HPRT1 — 268 ClinVar variants

All ClinVar germline HPRT1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 56 flagged for review →

64 Pathogenic · 1 Pathogenic/Likely pathogenic · 34 Likely pathogenic · 4 Conflicting · 18 Benign · 4 Benign/Likely benign · 77 Likely benign · 66 Uncertain significance

Full HPRT1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 56

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.

Predictors lean, ClinVar uncertain 43

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

Predictors split 11

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

All HPRT1 variants

Pathogenic 64

  • c.384+1G>A Multiple submitters Lesch-Nyhan syndrome
  • c.486-1G>A Multiple submitters Lesch-Nyhan syndrome
  • c.532+1G>A Multiple submitters HPRT1-related disorder
  • p.Arg48His Multiple submitters HPRT1-related disorder
  • p.Arg51Ter Multiple submitters Lesch-Nyhan syndrome
  • p.Gln109Ter Multiple submitters Lesch-Nyhan syndrome
  • p.Tyr72fs Multiple submitters Lesch-Nyhan syndrome
  • p.Val97fs Multiple submitters hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • c.28-2A>T Single submitter HPRT1-related disorder
  • c.319-2A>G Single submitter Lesch-Nyhan syndrome
  • c.385-2A>G Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • c.486-2A>G Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • c.486-3C>G Single submitter Lesch-Nyhan syndrome
  • c.532+2T>G Single submitter
  • c.533-1G>A Single submitter
  • c.609+1G>A Single submitter
  • c.610-1G>A Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • c.-147_384del Single submitter Lesch-Nyhan syndrome
  • p.Ala64Asp Single submitter Lesch-Nyhan syndrome
  • p.Arg4fs Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • p.Asp113fs Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • p.Asp135Tyr Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • p.Asp194Glu Single submitter HPRT1-related disorder
  • p.Asp194His Single submitter
  • p.Asp20Val Single submitter HPRT1-related disorder
  • p.Gln144Ter Single submitter Lesch-Nyhan syndrome
  • p.Gln152Ter Single submitter
  • p.Glu14fs Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • p.Gly16Val Single submitter Lesch-Nyhan syndrome
  • p.Gly190Ter Single submitter Lesch-Nyhan syndrome
  • p.Gly40Ter Single submitter Lesch-Nyhan syndrome
  • p.Gly70Arg Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • p.Gly70Glu Single submitter Lesch-Nyhan syndrome
  • p.Gly71fs Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • p.Gly71Val Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • p.His204Leu Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • p.Ile42fs Single submitter Lesch-Nyhan syndrome
  • p.Leu49Phe Single submitter
  • p.Leu68fs Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • p.Leu68Phe Single submitter
  • p.Leu68Pro Single submitter
  • p.Leu78Pro Single submitter Lesch-Nyhan syndrome
  • p.Lys186fs Single submitter Lesch-Nyhan syndrome
  • p.Lys215fs Single submitter
  • p.Met1Val Single submitter Lesch-Nyhan syndrome
  • p.Phe74Cys Single submitter Lesch-Nyhan syndrome
  • p.Ser89fs Single submitter
  • p.Val130Asp Single submitter Lesch-Nyhan syndrome
  • p.Val158fs Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • p.Val188_Val189insTer Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • c.317_318del No assertion criteria Lesch-Nyhan syndrome
  • c.532+5G>A No assertion criteria Lesch-Nyhan syndrome
  • c.610-4_610-2delinsTTT No assertion criteria Lesch-Nyhan syndrome
  • p.Arg45Lys No assertion criteria Lesch-Nyhan syndrome
  • p.Asp177Tyr No assertion criteria Lesch-Nyhan syndrome
  • p.Asp194Asn No assertion criteria Lesch-Nyhan syndrome
  • p.Gly180Glu No assertion criteria Lesch-Nyhan syndrome
  • p.Leu65Phe No assertion criteria hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • p.Met143Lys No assertion criteria Lesch-Nyhan syndrome
  • p.Met43fs No assertion criteria Lesch-Nyhan syndrome
  • p.Met54fs No assertion criteria Lesch-Nyhan syndrome
  • p.Pro176Leu No assertion criteria Lesch-Nyhan syndrome
  • p.Thr168Ile No assertion criteria hypoxanthine guanine phosphoribosyltransferase partial deficiency ⚠
  • p.Val130_Leu131insTer No assertion criteria Lesch-Nyhan syndrome

