PHC1 — 201 ClinVar variants
All ClinVar germline PHC1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 142 flagged for review →
1 Pathogenic · 1 Pathogenic/Likely pathogenic · 1 Likely pathogenic · 27 Benign · 1 Benign/Likely benign · 27 Likely benign · 143 Uncertain significance
Full PHC1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 142
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 lean, ClinVar uncertain 115
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
- PHC1 p.Arg876Gln Uncertain significance Multiple submitters
-
PHC1 p.Arg876Trp
Uncertain significance
Multiple submitters
microcephaly 11, primary, autosomal recessive
- PHC1 p.Arg939His Uncertain significance Multiple submitters
- PHC1 p.Glu684Ala Uncertain significance Multiple submitters
- PHC1 p.His629Asn Uncertain significance Multiple submitters
- PHC1 p.Ala125Gly Uncertain significance Single submitter
- PHC1 p.Ala202Pro Uncertain significance Single submitter
- PHC1 p.Ala243Ser Uncertain significance Single submitter
- PHC1 p.Ala247Ser Uncertain significance Single submitter
- PHC1 p.Ala253Ser Uncertain significance Single submitter
- PHC1 p.Ala287Thr Uncertain significance Single submitter
- PHC1 p.Ala357Gly Uncertain significance Single submitter
- PHC1 p.Ala442Thr Uncertain significance Single submitter
- PHC1 p.Ala518Pro Uncertain significance Single submitter
- PHC1 p.Ala704Ser Uncertain significance Single submitter
- PHC1 p.Ala71Ser Uncertain significance Single submitter
- PHC1 p.Ala906Thr Uncertain significance Single submitter
- PHC1 p.Ala996Thr Uncertain significance Single submitter
- PHC1 p.Arg355Gln Uncertain significance Single submitter
- PHC1 p.Arg410Gln Uncertain significance Single submitter
- PHC1 p.Arg556Gln Uncertain significance Single submitter
- PHC1 p.Arg556Trp Uncertain significance Single submitter
- PHC1 p.Arg649Ser Uncertain significance Single submitter
- PHC1 p.Arg649Thr Uncertain significance Single submitter
- PHC1 p.Arg82Gln Uncertain significance Single submitter
- PHC1 p.Arg854Cys Uncertain significance Single submitter
- PHC1 p.Arg856His Uncertain significance Single submitter
- PHC1 p.Arg860His Uncertain significance Single submitter
- PHC1 p.Arg867Cys Uncertain significance Single submitter
- PHC1 p.Asn104Ser Uncertain significance Single submitter
- PHC1 p.Asn13Ser Uncertain significance Single submitter
- PHC1 p.Asn692Asp Uncertain significance Single submitter
- PHC1 p.Asn828Ser Uncertain significance Single submitter
- PHC1 p.Asn849Ser Uncertain significance Single submitter
- PHC1 p.Gln100Arg Uncertain significance Single submitter
- PHC1 p.Gln25His Uncertain significance Single submitter
- PHC1 p.Gln439Pro Uncertain significance Single submitter
- PHC1 p.Gln449His Uncertain significance Single submitter
- PHC1 p.Gln452His Uncertain significance Single submitter
- PHC1 p.Gln457Pro Uncertain significance Single submitter
- PHC1 p.Gln463His Uncertain significance Single submitter
- PHC1 p.Gln871Arg Uncertain significance Single submitter
- PHC1 p.Gln95Pro Uncertain significance Single submitter
- PHC1 p.Glu681Gly Uncertain significance Single submitter
- PHC1 p.Glu684Gly Uncertain significance Single submitter
- PHC1 p.Glu775Asp Uncertain significance Single submitter
- PHC1 p.Glu844Gln Uncertain significance Single submitter
- PHC1 p.Glu947Val Uncertain significance Single submitter
- PHC1 p.Gly20Ser Uncertain significance Single submitter
- PHC1 p.Gly224Ser Uncertain significance Single submitter
- PHC1 p.Gly268Val Uncertain significance Single submitter
- PHC1 p.Gly282Ser Uncertain significance Single submitter
- PHC1 p.Gly608Glu Uncertain significance Single submitter
- PHC1 p.Gly720Asp Uncertain significance Single submitter
