PHF2 — 162 ClinVar variants
All ClinVar germline PHF2 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 120 flagged for review →
1 Likely pathogenic · 1 Conflicting · 15 Benign · 2 Benign/Likely benign · 19 Likely benign · 124 Uncertain significance
Full PHF2 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 120
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.
-
PHF2 p.Asn641Lys
Conflicting
Single submitter
autism spectrum disorder
Predictors lean, ClinVar uncertain 95
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
- PHF2 p.Ala25Val Uncertain significance Single submitter
- PHF2 p.Ala369Val Uncertain significance Single submitter
- PHF2 p.Ala445Thr Uncertain significance Single submitter
- PHF2 p.Ala457Thr Uncertain significance Single submitter
- PHF2 p.Ala538Val Uncertain significance Single submitter
- PHF2 p.Ala661Thr Uncertain significance Single submitter
- PHF2 p.Ala727Val Uncertain significance Single submitter
- PHF2 p.Ala76Val Uncertain significance Single submitter
- PHF2 p.Ala776Thr Uncertain significance Single submitter
- PHF2 p.Ala776Val Uncertain significance Single submitter
- PHF2 p.Ala841Thr Uncertain significance Single submitter
- PHF2 p.Ala984Thr Uncertain significance Single submitter
- PHF2 p.Arg1039His Uncertain significance Single submitter
- PHF2 p.Arg107His Uncertain significance Single submitter
- PHF2 p.Arg186Cys Uncertain significance Single submitter
- PHF2 p.Arg188Gln Uncertain significance Single submitter
- PHF2 p.Arg285Leu Uncertain significance Single submitter
- PHF2 p.Arg516Ser Uncertain significance Single submitter
- PHF2 p.Arg535Gln Uncertain significance Single submitter
- PHF2 p.Arg66Gln Uncertain significance Single submitter
- PHF2 p.Arg749Cys Uncertain significance Single submitter
- PHF2 p.Arg752Gly Uncertain significance Single submitter
- PHF2 p.Arg831Leu Uncertain significance Single submitter
- PHF2 p.Arg831Trp Uncertain significance Single submitter
- PHF2 p.Arg96Gln Uncertain significance Single submitter
- PHF2 p.Asn1062Ser Uncertain significance Single submitter
- PHF2 p.Asn544Ser Uncertain significance Single submitter
- PHF2 p.Asn630Ile Uncertain significance Single submitter
- PHF2 p.Asn641Ser Uncertain significance Single submitter
- PHF2 p.Asn641Tyr Uncertain significance Single submitter
- PHF2 p.Asp224Asn Uncertain significance Single submitter
- PHF2 p.Asp668Asn Uncertain significance Single submitter
- PHF2 p.Asp78Val Uncertain significance Single submitter
-
PHF2 p.Asp855Asn
Uncertain significance
Single submitter
prostate cancer
- PHF2 p.Gln362His Uncertain significance Single submitter
- PHF2 p.Gln583His Uncertain significance Single submitter
- PHF2 p.Glu207Gln Uncertain significance Single submitter
- PHF2 p.Glu861Asp Uncertain significance Single submitter
- PHF2 p.Gly465Arg Uncertain significance Single submitter
-
PHF2 p.Gly527Ser
Uncertain significance
Single submitter
PHF2-related disorder
- PHF2 p.Gly565Val Uncertain significance Single submitter
- PHF2 p.Gly72Cys Uncertain significance Single submitter
- PHF2 p.Gly748Ser Uncertain significance Single submitter
- PHF2 p.Gly816Val Uncertain significance Single submitter
- PHF2 p.Gly835Val Uncertain significance Single submitter
- PHF2 p.Gly836Cys Uncertain significance Single submitter
- PHF2 p.Gly842Ser Uncertain significance Single submitter
- PHF2 p.Gly911Ser Uncertain significance Single submitter
