PHIP — 1329 ClinVar variants

All ClinVar germline PHIP variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 506 flagged for review →

76 Pathogenic · 17 Pathogenic/Likely pathogenic · 91 Likely pathogenic · 44 Conflicting · 97 Benign · 23 Benign/Likely benign · 426 Likely benign · 555 Uncertain significance

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

⚑ Evidence disagreements 506

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 6

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

Predictors agree, ClinVar conflicts 32

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

Predictors lean, ClinVar uncertain 332

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 332

Predictors split 136

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

All PHIP variants

Pathogenic 76

  • p.Arg1229Ter Multiple submitters PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Arg1505Ter Multiple submitters PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Arg193Ter Multiple submitters Early onset severe obesity
  • p.Gln1211fs Multiple submitters PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Gln1468Ter Multiple submitters PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Gln274Ter Multiple submitters PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Glu886Ter Multiple submitters
  • p.Ile1268fs Multiple submitters PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Ile1318fs Multiple submitters PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Tyr285Ter Multiple submitters
  • c.1628_1653+13del Single submitter
  • c.1654-2A>C Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • c.1879+1G>A Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • c.2319+1del Single submitter
  • c.2537+2T>A Single submitter
  • c.3656+1242A>T Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • c.4370+1G>A Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • c.600+1del Single submitter
  • c.923+1G>A Single submitter Inborn genetic diseases
  • p.Ala124fs Single submitter
  • p.Arg110His Single submitter ⚠
  • p.Arg1167fs Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Arg1308Ter Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Arg250Ter Single submitter
  • p.Arg434Ter Single submitter
  • p.Arg81Ter Single submitter
  • p.Arg920fs Single submitter
  • p.Asn234_Tyr235insTer Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Asn308fs Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Cys1325_Glu1326delinsTer Single submitter
  • p.Gln1493fs Single submitter Early onset severe obesity
  • p.Gln1563Ter Single submitter
  • p.Gln171Ter Single submitter Inborn genetic diseases
  • p.Gln33Ter Single submitter
  • p.Gln890Ter Single submitter
  • p.Gln92Ter Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Gln98Ter Single submitter
  • p.Glu1132Ter Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Glu1685fs Single submitter Inborn genetic diseases
  • p.Glu976Ter Single submitter
  • p.Gly1154Ter Single submitter
  • p.Gly181fs Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Gly351fs Single submitter
  • p.Gly417fs Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Ile440fs Single submitter Inborn genetic diseases
  • p.Leu448fs Single submitter
  • p.Leu650fs Single submitter
  • p.Leu70Ter Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Lys788fs Single submitter Inborn genetic diseases
  • p.Lys891fs Single submitter PHIP-related disorder
  • p.Lys915fs Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Phe1100fs Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Phe1414fs Single submitter
  • p.Pro769fs Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Ser1037Ter Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Ser1392delinsTyrPheGlnTer Single submitter schizophrenia
  • p.Ser1524fs Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Ser1560fs Single submitter Inborn genetic diseases
  • p.Ser272Ter Single submitter
  • p.Ser287fs Single submitter
  • p.Ser484fs Single submitter
  • p.Ser600Ter Single submitter Inborn genetic diseases
  • p.Ser683Ter Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Thr1198_Val1199insTer Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Thr750fs Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Trp1081Ter Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Tyr235fs Single submitter
  • p.Tyr235Ter Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Val1048fs Single submitter
  • p.Val1053_Leu1054insTer Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Val902fs Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Arg110Ser No assertion criteria PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome ⚠
  • p.Gln29fs No assertion criteria PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Gln579Ter No assertion criteria PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Leu100fs No assertion criteria PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Tyr1149Ter No assertion criteria PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome

Pathogenic/Likely pathogenic 17

  • p.Arg1065Ter Multiple submitters PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Arg110Cys Multiple submitters intellectual disability
  • p.Arg1236Ter Multiple submitters PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Arg1298Ter Multiple submitters syndromic intellectual disability
  • p.Arg1483Ter Multiple submitters Inborn genetic diseases
  • p.Arg1510Ter Multiple submitters PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Arg178Ter Multiple submitters PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Arg255Ter Multiple submitters PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Arg396Ter Multiple submitters PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Arg503Ter Multiple submitters PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Arg721Ter Multiple submitters PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Arg968Ter Multiple submitters PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Gly223Val Multiple submitters PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Ile307fs Multiple submitters PHIP-related disorder
  • p.Thr200fs Multiple submitters PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Tyr1316Ter Multiple submitters PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Gln1191Ter No assertion criteria PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome

Likely pathogenic 91

  • c.3782+3_3782+6del Multiple submitters PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Asn507Ser Multiple submitters PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome ⚠
  • p.His266Arg Multiple submitters PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Lys521Arg Multiple submitters PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Ser287Tyr Multiple submitters PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome ⚠
  • p.Ser484Phe Multiple submitters PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • c.1096-2A>C Single submitter PHIP-related disorder
  • c.1137-2A>G Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • c.1137-7_1140del Single submitter
  • c.121_129+18del Single submitter
  • c.122_129+39delinsCGAGGCGGCCCGGGGCGCGGGGCTCAGCTCTCCCCGCTTTGTTGTTGCAGGTGCTGATCCGCGAGAA Single submitter Inborn genetic diseases
  • c.129+1G>A Single submitter
  • c.1654-1G>A Single submitter
  • c.2201+1G>A Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • c.2320-2A>G Single submitter
  • c.2770-1G>C Single submitter Early onset severe obesity
  • c.2890-2A>G Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • c.2890-8T>G Single submitter
  • c.3122+1_3122+8delinsATGTAAA Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • c.3122+2T>C Single submitter PHIP-related disorder
  • c.3205+1G>A Single submitter
  • c.3318-1G>C Single submitter
  • c.3379+1G>A Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • c.341-1G>A Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • c.3535+1G>A Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • c.3852+1G>A Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • c.41-7C>A Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • c.439+5G>T Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • c.4630+2_4630+5del Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • c.4631-2A>T Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • c.600+1G>C Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • c.822+1G>A Single submitter PHIP-related disorder
  • p.Ala485fs Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Arg1402Ser Single submitter ⚠
  • p.Arg163Ter Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Asp1302fs Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Asp488Gly Single submitter
  • p.Cys1106Tyr Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome ⚠
  • p.Cys520fs Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Cys79Arg Single submitter
  • p.Gln790Ter Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Gln922Ter Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Gln98_Leu100del Single submitter
  • p.Glu1368Ter Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Glu55Ter Single submitter PHIP-related disorder
  • p.Glu680fs Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Glu755Ter Single submitter PHIP-related disorder
  • p.Glu904fs Single submitter PHIP-related disorder
  • p.Gly1660fs Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Gly387Arg Single submitter Inborn genetic diseases
  • p.His182Arg Single submitter
  • p.His465Arg Single submitter Inborn genetic diseases
  • p.Ile1009Met Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome ⚠
  • p.Ile1168fs Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Ile509Phe Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Leu260fs Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Leu462fs Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Lys1114_Met1115insTer Single submitter PHIP-related disorder
  • p.Lys1288Ter Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Lys901_Val902insTer Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Met1589fs Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Met429Val Single submitter ⚠
  • p.Met508Arg Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Met508fs Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Met508Ile Single submitter Neurodevelopmental delay ⚠
  • p.Phe1072_Ile1076delinsLeu Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Phe1530fs Single submitter
  • p.Phe17Cys Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Phe17Ser Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome ⚠
  • p.Pro144fs Single submitter
  • p.Pro726Ser Single submitter ⚠
  • p.Ser229Leu Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome ⚠
  • p.Thr423fs Single submitter PHIP-related disorder
  • p.Thr428fs Single submitter Inborn genetic diseases
  • p.Thr428Ser Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome ⚠
  • p.Trp298Ter Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Trp300Ter Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Trp399Ter Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Trp719Ter Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Trp739Ter Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Trp855Ter Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Trp993fs Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Trp993Ter Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Tyr187Cys Single submitter
  • p.Tyr348fs Single submitter PHIP-related disorder
  • p.Tyr602Ter Single submitter PHIP-related disorder
  • p.Val138Gly Single submitter Inborn genetic diseases ⚠
  • p.Val427Phe Single submitter
  • c.995-18_1005del No assertion criteria PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Asp488Val No assertion criteria PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Glu963Gly No assertion criteria PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome

Conflicting classifications of pathogenicity 44

  • p.Ala1597Val Single submitter Inborn genetic diseases ⚠
  • p.Ala1616Thr Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome ⚠
  • p.Ala516Thr Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome ⚠
  • p.Ala569Val Single submitter Inborn genetic diseases ⚠
  • p.Arg1310His Single submitter Early onset severe obesity ⚠
  • p.Arg1773Ter Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Arg669Cys Single submitter Inborn genetic diseases ⚠
  • p.Arg797His Single submitter Inborn genetic diseases ⚠
  • p.Arg952Ter Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Asn1693Ser Single submitter Inborn genetic diseases ⚠
  • p.Asn872Ser Single submitter Inborn genetic diseases ⚠
  • p.Asn903Lys Single submitter Inborn genetic diseases ⚠
  • p.Asp1704Glu Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome ⚠
  • p.Asp594Glu Single submitter Early onset severe obesity ⚠
  • p.Gln33Glu Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome ⚠
  • p.Gln616His Single submitter Inborn genetic diseases ⚠
  • p.Glu1499fs Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Glu1755Gln Single submitter Inborn genetic diseases ⚠
  • p.Glu680Asp Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome ⚠
  • p.Glu836del Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
  • p.Gly201Val Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome ⚠
  • p.Gly464Arg Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome ⚠
  • p.Gly660Val Single submitter Inborn genetic diseases ⚠
  • p.His514Arg Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome ⚠
  • p.Leu1257del Single submitter Inborn genetic diseases
  • p.Leu1271Val Single submitter Inborn genetic diseases ⚠
  • p.Leu44= Single submitter
  • p.Lys889Asn Single submitter Inborn genetic diseases ⚠
  • p.Lys989Arg Single submitter PHIP-related disorder ⚠
  • p.Met1275Val Single submitter Inborn genetic diseases ⚠
  • p.Met1361Val Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome ⚠
  • p.Met1379Val Single submitter PHIP-related disorder ⚠
  • p.Pro410Ala Single submitter Inborn genetic diseases ⚠
  • p.Ser1762Pro Single submitter Inborn genetic diseases ⚠
  • p.Thr1506Ala Single submitter ⚠
  • p.Thr167Ala Single submitter intellectual disability, X-linked 102 ⚠
  • p.Thr438Ala Single submitter Inborn genetic diseases ⚠
  • p.Thr944Ala Single submitter Inborn genetic diseases ⚠
  • p.Thr949Ala Single submitter PHIP-related disorder ⚠
  • p.Thr949Ser Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome ⚠
  • p.Val1169Ala Single submitter PHIP-related disorder ⚠
  • p.Val1366Ile Single submitter Inborn genetic diseases ⚠
  • p.Val1647= Single submitter
  • p.Val681Ile Single submitter PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome ⚠

Benign 97

Benign/Likely benign 23

Likely benign 426

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

Uncertain significance 555

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