Pathogenic/Likely pathogenic 1

  • p.Arg170Ter Multiple submitters HPRT1-related disorder

Likely pathogenic 34

  • c.532+1_532+2del Multiple submitters hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • c.134+1G>C Single submitter Lesch-Nyhan syndrome
  • c.27+174G>T Single submitter Lesch-Nyhan syndrome
  • c.384+1G>T Single submitter Lesch-Nyhan syndrome
  • c.402+1229A>G Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • c.609+5G>A Single submitter Lesch-Nyhan syndrome
  • p.Ala161Ser Single submitter Lesch-Nyhan syndrome ⚠
  • p.Ala161Thr Single submitter Lesch-Nyhan syndrome ⚠
  • p.Ala50Pro Single submitter Nephrolithiasis/nephrocalcinosis
  • p.Arg167Met Single submitter
  • p.Arg200fs Single submitter Lesch-Nyhan syndrome
  • p.Asp194Tyr Single submitter Lesch-Nyhan syndrome
  • p.Asp44Gly Single submitter HPRT1-related disorder
  • p.Asp80Gly Single submitter Lesch-Nyhan syndrome
  • p.Asp80Tyr Single submitter Lesch-Nyhan syndrome
  • p.Asp80Val Single submitter Lesch-Nyhan syndrome
  • p.Glu47Val Single submitter Nephrolithiasis/nephrocalcinosis
  • p.Gly16Ala Single submitter Lesch-Nyhan syndrome
  • p.Gly71Arg Single submitter Lesch-Nyhan syndrome
  • p.His204Asp Single submitter Lesch-Nyhan syndrome
  • p.His204fs Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • p.His204Tyr Single submitter Lesch-Nyhan syndrome
  • p.Leu147Pro Single submitter
  • p.Leu41fs Single submitter HPRT1-related disorder
  • p.Pro38Ala Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • p.Pro38Leu Single submitter HPRT1-related disorder
  • p.Ser110Leu Single submitter Lesch-Nyhan syndrome
  • p.Ser162Arg Single submitter Lesch-Nyhan syndrome
  • p.Thr139Asn Single submitter Lesch-Nyhan syndrome
  • p.Tyr17Cys Single submitter HPRT1-related disorder
  • p.Val189Ala Single submitter
  • p.Val207fs Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • c.28-2A>G No assertion criteria Lesch-Nyhan syndrome
  • p.Ser123Ter No assertion criteria Lesch-Nyhan spectrum

Conflicting classifications of pathogenicity 4

  • c.134+18A>G Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • c.134+6_134+9del Single submitter Nephrolithiasis/nephrocalcinosis
  • c.384+9C>T Single submitter Lesch-Nyhan syndrome
  • p.Glu182= Single submitter HPRT1-related disorder

Benign 18

  • c.319-7del Multiple submitters
  • c.319-7dup Multiple submitters Lesch-Nyhan syndrome
  • p.Val160= Multiple submitters Nephrolithiasis/nephrocalcinosis
  • c.135-101= Single submitter
  • c.28-14del Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • c.384+304dup Single submitter
  • c.402+297TA[6] Single submitter
  • c.403-12C>A Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • c.485+291A>G Single submitter
  • c.486-12dup Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • c.609+20T>C Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • c.610-221A>C Single submitter
  • c.610-5del Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • c.610-5dup Single submitter Lesch-Nyhan syndrome
  • c.610-6_610-5del Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • p.Arg170= Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • p.Asp77= Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • p.Tyr174= Single submitter Lesch-Nyhan syndrome

Benign/Likely benign 4

  • c.384+19A>G Multiple submitters Lesch-Nyhan syndrome
  • c.486-11G>A Multiple submitters hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • p.Gly140= Multiple submitters hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • p.Pro169Ala Multiple submitters hypoxanthine guanine phosphoribosyltransferase partial deficiency ⚠

Likely benign 77

  • c.319-17T>G Multiple submitters hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • c.319-18T>G Multiple submitters Lesch-Nyhan syndrome
  • c.319-8_319-7dup Multiple submitters hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • c.532+45C>A Multiple submitters
  • p.Ile208= Multiple submitters hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • p.Thr168= Multiple submitters Lesch-Nyhan syndrome
  • c.134+12C>G Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • c.135-121dup Single submitter
  • c.135-6C>T Single submitter Lesch-Nyhan syndrome
  • c.27+19C>G Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • c.27+55G>A Single submitter
  • c.27+7A>G Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • c.28-13A>G Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • c.28-15A>G Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • c.28-19A>G Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • c.28-208A>G Single submitter
  • c.318+18A>C Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • c.318+3362C>T Single submitter
  • c.318+7A>G Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • c.318+9A>G Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • c.319-124C>A Single submitter
  • c.319-16T>A Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • c.319-16T>G Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • c.319-17_319-16insCT Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • c.319-18_319-17insG Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • c.319-19_319-18insG Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • c.319-19_319-18insGT Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • c.319-213C>G Single submitter
  • c.319-7T>C Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • c.384+11T>C Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • c.384+13A>G Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • c.384+147G>A Single submitter
  • c.385-5T>C Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • c.402+1211T>C Single submitter
  • c.402+1346G>A Single submitter
  • c.402+297TA[5] Single submitter
  • c.402+8C>G Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • c.403-17G>A Single submitter Lesch-Nyhan syndrome
  • c.403-18T>C Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • c.403-228C>T Single submitter
  • c.403-7T>A Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • c.485+1206A>G Single submitter
  • c.485+1206dup Single submitter
  • c.485+1213G>A Single submitter
  • c.485+15T>A Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • c.485+862G>A Single submitter
  • c.532+18T>C Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • c.532+20T>C Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • c.533-11A>G Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • c.533-12G>T Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • c.533-13T>C Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • c.609+14T>G Single submitter Lesch-Nyhan syndrome
  • c.610-4A>G Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • p.Ala50= Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • p.Ala64= Single submitter
  • p.Arg34= Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • p.Arg87= Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • p.Asn86= Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • p.Cys23= Single submitter Lesch-Nyhan syndrome
  • p.Glu47= Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • p.Gly112= Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • p.Gly173= Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • p.Gly58= Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • p.Gly59= Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • p.His39= Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • p.Leu131= Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • p.Leu147= Single submitter Lesch-Nyhan syndrome
  • p.Leu164= Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • p.Leu19= Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • p.Leu68= Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • p.Ser148= Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • p.Thr139= Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • p.Thr3= Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • p.Val133= Single submitter Lesch-Nyhan syndrome
  • p.Val205= Single submitter hypoxanthine guanine phosphoribosyltransferase partial deficiency
  • p.Val53= Single submitter Lesch-Nyhan syndrome
  • c.319-9_319-7dup No assertion criteria HPRT1-related disorder

Uncertain significance 66