Sugi Variant

Sugi Variant/POGZ

POGZ — 884 ClinVar variants

All ClinVar germline POGZ variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 380 flagged for review →

103 Pathogenic · 17 Pathogenic/Likely pathogenic · 84 Likely pathogenic · 27 Conflicting · 57 Benign · 33 Benign/Likely benign · 166 Likely benign · 397 Uncertain significance

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

⚑ Evidence disagreements 380

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 3

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

Predictors agree, ClinVar conflicts 20

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 254

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 254

Predictors split 102

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

All POGZ variants

Pathogenic 103

  • p.Arg1001Ter Multiple submitters intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Arg1008Ter Multiple submitters intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Arg238Ter Multiple submitters intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Arg508Ter Multiple submitters Inborn genetic diseases
  • p.Arg698Ter Multiple submitters intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Arg784Ter Multiple submitters intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Arg979Ter Multiple submitters intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Asn882fs Multiple submitters intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.His923fs Multiple submitters intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Met394fs Multiple submitters POGZ-related disorder
  • p.Phe1104fs Multiple submitters
  • p.Pro903_Leu904insTer Multiple submitters intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Ser774fs Multiple submitters Smith-Magenis Syndrome-like
  • p.Tyr770Ter Multiple submitters Inborn genetic diseases
  • c.125-1G>T Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • c.1679-3C>G Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • c.2545+1G>C Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • c.2546-1G>A Single submitter
  • c.2570+1G>T Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • c.460-1G>A Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • c.460-2A>C Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Ala905fs Single submitter Inborn genetic diseases
  • p.Ala915fs Single submitter
  • p.Arg350fs Single submitter
  • p.Arg495Ter Single submitter
  • p.Arg674fs Single submitter Inborn genetic diseases
  • p.Asn705Ter Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Asn872fs Single submitter
  • p.Cys753Ter Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Cys782fs Single submitter intellectual disability
  • p.Cys939_Asp944delinsTer Single submitter
  • p.Gln1014Ter Single submitter Inborn genetic diseases
  • p.Gln1041Ter Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Gln1042Arg Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome ⚠
  • p.Gln123fs Single submitter
  • p.Gln177Ter Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Gln245Ter Single submitter
  • p.Gln593His Single submitter ⚠
  • p.Gln635Ter Single submitter Inborn genetic diseases
  • p.Gln668fs Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Gln953Ter Single submitter
  • p.Glu1033fs Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Glu26fs Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Glu525fs Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Glu604Ter Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Gly116fs Single submitter Inborn genetic diseases
  • p.Gly179Val Single submitter ⚠
  • p.Gly201fs Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Gly936Ter Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Gly962fs Single submitter Inborn genetic diseases
  • p.Gly965fs Single submitter
  • p.His1234fs Single submitter
  • p.His137fs Single submitter
  • p.His613Arg Single submitter
  • p.His613Tyr Single submitter
  • p.Ile237fs Single submitter
  • p.Leu1119Ter Single submitter Inborn genetic diseases
  • p.Leu126fs Single submitter
  • p.Leu235fs Single submitter Inborn genetic diseases
  • p.Leu576fs Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Leu775fs Single submitter autism spectrum disorder
  • p.Leu901fs Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Leu927fs Single submitter Inborn genetic diseases
  • p.Leu940fs Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Lys422fs Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Lys675Ter Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Lys807Ter Single submitter
  • p.Met510fs Single submitter
  • p.Met722fs Single submitter
  • p.Phe1065fs Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Phe1107fs Single submitter
  • p.Phe206fs Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Phe879fs Single submitter
  • p.Pro156fs Single submitter
  • p.Pro189fs Single submitter
  • p.Pro211fs Single submitter
  • p.Pro488fs Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Pro732fs Single submitter
  • p.Pro918fs Single submitter
  • p.Pro924fs Single submitter sensorineural hearing loss disorder
  • p.Ser278Ter Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Ser352fs Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Ser603fs Single submitter Inborn genetic diseases
  • p.Ser856Ter Single submitter
  • p.Thr258fs Single submitter
  • p.Thr559fs Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Thr922fs Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Trp1208fs Single submitter
  • p.Trp852Ter Single submitter
  • p.Tyr1199_Ser1200delinsTer Single submitter
  • p.Tyr536Ter Single submitter
  • p.Tyr623fs Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Val1150fs Single submitter Inborn genetic diseases
  • p.Val733fs Single submitter
  • p.Val975fs Single submitter
  • c.2433-2A>T No assertion criteria intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • c.2545+1G>T No assertion criteria intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Gln1283Ter No assertion criteria intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Leu1119fs No assertion criteria intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Leu904Ter No assertion criteria intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Pro1118fs No assertion criteria intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Pro426_Glu427insTer No assertion criteria intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Tyr536fs No assertion criteria intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome

