Sugi Variant

Sugi Variant/HNF4A

HNF4A — 752 ClinVar variants

All ClinVar germline HNF4A variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 229 flagged for review →

65 Pathogenic · 3 Pathogenic/Likely pathogenic · 91 Likely pathogenic · 100 Conflicting · 53 Benign · 46 Benign/Likely benign · 132 Likely benign · 262 Uncertain significance

Full HNF4A gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 229

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 5

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

Predictors agree, ClinVar conflicts 16

ClinVar submitters conflict, but the independent predictors unanimously agree — a QC review flag, not a reclassification.

Predicted LoF vs a conflicting call 1

ClinVar submitters conflict, and it's a predicted loss-of-function change in a gene where LoF causes disease — flagged for review, not resolved (verify NMD-escape for C-terminal truncations). Non-missense.

Predictors lean, ClinVar uncertain 158

ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification. · showing the 150 best-reviewed of 158

Predictors split 49

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

All HNF4A variants

Pathogenic 65

Pathogenic/Likely pathogenic 3

  • c.224+1G>A Multiple submitters maturity-onset diabetes of the young
  • c.319+2T>C Multiple submitters maturity-onset diabetes of the young
  • p.Leu352fs Multiple submitters maturity-onset diabetes of the young

Likely pathogenic 91

Conflicting classifications of pathogenicity 100

  • c.1063+120G>A Single submitter type 2 diabetes mellitus
  • c.1217-145T>C Single submitter maturity-onset diabetes of the young
  • c.1217-151A>C Single submitter maturity-onset diabetes of the young
  • c.426+6G>A Single submitter familial hyperinsulinism
  • c.427-20C>T Single submitter Fanconi renotubular syndrome 4 with maturity-onset diabetes of the young
  • c.427-4G>A Single submitter maturity-onset diabetes of the young
  • c.49+13G>A Single submitter maturity-onset diabetes of the young
  • c.50-4753G>A Single submitter maturity-onset diabetes of the young
  • c.582+12C>T Single submitter maturity-onset diabetes of the young type 1
  • c.582+20G>C Single submitter maturity-onset diabetes of the young
  • c.582+4A>G Single submitter maturity-onset diabetes of the young
  • c.-401G>A Single submitter maturity-onset diabetes of the young
  • c.-565T>C Single submitter maturity-onset diabetes of the young
  • c.-79C>T Single submitter type 2 diabetes mellitus
  • c.*1013G>A Single submitter maturity-onset diabetes of the young
  • c.*1078G>A Single submitter familial hyperinsulinism
  • c.*1087G>C Single submitter familial hyperinsulinism
  • c.*1106G>A Single submitter familial hyperinsulinism
  • c.*1127T>C Single submitter maturity-onset diabetes of the young
  • c.*1291TCCTCCCT[1] Single submitter maturity-onset diabetes of the young
  • c.*1293C>T Single submitter maturity-onset diabetes of the young type 1
  • c.*1363C>T Single submitter maturity-onset diabetes of the young type 1
  • c.*1364G>A Single submitter maturity-onset diabetes of the young type 1
  • c.*1395C>T Single submitter maturity-onset diabetes of the young type 1
  • c.*145T>A Single submitter familial hyperinsulinism
  • c.*1616G>A Single submitter familial hyperinsulinism
  • c.*168G>T Single submitter maturity-onset diabetes of the young type 1
  • c.*1783G>T Single submitter maturity-onset diabetes of the young
  • c.*1809C>G Single submitter maturity-onset diabetes of the young
  • c.*1821C>T Single submitter familial hyperinsulinism
  • c.*1826G>A Single submitter maturity-onset diabetes of the young
  • c.*1828G>A Single submitter familial hyperinsulinism
  • c.*1C>A Single submitter maturity-onset diabetes of the young
  • c.*2153T>C Single submitter familial hyperinsulinism
  • c.*2167T>G Single submitter familial hyperinsulinism
  • c.*217C>T Single submitter maturity-onset diabetes of the young type 1
  • c.*2193T>C Single submitter familial hyperinsulinism
  • c.*226C>A Single submitter maturity-onset diabetes of the young type 1