- PHC1 p.Gly740Ala Uncertain significance Single submitter
- PHC1 p.Gly909Glu Uncertain significance Single submitter
- PHC1 p.His908Arg Uncertain significance Single submitter
- PHC1 p.His908Tyr Uncertain significance Single submitter
- PHC1 p.Ile733Thr Uncertain significance Single submitter
- PHC1 p.Leu248Gln Uncertain significance Single submitter
- PHC1 p.Leu262Phe Uncertain significance Single submitter
- PHC1 p.Leu291Val Uncertain significance Single submitter
- PHC1 p.Leu637Phe Uncertain significance Single submitter
- PHC1 p.Leu698Val Uncertain significance Single submitter
- PHC1 p.Leu975Val Uncertain significance Single submitter
- PHC1 p.Lys491Glu Uncertain significance Single submitter
- PHC1 p.Lys676Arg Uncertain significance Single submitter
- PHC1 p.Lys838Thr Uncertain significance Single submitter
- PHC1 p.Lys873Arg Uncertain significance Single submitter
- PHC1 p.Met279Val Uncertain significance Single submitter
- PHC1 p.Met558Thr Uncertain significance Single submitter
-
PHC1 p.Met593Leu
Uncertain significance
Single submitter
microcephaly 11, primary, autosomal recessive
- PHC1 p.Met673Thr Uncertain significance Single submitter
- PHC1 p.Pro123Leu Uncertain significance Single submitter
- PHC1 p.Pro123Ser Uncertain significance Single submitter
- PHC1 p.Pro236Arg Uncertain significance Single submitter
- PHC1 p.Pro461Leu Uncertain significance Single submitter
- PHC1 p.Pro461Ser Uncertain significance Single submitter
- PHC1 p.Pro507Leu Uncertain significance Single submitter
- PHC1 p.Pro587Leu Uncertain significance Single submitter
- PHC1 p.Pro631Leu Uncertain significance Single submitter
- PHC1 p.Pro770Leu Uncertain significance Single submitter
- PHC1 p.Pro858Leu Uncertain significance Single submitter
- PHC1 p.Pro920Ser Uncertain significance Single submitter
- PHC1 p.Pro921Arg Uncertain significance Single submitter
- PHC1 p.Ser109Pro Uncertain significance Single submitter
- PHC1 p.Ser21Thr Uncertain significance Single submitter
- PHC1 p.Ser225Pro Uncertain significance Single submitter
- PHC1 p.Ser265Gly Uncertain significance Single submitter
- PHC1 p.Ser271Thr Uncertain significance Single submitter
- PHC1 p.Ser303Gly Uncertain significance Single submitter
- PHC1 p.Ser555Cys Uncertain significance Single submitter
- PHC1 p.Ser572Leu Uncertain significance Single submitter
- PHC1 p.Ser685Leu Uncertain significance Single submitter
- PHC1 p.Ser722Leu Uncertain significance Single submitter
- PHC1 p.Ser755Cys Uncertain significance Single submitter
- PHC1 p.Thr129Ala Uncertain significance Single submitter
- PHC1 p.Thr320Ile Uncertain significance Single submitter
- PHC1 p.Thr370Ala Uncertain significance Single submitter
- PHC1 p.Thr444Asn Uncertain significance Single submitter
- PHC1 p.Thr654Pro Uncertain significance Single submitter
- PHC1 p.Thr693Ile Uncertain significance Single submitter
- PHC1 p.Thr767Ile Uncertain significance Single submitter
- PHC1 p.Thr897Ala Uncertain significance Single submitter
- PHC1 p.Thr91Ile Uncertain significance Single submitter
- PHC1 p.Thr99Asn Uncertain significance Single submitter
- PHC1 p.Val198Ala Uncertain significance Single submitter
- PHC1 p.Val237Gly Uncertain significance Single submitter
- PHC1 p.Val459Phe Uncertain significance Single submitter
- PHC1 p.Val473Ile Uncertain significance Single submitter
- PHC1 p.Val628Leu Uncertain significance Single submitter
- PHC1 p.Val666Ile Uncertain significance Single submitter
- PHC1 p.Val689Ala Uncertain significance Single submitter
- PHC1 p.Val73Ile Uncertain significance Single submitter
- PHC1 p.Val904Leu Uncertain significance Single submitter
Predictors split 27
The independent predictors disagree with each other — read with care.