Pathogenic/Likely pathogenic 17

  • c.1679-1G>A Multiple submitters intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • c.1679-2A>G Multiple submitters intellectual disability
  • p.Arg1087Ter Multiple submitters Inborn genetic diseases
  • p.Arg1142Ter Multiple submitters intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Arg1211Ter Multiple submitters POGZ-related disorder
  • p.Arg306Ter Multiple submitters Inborn genetic diseases
  • p.Arg379Ter Multiple submitters intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Arg694Ter Multiple submitters intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Arg864Ter Multiple submitters intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Arg997Ter Multiple submitters intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Gln1014fs Multiple submitters Inborn genetic diseases
  • p.Gln972Ter Multiple submitters intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Glu1040Lys Multiple submitters intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome ⚠
  • p.Glu1154fs Multiple submitters neurodevelopmental disorder
  • p.His840fs Multiple submitters intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Lys1281fs Multiple submitters intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Ser721Ter Multiple submitters intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome

Likely pathogenic 84

  • p.Arg997fs Multiple submitters intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Val951fs Multiple submitters intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • c.1524-3C>G Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • c.1678_1678+1delinsTT Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • c.2062-2A>G Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • c.2234+5G>C Single submitter
  • c.2433-1G>C Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • c.2545+1del Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • c.2545+2del Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • c.2570+3A>C Single submitter
  • c.460-2A>G Single submitter POGZ-related disorder
  • c.568+2T>C Single submitter Inborn genetic diseases
  • p.Ala659fs Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Ala928fs Single submitter
  • p.Arg306Gln Single submitter ⚠
  • p.Arg740fs Single submitter intellectual disability
  • p.Arg777fs Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Arg857Gly Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome ⚠
  • p.Asn322Ser Single submitter POGZ-related disorder ⚠
  • p.Asn869fs Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Asp3fs Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Asp520fs Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Asp946fs Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Cys1267Ter Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Cys496Arg Single submitter
  • p.Cys621Ter Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Cys652Trp Single submitter POGZ-related disorder
  • p.Cys820Ser Single submitter
  • p.Gln1000fs Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Gln1042Ter Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Gln1262Ter Single submitter
  • p.Gln164Ter Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Gln655Ter Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Gln751Ter Single submitter POGZ-related disorder
  • p.Gln925fs Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Glu1016fs Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Glu1062Lys Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Glu570Ter Single submitter POGZ-related disorder
  • p.Gly1063fs Single submitter POGZ-related disorder
  • p.His512Arg Single submitter neurodevelopmental disorder
  • p.His858fs Single submitter intellectual disability
  • p.Ile21fs Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Ile231fs Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Ile25fs Single submitter
  • p.Leu1117fs Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Leu1164fs Single submitter POGZ-related disorder
  • p.Lys1066Ter Single submitter
  • p.Lys1273fs Single submitter
  • p.Lys406fs Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Lys677fs Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Lys801fs Single submitter intellectual disability
  • p.Met1121fs Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Met1180fs Single submitter Inborn genetic diseases
  • p.Phe367fs Single submitter POGZ-related disorder
  • p.Phe728fs Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Phe836fs Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Phe983fs Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Ser1060fs Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Ser1068_Tyr1069insTer Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Ser1197fs Single submitter Inborn genetic diseases
  • p.Ser22fs Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Ser425fs Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Ser839fs Single submitter
  • p.Ser910fs Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Ser910Ter Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Thr186fs Single submitter POGZ-related disorder
  • p.Thr824fs Single submitter intellectual disability
  • p.Thr881fs Single submitter
  • p.Thr886fs Single submitter
  • p.Trp1156Ter Single submitter POGZ-related disorder
  • p.Trp1280Ter Single submitter intellectual disability
  • p.Tyr1176Ter Single submitter Inborn genetic diseases
  • p.Tyr1199fs Single submitter
  • p.Tyr473Cys Single submitter autism spectrum disorder
  • p.Tyr473His Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Tyr647Ter Single submitter
  • p.Val700fs Single submitter
  • c.1079-1G>A No assertion criteria
  • c.2433-2A>G No assertion criteria intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Leu1050fs No assertion criteria intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Leu576Pro No assertion criteria intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Pro726fs No assertion criteria intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Ser141fs No assertion criteria intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Trp1213Ter No assertion criteria obesity disorder