- PHF2 p.His394Tyr Uncertain significance Single submitter
- PHF2 p.Ile211Val Uncertain significance Single submitter
- PHF2 p.Ile542Val Uncertain significance Single submitter
- PHF2 p.Ile741Met Uncertain significance Single submitter
- PHF2 p.Ile741Val Uncertain significance Single submitter
- PHF2 p.Leu1021Arg Uncertain significance Single submitter
- PHF2 p.Leu1021Val Uncertain significance Single submitter
- PHF2 p.Leu228Pro Uncertain significance Single submitter
- PHF2 p.Leu357Val Uncertain significance Single submitter
- PHF2 p.Lys168Asn Uncertain significance Single submitter
- PHF2 p.Lys447Arg Uncertain significance Single submitter
- PHF2 p.Lys529Arg Uncertain significance Single submitter
- PHF2 p.Lys558Arg Uncertain significance Single submitter
- PHF2 p.Lys671Thr Uncertain significance Single submitter
- PHF2 p.Lys722Glu Uncertain significance Single submitter
- PHF2 p.Lys895Arg Uncertain significance Single submitter
- PHF2 p.Met499Ile Uncertain significance Single submitter
- PHF2 p.Pro1013Leu Uncertain significance Single submitter
- PHF2 p.Pro109Leu Uncertain significance Single submitter
- PHF2 p.Pro140Leu Uncertain significance Single submitter
- PHF2 p.Pro393Arg Uncertain significance Single submitter
- PHF2 p.Pro451Leu Uncertain significance Single submitter
- PHF2 p.Pro652Thr Uncertain significance Single submitter
- PHF2 p.Pro653Leu Uncertain significance Single submitter
- PHF2 p.Pro700Arg Uncertain significance Single submitter
- PHF2 p.Pro77Thr Uncertain significance Single submitter
- PHF2 p.Ser1009Leu Uncertain significance Single submitter
- PHF2 p.Ser1020Ile Uncertain significance Single submitter
-
PHF2 p.Ser1020Thr
Uncertain significance
Single submitter
PHF2-related disorder
- PHF2 p.Ser458Leu Uncertain significance Single submitter
- PHF2 p.Ser612Cys Uncertain significance Single submitter
- PHF2 p.Ser757Asn Uncertain significance Single submitter
- PHF2 p.Ser823Asn Uncertain significance Single submitter
- PHF2 p.Ser949Asn Uncertain significance Single submitter
- PHF2 p.Thr1033Ile Uncertain significance Single submitter
- PHF2 p.Thr1064Ile Uncertain significance Single submitter
- PHF2 p.Thr520Met Uncertain significance Single submitter
- PHF2 p.Thr56Ser Uncertain significance Single submitter
- PHF2 p.Thr716Met Uncertain significance Single submitter
- PHF2 p.Thr719Met Uncertain significance Single submitter
- PHF2 p.Thr814Met Uncertain significance Single submitter
- PHF2 p.Thr960Ser Uncertain significance Single submitter
- PHF2 p.Tyr48His Uncertain significance Single submitter
- PHF2 p.Val161Met Uncertain significance Single submitter
- PHF2 p.Val192Ile Uncertain significance Single submitter
- PHF2 p.Val673Met Uncertain significance Single submitter
- PHF2 p.Val914Met Uncertain significance Single submitter
Predictors split 24
The independent predictors disagree with each other — read with care.
- PHF2 p.Ala935Val Uncertain significance Single submitter
- PHF2 p.Arg1054Trp Uncertain significance Single submitter
- PHF2 p.Arg1070His Uncertain significance Single submitter
- PHF2 p.Arg157Trp Uncertain significance Single submitter
- PHF2 p.Arg66Trp Uncertain significance Single submitter
- PHF2 p.Asp169Tyr Uncertain significance Single submitter
- PHF2 p.Asp300Asn Uncertain significance Single submitter
- PHF2 p.Cys240Arg Uncertain significance Single submitter
- PHF2 p.Gly398Ala Uncertain significance Single submitter
