Thr229Ile Single submitter histidinemia ⚠
- p.Thr350Ser Single submitter ⚠
- p.Thr410Ile Single submitter ⚠
- p.Thr426Arg Single submitter histidinemia ⚠
- p.Thr46Pro Single submitter ⚠
- p.Thr502Met Single submitter ⚠
- p.Trp26Arg Single submitter ⚠
- p.Trp280Ter Single submitter
- p.Trp537Arg Single submitter histidinemia ⚠
- p.Val146= Single submitter histidinemia
- p.Val251Ile Single submitter histidinemia
- p.Val268Ala Single submitter ⚠
- p.Val32Met Single submitter ⚠
- p.Val340Met Single submitter histidinemia ⚠
- p.Val364Ile Single submitter histidinemia ⚠
- p.Val414Leu Single submitter ⚠
- p.Val487Met Single submitter ⚠
- p.Val532Ile Single submitter histidinemia ⚠
- p.Val549Met Single submitter histidinemia ⚠
- p.Val80Met Single submitter ⚠
- p.Val8Ile Single submitter ⚠