  • c.*2297C>A Single submitter maturity-onset diabetes of the young type 1
  • c.*2374G>C Single submitter familial hyperinsulinism
  • c.*2511A>G Single submitter maturity-onset diabetes of the young
  • c.*2558T>C Single submitter familial hyperinsulinism
  • c.*2639T>G Single submitter familial hyperinsulinism
  • c.*271C>T Single submitter maturity-onset diabetes of the young type 1
  • c.*2779A>C Single submitter familial hyperinsulinism
  • c.*2782A>C Single submitter maturity-onset diabetes of the young type 1
  • c.*2992C>T Single submitter familial hyperinsulinism
  • c.*3013A>G Single submitter familial hyperinsulinism
  • c.*3018G>A Single submitter familial hyperinsulinism
  • c.*3024C>T Single submitter familial hyperinsulinism
  • c.*3052G>A Single submitter maturity-onset diabetes of the young type 1
  • c.*3068C>T Single submitter familial hyperinsulinism
  • c.*3086C>T Single submitter maturity-onset diabetes of the young
  • c.*3104A>C Single submitter familial hyperinsulinism
  • c.*3120T>C Single submitter familial hyperinsulinism
  • c.*3153C>A Single submitter familial hyperinsulinism
  • c.*35C>A Single submitter maturity-onset diabetes of the young type 1
  • c.*446G>A Single submitter maturity-onset diabetes of the young type 1
  • c.*547G>A Single submitter maturity-onset diabetes of the young
  • c.*572C>A Single submitter maturity-onset diabetes of the young type 1
  • c.*764C>T Single submitter maturity-onset diabetes of the young type 1
  • c.*765G>A Single submitter familial hyperinsulinism
  • c.*76G>A Single submitter maturity-onset diabetes of the young type 1
  • c.*782G>A Single submitter familial hyperinsulinism
  • c.*867G>A Single submitter maturity-onset diabetes of the young
  • c.*965G>T Single submitter familial hyperinsulinism
  • c.*977C>G Single submitter familial hyperinsulinism
  • c.*987G>T Single submitter familial hyperinsulinism
  • p.Ala107Pro Single submitter maturity-onset diabetes of the young ⚠
  • p.Ala28= Single submitter maturity-onset diabetes of the young
  • p.Arg112Pro Single submitter maturity-onset diabetes of the young ⚠
  • p.Arg118Gln Single submitter maturity-onset diabetes of the young type 1 ⚠
  • p.Arg155Gln Single submitter Fanconi renotubular syndrome 4 with maturity-onset diabetes of the young ⚠
  • p.Arg290Gly Single submitter ⚠
  • p.Arg400Ter Single submitter maturity-onset diabetes of the young type 1 ⚠
  • p.Arg44Gln Single submitter monogenic diabetes ⚠
  • p.Arg67= Single submitter type 2 diabetes mellitus
  • p.Asn131= Single submitter maturity-onset diabetes of the young
  • p.Asn392= Single submitter maturity-onset diabetes of the young type 1
  • p.Asp219= Single submitter maturity-onset diabetes of the young
  • p.Cys80Tyr Single submitter ⚠
  • p.Gly203= Single submitter Fanconi renotubular syndrome 4 with maturity-onset diabetes of the young
  • p.Gly209Arg Single submitter maturity-onset diabetes of the young type 1 ⚠
  • p.Gly340= Single submitter maturity-onset diabetes of the young
  • p.His205Pro Single submitter maturity-onset diabetes of the young type 1 ⚠
  • p.Leu127= Single submitter maturity-onset diabetes of the young
  • p.Leu208= Single submitter maturity-onset diabetes of the young
  • p.Leu317Arg Single submitter maturity-onset diabetes of the young type 1 ⚠
  • p.Pro190Leu Single submitter ⚠
  • p.Pro234= Single submitter type 2 diabetes mellitus
  • p.Pro29His Single submitter ⚠
  • p.Pro357Ala Single submitter monogenic diabetes ⚠
  • p.Pro415Ser Single submitter maturity-onset diabetes of the young ⚠
  • p.Ser281Gly Single submitter Fanconi renotubular syndrome 4 with maturity-onset diabetes of the young ⚠
  • p.Tyr264Cys Single submitter maturity-onset diabetes of the young type 1 ⚠
  • p.Val147Ile Single submitter familial hyperinsulinism ⚠
  • p.Val177Ile Single submitter maturity-onset diabetes of the young type 1
  • p.Val242= Single submitter maturity-onset diabetes of the young
  • p.Val66Met Single submitter maturity-onset diabetes of the young ⚠
  • p.Val81Met Single submitter ⚠