- PHF2 p.Gly933Arg Uncertain significance Single submitter
- PHF2 p.His1089Arg Uncertain significance Single submitter
- PHF2 p.Lys498Thr Uncertain significance Single submitter
- PHF2 p.Lys697Asn Uncertain significance Single submitter
- PHF2 p.Lys951Glu Uncertain significance Single submitter
- PHF2 p.Pro508His Uncertain significance Single submitter
- PHF2 p.Pro509Leu Uncertain significance Single submitter
- PHF2 p.Pro988Leu Uncertain significance Single submitter
- PHF2 p.Ser1020Arg Uncertain significance Single submitter
- PHF2 p.Ser853Arg Uncertain significance Single submitter
- PHF2 p.Ser973Tyr Uncertain significance Single submitter
- PHF2 p.Thr982Met Uncertain significance Single submitter
- PHF2 p.Tyr117Cys Uncertain significance Single submitter
- PHF2 p.Val680Met Uncertain significance Single submitter
- PHF2 p.Val6Met Uncertain significance Single submitter
All PHF2 variants
Likely pathogenic 1
- p.Gln917Ter Single submitter
Conflicting classifications of pathogenicity 1
- p.Asn641Lys Single submitter autism spectrum disorder ⚠
Benign 15
- c.299+7T>A Multiple submitters
- p.Asp103= Multiple submitters
- p.Pro786= Multiple submitters
- p.Pro988= Multiple submitters
- p.Ser725= Multiple submitters
- p.Ser738= Multiple submitters
- p.Thr124= Multiple submitters
- p.Val449Ile Multiple submitters
- p.982TPAST[4] Single submitter
- p.Pro109Ser Single submitter
- p.Ser893= Single submitter
- p.Leu548= No assertion criteria PHF2-related disorder
- p.Ser275= No assertion criteria PHF2-related disorder
- p.Ser840Asn No assertion criteria PHF2-related disorder
- p.Thr114= No assertion criteria PHF2-related disorder
Benign/Likely benign 2
- c.789+10G>A Multiple submitters
- p.Leu645= Multiple submitters
Likely benign 19
- c.2349-2312_2349-2310del Single submitter
- p.Ala106= Single submitter
- p.Gly646Ser Single submitter
- p.Ile888Val Single submitter
- p.Ser291= Single submitter
- p.Ser782Asn Single submitter
- p.Ser807= Single submitter
- p.Thr1033= Single submitter
- p.Thr992= Single submitter
- p.Val1048Ile Single submitter autism spectrum disorder
- c.-18GCGGC[4] No assertion criteria PHF2-related disorder
- p.Asp133= No assertion criteria PHF2-related disorder
- p.Gly629= No assertion criteria PHF2-related disorder
- p.His865= No assertion criteria PHF2-related disorder
- p.Lys890= No assertion criteria PHF2-related disorder
- p.Pro273= No assertion criteria PHF2-related disorder
- p.Pro480Leu No assertion criteria PHF2-related disorder
- p.Ser725Leu No assertion criteria PHF2-related disorder
- p.Thr1077= No assertion criteria PHF2-related disorder
Uncertain significance 124
- p.Ala25Val Single submitter ⚠
- p.Ala369Val Single submitter ⚠
- p.Ala445Thr Single submitter ⚠
- p.Ala457Thr Single submitter ⚠
- p.Ala538Val Single submitter ⚠
- p.Ala661Thr Single submitter ⚠
- p.Ala727Val Single submitter ⚠
- p.Ala76Val Single submitter ⚠
- p.Ala776Thr Single submitter ⚠
- p.Ala776Val Single submitter ⚠
- p.Ala841Thr Single submitter ⚠
- p.Ala935Val Single submitter ⚠
- p.Ala984Thr Single submitter ⚠
- p.Arg1039His Single submitter ⚠
- p.Arg1054Trp Single submitter ⚠
- p.Arg1070His Single submitter ⚠
- p.Arg107His Single submitter ⚠
- p.Arg157Trp Single submitter ⚠
- p.Arg186Cys Single submitter ⚠
- p.Arg188Gln Single submitter ⚠
- p.Arg285Leu Single submitter ⚠
- p.Arg516Ser Single submitter ⚠
- p.Arg535Gln Single submitter ⚠