- PHC1 p.Arg34Gln Uncertain significance Single submitter
- PHC1 p.Arg45Gln Uncertain significance Single submitter
- PHC1 p.Asn207Lys Uncertain significance Single submitter
- PHC1 p.Asn48Lys Uncertain significance Single submitter
- PHC1 p.Gln148His Uncertain significance Single submitter
- PHC1 p.Gln174His Uncertain significance Single submitter
- PHC1 p.Gln413Arg Uncertain significance Single submitter
- PHC1 p.Gln427Leu Uncertain significance Single submitter
- PHC1 p.Gln430His Uncertain significance Single submitter
- PHC1 p.Gln474Lys Uncertain significance Single submitter
- PHC1 p.Gly753Asp Uncertain significance Single submitter
- PHC1 p.Ile78Thr Uncertain significance Single submitter
- PHC1 p.Ile986Val Uncertain significance Single submitter
- PHC1 p.Leu291Trp Uncertain significance Single submitter
- PHC1 p.Leu353Pro Uncertain significance Single submitter
- PHC1 p.Leu365Phe Uncertain significance Single submitter
- PHC1 p.Leu589Trp Uncertain significance Single submitter
- PHC1 p.Lys337Asn Uncertain significance Single submitter
- PHC1 p.Lys869Glu Uncertain significance Single submitter
- PHC1 p.Met178Ile Uncertain significance Single submitter
-
PHC1 p.Pro24Leu
Uncertain significance
Single submitter
microcephaly 11, primary, autosomal recessive
- PHC1 p.Pro376Thr Uncertain significance Single submitter
- PHC1 p.Ser5Arg Uncertain significance Single submitter
- PHC1 p.Thr1004Ile Uncertain significance Single submitter
- PHC1 p.Thr419Ile Uncertain significance Single submitter
- PHC1 p.Tyr32His Uncertain significance Single submitter
- PHC1 p.Val1000Asp Likely benign Single submitter
All PHC1 variants
Pathogenic 1
- p.Arg34Ter Single submitter microcephaly 11, primary, autosomal recessive
Pathogenic/Likely pathogenic 1
- p.Leu992Phe No assertion criteria microcephaly 11, primary, autosomal recessive
Likely pathogenic 1
- p.Ser303fs Single submitter PHC1-related disorders
Benign 27
- c.1106-60G>A Multiple submitters
- c.114+191T>C Multiple submitters
- c.1894-221A>G Multiple submitters
- c.2041+75A>T Multiple submitters
- c.2253+7G>A Multiple submitters
- c.2368+32A>T Multiple submitters
- c.2628+164G>A Multiple submitters
- c.2629-127G>A Multiple submitters
- c.2860+12C>T Multiple submitters microcephaly 11, primary, autosomal recessive
- c.613-176A>G Multiple submitters
- p.Arg306= Multiple submitters microcephaly 11, primary, autosomal recessive
- p.Arg911His Multiple submitters
- p.Leu31= Multiple submitters microcephaly 11, primary, autosomal recessive
- p.Lys662= Multiple submitters
- p.Pro123= Multiple submitters microcephaly 11, primary, autosomal recessive
- p.Thr693Ala Multiple submitters microcephaly 11, primary, autosomal recessive
- c.1106-228G>A Single submitter
- c.115-190C>T Single submitter
- c.2369-180A>C Single submitter
- c.2860+203G>A Single submitter
- c.2860+236C>T Single submitter
- c.2861-314G>A Single submitter
- c.457-215G>T Single submitter
- c.613-274C>T Single submitter
- c.*243C>T Single submitter