Conflicting classifications of pathogenicity 27

  • c.1079-20A>G Single submitter intellectual disability
  • p.Ala711Thr Single submitter Inborn genetic diseases ⚠
  • p.Arg1232Cys Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Arg476Gln Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome ⚠
  • p.Arg502Lys Single submitter Inborn genetic diseases ⚠
  • p.Arg653Trp Single submitter Inborn genetic diseases ⚠
  • p.Asn136Ser Single submitter Inborn genetic diseases ⚠
  • p.Asp1333Asn Single submitter POGZ-related disorder ⚠
  • p.Glu1401Val Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome ⚠
  • p.Glu518Ala Single submitter Inborn genetic diseases ⚠
  • p.Glu759Lys Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome ⚠
  • p.His1363Arg Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome ⚠
  • p.His583Arg Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome ⚠
  • p.Ile1312Thr Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome ⚠
  • p.Ile1379Val Single submitter Inborn genetic diseases ⚠
  • p.Leu1103Phe Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome ⚠
  • p.Leu86fs Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome ⚠
  • p.Met120Val Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome ⚠
  • p.Pro291Ser Single submitter Inborn genetic diseases ⚠
  • p.Pro717Leu Single submitter POGZ-related disorder ⚠
  • p.Pro726Ala Single submitter Inborn genetic diseases ⚠
  • p.Pro931Leu Single submitter Inborn genetic diseases ⚠
  • p.Ser343Asn Single submitter Inborn genetic diseases ⚠
  • p.Ser438Tyr Single submitter intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome ⚠
  • p.Thr1134Arg Single submitter Inborn genetic diseases ⚠
  • p.Thr258Ala Single submitter Inborn genetic diseases ⚠
  • p.Thr310Ala Single submitter Inborn genetic diseases ⚠

Benign 57

Benign/Likely benign 33

  • c.1186-4A>G Multiple submitters Inborn genetic diseases
  • c.1524-10T>A Multiple submitters
  • c.2433-3T>C Multiple submitters intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • c.860-5C>T Multiple submitters Inborn genetic diseases
  • p.Ala831= Multiple submitters Inborn genetic diseases
  • p.Ala890Val Multiple submitters Inborn genetic diseases
  • p.Asp368= Multiple submitters Inborn genetic diseases
  • p.Cys817= Multiple submitters intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Gln596= Multiple submitters Inborn genetic diseases
  • p.Glu1099= Multiple submitters intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Glu1402Asp Multiple submitters Inborn genetic diseases
  • p.Glu971= Multiple submitters Inborn genetic diseases
  • p.His1079= Multiple submitters intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.His1363Gln Multiple submitters intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.His516= Multiple submitters Inborn genetic diseases
  • p.Ile853Met Multiple submitters intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Leu1043= Multiple submitters Inborn genetic diseases
  • p.Leu1093= Multiple submitters intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Leu1300= Multiple submitters
  • p.Pro54= Multiple submitters Inborn genetic diseases
  • p.Pro930Arg Multiple submitters intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Pro930Leu Multiple submitters intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Ser1200Gly Multiple submitters Inborn genetic diseases
  • p.Ser251= Multiple submitters Inborn genetic diseases
  • p.Ser721del Multiple submitters intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Ser74= Multiple submitters Inborn genetic diseases
  • p.Ser878= Multiple submitters Inborn genetic diseases
  • p.Thr119= Multiple submitters intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Thr229= Multiple submitters
  • p.Thr249= Multiple submitters Inborn genetic diseases
  • p.Thr541= Multiple submitters intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
  • p.Tyr770= Multiple submitters Inborn genetic diseases
  • p.Val24Ile Multiple submitters Inborn genetic diseases

Likely benign 166

Uncertain significance 397

Showing the top 300 by review status; the full set is in the sitemap.