- p.Arg66Gln Single submitter ⚠
- p.Arg66Trp Single submitter ⚠
- p.Arg749Cys Single submitter ⚠
- p.Arg752Gly Single submitter ⚠
- p.Arg831Leu Single submitter ⚠
- p.Arg831Trp Single submitter ⚠
- p.Arg96Gln Single submitter ⚠
- p.Asn1062Ser Single submitter ⚠
- p.Asn544Ser Single submitter ⚠
- p.Asn630Ile Single submitter ⚠
- p.Asn641Ser Single submitter ⚠
- p.Asn641Tyr Single submitter ⚠
- p.Asp169Tyr Single submitter ⚠
- p.Asp224Asn Single submitter ⚠
- p.Asp300Asn Single submitter ⚠
- p.Asp668Asn Single submitter ⚠
- p.Asp78Val Single submitter ⚠
- p.Asp855Asn Single submitter prostate cancer ⚠
- p.Cys240Arg Single submitter ⚠
- p.Gln362His Single submitter ⚠
- p.Gln583His Single submitter ⚠
- p.Glu207Gln Single submitter ⚠
- p.Glu861Asp Single submitter ⚠
- p.Gly398Ala Single submitter ⚠
- p.Gly465Arg Single submitter ⚠
- p.Gly527Ser Single submitter PHF2-related disorder ⚠
- p.Gly565Val Single submitter ⚠
- p.Gly72Cys Single submitter ⚠
- p.Gly748Ser Single submitter ⚠
- p.Gly816Val Single submitter ⚠
- p.Gly835Val Single submitter ⚠
- p.Gly836Cys Single submitter ⚠
- p.Gly842Ser Single submitter ⚠
- p.Gly911Ser Single submitter ⚠
- p.Gly933Arg Single submitter ⚠
- p.His1089Arg Single submitter ⚠
- p.His394Tyr Single submitter ⚠
- p.Ile211Val Single submitter ⚠
- p.Ile542Val Single submitter ⚠
- p.Ile741Met Single submitter ⚠
- p.Ile741Val Single submitter ⚠
- p.Leu1021Arg Single submitter ⚠
- p.Leu1021Val Single submitter ⚠
- p.Leu228Pro Single submitter ⚠
- p.Leu357Val Single submitter ⚠
- p.Lys168Asn Single submitter ⚠
- p.Lys447Arg Single submitter ⚠
- p.Lys498Thr Single submitter ⚠
- p.Lys529Arg Single submitter ⚠
- p.Lys558Arg Single submitter ⚠
- p.Lys671Thr Single submitter ⚠
- p.Lys697Asn Single submitter ⚠
- p.Lys722Glu Single submitter ⚠
- p.Lys895Arg Single submitter ⚠
- p.Lys951Glu Single submitter ⚠
- p.Lys953fs Single submitter
- p.Met499Ile Single submitter ⚠
- p.Pro1013Leu Single submitter ⚠
- p.Pro109Leu Single submitter ⚠
- p.Pro140Leu Single submitter ⚠
- p.Pro393Arg Single submitter ⚠
- p.Pro451Leu Single submitter ⚠
- p.Pro508His Single submitter ⚠
- p.Pro509Leu Single submitter ⚠
- p.Pro652Thr Single submitter ⚠
- p.Pro653Leu Single submitter ⚠
- p.Pro700Arg Single submitter ⚠
- p.Pro77Thr Single submitter ⚠
- p.Pro988Leu Single submitter ⚠
- p.Ser1009Leu Single submitter ⚠
- p.Ser1020Arg Single submitter ⚠
- p.Ser1020Ile Single submitter ⚠
- p.Ser1020Thr Single submitter PHF2-related disorder ⚠
- p.Ser458Leu Single submitter ⚠
- p.Ser474fs Single submitter
- p.Ser612Cys Single submitter ⚠
- p.Ser757Asn Single submitter ⚠
- p.Ser823Asn Single submitter ⚠
- p.Ser853Arg Single submitter ⚠
- p.Ser949Asn Single submitter ⚠
- p.Ser973Tyr Single submitter ⚠
- p.Thr1033Ile Single submitter ⚠
- p.Thr1064Ile Single submitter ⚠
- p.Thr493fs Single submitter neurodevelopmental disorder
- p.Thr520Met Single submitter ⚠
- p.Thr56Ser Single submitter ⚠
- p.Thr716Met Single submitter ⚠
- p.Thr719Met Single submitter ⚠
- p.Thr814Met Single submitter ⚠
- p.Thr960Ser Single submitter ⚠
- p.Thr982Met Single submitter ⚠
- p.Trp815Leu Single submitter
- p.Tyr117Cys Single submitter ⚠
- p.Tyr48His Single submitter ⚠
- p.Val161Met Single submitter ⚠
- p.Val192Ile Single submitter ⚠
- p.Val673Met Single submitter ⚠
- p.Val680Met Single submitter ⚠
- p.Val6Met Single submitter ⚠
- p.Val82Met Single submitter
- p.Val914Met Single submitter ⚠