- p.Gln438_Gln439del Single submitter
- p.Gln467Lys Single submitter
Benign/Likely benign 1
- p.Val615= Multiple submitters
Likely benign 27
- p.Ala512= Multiple submitters
- p.Ala704Thr Multiple submitters
- p.Gln389Ter Multiple submitters
- p.Gln434= Multiple submitters
- p.His54= Multiple submitters
- c.1106-11del Single submitter
- c.1893+12C>A Single submitter
- c.1894-8C>T Single submitter
- c.2629-4A>G Single submitter
- c.457-14C>G Single submitter
- c.612+9C>T Single submitter
- p.Ala27= Single submitter
- p.Ala700= Single submitter
- p.Arg533Gln Single submitter
- p.Gln435= Single submitter
- p.Gly746= Single submitter
- p.Leu548= Single submitter
- p.Pro440= Single submitter
- p.Pro501= Single submitter
- p.Pro579Ala Single submitter
- p.Ser115= Single submitter
- p.Thr164= Single submitter
- p.Val1000Asp Single submitter ⚠
- c.2253+8C>T No assertion criteria PHC1-related disorder
- p.Gln408= No assertion criteria PHC1-related disorder
- p.Gly927= No assertion criteria PHC1-related disorder
- p.Val73= No assertion criteria PHC1-related disorder
Uncertain significance 143
- p.Arg876Gln Multiple submitters ⚠
- p.Arg876Trp Multiple submitters microcephaly 11, primary, autosomal recessive ⚠
- p.Arg939His Multiple submitters ⚠
- p.Glu684Ala Multiple submitters ⚠
- p.His629Asn Multiple submitters ⚠
- c.306+7A>G Single submitter
- p.Ala125Gly Single submitter ⚠
- p.Ala202Pro Single submitter ⚠
- p.Ala243Ser Single submitter ⚠
- p.Ala247Ser Single submitter ⚠
- p.Ala253Ser Single submitter ⚠
- p.Ala287Thr Single submitter ⚠
- p.Ala357Gly Single submitter ⚠
- p.Ala442Thr Single submitter ⚠
- p.Ala518Pro Single submitter ⚠
- p.Ala704Ser Single submitter ⚠
- p.Ala71Ser Single submitter ⚠
- p.Ala906Thr Single submitter ⚠
- p.Ala996Thr Single submitter ⚠
- p.Arg34Gln Single submitter ⚠
- p.Arg355Gln Single submitter ⚠
- p.Arg410Gln Single submitter ⚠
- p.Arg45Gln Single submitter ⚠
- p.Arg556Gln Single submitter ⚠
- p.Arg556Trp Single submitter ⚠
- p.Arg649Ser Single submitter ⚠
- p.Arg649Thr Single submitter ⚠
- p.Arg82Gln Single submitter ⚠
- p.Arg854Cys Single submitter ⚠
- p.Arg856His Single submitter ⚠
- p.Arg860His Single submitter ⚠
- p.Arg867Cys Single submitter ⚠
- p.Asn104Ser Single submitter ⚠
- p.Asn13Ser Single submitter ⚠
- p.Asn162= Single submitter
- p.Asn207Lys Single submitter ⚠
- p.Asn48Lys Single submitter ⚠
- p.Asn692Asp Single submitter ⚠
- p.Asn828Ser Single submitter ⚠
- p.Asn849Ser Single submitter ⚠
- p.Gln100Arg Single submitter ⚠
- p.Gln148His Single submitter ⚠
- p.Gln174His Single submitter ⚠
- p.Gln25His Single submitter ⚠
- p.Gln413Arg Single submitter ⚠
- p.Gln427Leu Single submitter ⚠
- p.Gln430His Single submitter ⚠
- p.Gln439Pro Single submitter ⚠
- p.Gln449His Single submitter ⚠
- p.Gln452His Single submitter ⚠
- p.Gln457Pro Single submitter ⚠
- p.Gln463His Single submitter ⚠
- p.Gln474Lys Single submitter ⚠
- p.Gln871Arg Single submitter ⚠
- p.Gln95Pro Single submitter ⚠