Benign 53

Benign/Likely benign 46

  • c.1064-19C>T Multiple submitters maturity-onset diabetes of the young
  • c.319+10G>A Multiple submitters maturity-onset diabetes of the young
  • c.426+7G>C Multiple submitters maturity-onset diabetes of the young
  • c.427-16C>T Multiple submitters maturity-onset diabetes of the young
  • c.50-4496C>T Multiple submitters maturity-onset diabetes of the young
  • c.50-4538G>A Multiple submitters maturity-onset diabetes of the young
  • c.50-4751_50-4745del Multiple submitters
  • c.50-5C>T Multiple submitters Glycosuria
  • c.583-27G>A Multiple submitters maturity-onset diabetes of the young
  • c.-278G>A Multiple submitters maturity-onset diabetes of the young
  • c.*1095G>A Multiple submitters familial hyperinsulinism
  • c.*167T>A Multiple submitters maturity-onset diabetes of the young type 1
  • c.*1832G>A Multiple submitters familial hyperinsulinism
  • c.*1975G>A Multiple submitters maturity-onset diabetes of the young type 1
  • c.*2182G>A Multiple submitters familial hyperinsulinism
  • c.*2256C>G Multiple submitters maturity-onset diabetes of the young type 1
  • c.*242T>C Multiple submitters maturity-onset diabetes of the young type 1
  • c.*2656G>A Multiple submitters maturity-onset diabetes of the young
  • c.*277T>C Multiple submitters familial hyperinsulinism
  • c.*2786C>T Multiple submitters maturity-onset diabetes of the young type 1
  • c.*305A>G Multiple submitters familial hyperinsulinism
  • c.*3143G>T Multiple submitters maturity-onset diabetes of the young type 1
  • c.*393G>A Multiple submitters familial hyperinsulinism
  • c.*427G>T Multiple submitters maturity-onset diabetes of the young type 1
  • c.*521G>A Multiple submitters familial hyperinsulinism
  • c.*568G>A Multiple submitters maturity-onset diabetes of the young
  • c.*657G>A Multiple submitters maturity-onset diabetes of the young
  • c.*785G>A Multiple submitters maturity-onset diabetes of the young type 1
  • c.*7G>A Multiple submitters maturity-onset diabetes of the young type 1
  • p.Ala132= Multiple submitters maturity-onset diabetes of the young
  • p.Ala163= Multiple submitters maturity-onset diabetes of the young
  • p.Arg304= Multiple submitters maturity-onset diabetes of the young type 1
  • p.Asn27= Multiple submitters maturity-onset diabetes of the young
  • p.Asn379= Multiple submitters maturity-onset diabetes of the young type 1
  • p.Asp192= Multiple submitters maturity-onset diabetes of the young
  • p.Asp248= Multiple submitters maturity-onset diabetes of the young type 1
  • p.Asp307= Multiple submitters maturity-onset diabetes of the young
  • p.His232= Multiple submitters maturity-onset diabetes of the young
  • p.Ile333= Multiple submitters maturity-onset diabetes of the young
  • p.Ile344= Multiple submitters type 2 diabetes mellitus
  • p.Ile434= Multiple submitters maturity-onset diabetes of the young
  • p.Leu221= Multiple submitters
  • p.Leu223= Multiple submitters type 2 diabetes mellitus
  • p.Ser308= Multiple submitters maturity-onset diabetes of the young
  • p.Thr117Ile Multiple submitters monogenic diabetes
  • c.*76G>T Single submitter familial hyperinsulinism

Likely benign 132

Uncertain significance 262