- p.Glu681Gly Single submitter ⚠
- p.Glu684Gly Single submitter ⚠
- p.Glu775Asp Single submitter ⚠
- p.Glu844Gln Single submitter ⚠
- p.Glu947Val Single submitter ⚠
- p.Gly20Ser Single submitter ⚠
- p.Gly224Ser Single submitter ⚠
- p.Gly268Val Single submitter ⚠
- p.Gly282Ser Single submitter ⚠
- p.Gly608Glu Single submitter ⚠
- p.Gly720Asp Single submitter ⚠
- p.Gly740Ala Single submitter ⚠
- p.Gly753Asp Single submitter ⚠
- p.Gly909Glu Single submitter ⚠
- p.His908Arg Single submitter ⚠
- p.His908Tyr Single submitter ⚠
- p.Ile733Thr Single submitter ⚠
- p.Ile78Thr Single submitter ⚠
- p.Ile986Val Single submitter ⚠
- p.Leu248Gln Single submitter ⚠
- p.Leu262Phe Single submitter ⚠
- p.Leu291Trp Single submitter ⚠
- p.Leu291Val Single submitter ⚠
- p.Leu353Pro Single submitter ⚠
- p.Leu365Phe Single submitter ⚠
- p.Leu589Trp Single submitter ⚠
- p.Leu637Phe Single submitter ⚠
- p.Leu698Val Single submitter ⚠
- p.Leu975Val Single submitter ⚠
- p.Lys337Asn Single submitter ⚠
- p.Lys491Glu Single submitter ⚠
- p.Lys676Arg Single submitter ⚠
- p.Lys838Thr Single submitter ⚠
- p.Lys869Glu Single submitter ⚠
- p.Lys873Arg Single submitter ⚠
- p.Met178Ile Single submitter ⚠
- p.Met279Val Single submitter ⚠
- p.Met558Thr Single submitter ⚠
- p.Met593Leu Single submitter microcephaly 11, primary, autosomal recessive ⚠
- p.Met673Thr Single submitter ⚠
- p.Pro123Leu Single submitter ⚠
- p.Pro123Ser Single submitter ⚠
- p.Pro236Arg Single submitter ⚠
- p.Pro24Leu Single submitter microcephaly 11, primary, autosomal recessive ⚠
- p.Pro376Thr Single submitter ⚠
- p.Pro461Leu Single submitter ⚠
- p.Pro461Ser Single submitter ⚠
- p.Pro507Leu Single submitter ⚠
- p.Pro587Leu Single submitter ⚠
- p.Pro631Leu Single submitter ⚠
- p.Pro770Leu Single submitter ⚠
- p.Pro858Leu Single submitter ⚠
- p.Pro920Ser Single submitter ⚠
- p.Pro921Arg Single submitter ⚠
- p.Ser109Pro Single submitter ⚠
- p.Ser21Thr Single submitter ⚠
- p.Ser225Pro Single submitter ⚠
- p.Ser265Gly Single submitter ⚠
- p.Ser271Thr Single submitter ⚠
- p.Ser303Gly Single submitter ⚠
- p.Ser555Cys Single submitter ⚠
- p.Ser572Leu Single submitter ⚠
- p.Ser5Arg Single submitter ⚠
- p.Ser685Leu Single submitter ⚠
- p.Ser722Leu Single submitter ⚠
- p.Ser755Cys Single submitter ⚠
- p.Thr1004Ile Single submitter ⚠
- p.Thr129Ala Single submitter ⚠
- p.Thr320Ile Single submitter ⚠
- p.Thr370Ala Single submitter ⚠
- p.Thr419Ile Single submitter ⚠
- p.Thr444Asn Single submitter ⚠
- p.Thr654Pro Single submitter ⚠
- p.Thr693Ile Single submitter ⚠
- p.Thr767Ile Single submitter ⚠
- p.Thr897Ala Single submitter ⚠
- p.Thr91Ile Single submitter ⚠
- p.Thr99Asn Single submitter ⚠
- p.Tyr32His Single submitter ⚠
- p.Val198Ala Single submitter ⚠
- p.Val237Gly Single submitter ⚠
- p.Val459Phe Single submitter ⚠
- p.Val473Ile Single submitter ⚠
- p.Val628Leu Single submitter ⚠
- p.Val666Ile Single submitter ⚠
- p.Val689Ala Single submitter ⚠
- p.Val73Ile Single submitter ⚠
- p.Val904Leu Single submitter ⚠