PSPH — 181 ClinVar variants
All ClinVar germline PSPH variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 61 flagged for review →
3 Pathogenic · 1 Likely pathogenic · 8 Conflicting · 16 Benign · 6 Benign/Likely benign · 52 Likely benign · 95 Uncertain significance
Full PSPH gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 61
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 4
ClinVar submitters conflict, but the independent predictors unanimously agree — a QC review flag, not a reclassification.
-
PSPH p.Ala192Val
Conflicting
Single submitter
Inborn genetic diseases
-
PSPH p.Arg50Gln
Conflicting
Single submitter
PSPH deficiency
-
PSPH p.Thr152Ile
Conflicting
Single submitter
PSPH deficiency
-
PSPH p.Val217Ala
Conflicting
Single submitter
PSPH deficiency
Predictors lean, ClinVar uncertain 45
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
-
PSPH p.Asn124Ser
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
PSPH p.Asp32Asn
Uncertain significance
Multiple submitters
PSPH deficiency
-
PSPH p.Gln204His
Uncertain significance
Multiple submitters
PSPH deficiency
-
PSPH p.Glu117Asp
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
PSPH p.Glu225Lys
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
PSPH p.Tyr212Cys
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
PSPH p.Ala127Thr
Uncertain significance
Single submitter
PSPH deficiency
-
PSPH p.Ala190Pro
Uncertain significance
Single submitter
PSPH deficiency
-
PSPH p.Ala192Thr
Uncertain significance
Single submitter
Inborn genetic diseases
-
PSPH p.Ala209Thr
Uncertain significance
Single submitter
Inborn genetic diseases
-
PSPH p.Ala43Val
Uncertain significance
Single submitter
Inborn genetic diseases
-
PSPH p.Ala67Asp
Uncertain significance
Single submitter
Inborn genetic diseases
-
PSPH p.Arg101Gln
Uncertain significance
Single submitter
PSPH deficiency
-
PSPH p.Asn102Ser
Uncertain significance
Single submitter
PSPH deficiency
-
PSPH p.Asn124His
Uncertain significance
Single submitter
Inborn genetic diseases
-
PSPH p.Asn133His
Uncertain significance
Single submitter
Inborn genetic diseases
-
PSPH p.Asn133Ser
Uncertain significance
Single submitter
PSPH deficiency
-
PSPH p.Asn199His
Uncertain significance
Single submitter
PSPH deficiency
-
PSPH p.Asn199Ile
Uncertain significance
Single submitter
PSPH deficiency
-
PSPH p.Asn199Lys
Uncertain significance
Single submitter
PSPH deficiency
-
PSPH p.Asp191His
Uncertain significance
Single submitter
Inborn genetic diseases
-
PSPH p.Asp42Val
Uncertain significance
Single submitter
Inborn genetic diseases
- PSPH p.Cys18Arg Uncertain significance Single submitter
-
PSPH p.Glu142Lys
Uncertain significance
Single submitter
PSPH deficiency
-
PSPH p.Glu225Ala
Uncertain significance
Single submitter
PSPH deficiency
-
PSPH p.Glu225Gln
Uncertain significance
Single submitter
PSPH deficiency
-
PSPH p.Glu64Gly
Uncertain significance
Single submitter
Inborn genetic diseases
-
PSPH p.Glu6Val
Uncertain significance
Single submitter
Inborn genetic diseases
-
PSPH p.Gly141Ser
Uncertain significance
Single submitter
PSPH deficiency
-
PSPH p.Gly156Asp
Uncertain significance
Single submitter
PSPH deficiency
-
PSPH p.His170Arg
Uncertain significance
Single submitter
PSPH deficiency
-
PSPH p.Ile162Val
Uncertain significance
Single submitter
PSPH deficiency
-
PSPH p.Ile175Leu
Uncertain significance
Single submitter
Inborn genetic diseases
-
PSPH p.Leu62Pro
Uncertain significance
Single submitter
Inborn genetic diseases
-
PSPH p.Lys122Asn
Uncertain significance
Single submitter
PSPH deficiency
-
PSPH p.Lys160Arg
Uncertain significance
Single submitter
PSPH deficiency
-
PSPH p.Phe106Leu
Uncertain significance
Single submitter
PSPH deficiency
-
PSPH p.Phe216Cys
Uncertain significance
Single submitter
PSPH deficiency
-
PSPH p.Phe58Leu
Uncertain significance
Single submitter
Inborn genetic diseases
-
PSPH p.Ser114Ile
Uncertain significance
Single submitter
PSPH deficiency
-
PSPH p.Ser155Phe
Uncertain significance
Single submitter
PSPH deficiency
-
PSPH p.Thr48Ile
Uncertain significance
Single submitter
Inborn genetic diseases
-
PSPH p.Tyr12Asn
Uncertain significance
Single submitter
Inborn genetic diseases
-
PSPH p.Val116Ile
Uncertain significance
Single submitter
PSPH deficiency
-
PSPH p.Val161Met
Uncertain significance
Single submitter
PSPH deficiency
Predictors split 12
The independent predictors disagree with each other — read with care.
-
PSPH p.His118Arg
Uncertain significance
Multiple submitters
PSPH deficiency
-
PSPH p.Pro57Ser
Benign
Multiple submitters
PSPH deficiency
-
PSPH p.Ala120Ser
Uncertain significance
Single submitter
PSPH deficiency
-
PSPH p.Arg134Ser
Uncertain significance
Single submitter
PSPH deficiency
-
PSPH p.Arg97Cys
Uncertain significance
Single submitter
PSPH deficiency
-
PSPH p.Asn129Ser
Uncertain significance
Single submitter
PSPH deficiency
-
PSPH p.Gly198Glu
Uncertain significance
Single submitter
PSPH deficiency
-
PSPH p.Gly39Ser
Conflicting
Single submitter
PSPH deficiency
-
PSPH p.Leu79Phe
Uncertain significance
Single submitter
PSPH deficiency
-
PSPH p.Thr149Met
Uncertain significance
Single submitter
PSPH deficiency
-
PSPH p.Thr214Pro
Uncertain significance
Single submitter
PSPH deficiency
-
PSPH p.Thr214Ser
Uncertain significance
Single submitter
PSPH deficiency
All PSPH variants
Pathogenic 3
- p.Arg50Ter Single submitter
- p.Ala35Thr No assertion criteria PSPH deficiency
- p.Met52Thr No assertion criteria PSPH deficiency
Likely pathogenic 1
- p.Arg101Ter Multiple submitters PSPH deficiency
Conflicting classifications of pathogenicity 8
- c.275+1del Single submitter neurometabolic disorder due to serine deficiency
- p.Ala192Val Single submitter Inborn genetic diseases ⚠
- p.Ala43= Single submitter PSPH deficiency
- p.Arg50Gln Single submitter PSPH deficiency ⚠
- p.Gly39Ser Single submitter PSPH deficiency ⚠
- p.Ser114fs Single submitter PSPH deficiency
- p.Thr152Ile Single submitter PSPH deficiency ⚠
- p.Val217Ala Single submitter PSPH deficiency ⚠
Benign 16
- c.-19-4G>A Multiple submitters PSPH deficiency
- c.*11C>T Multiple submitters PSPH deficiency
- c.*361A>G Multiple submitters PSPH deficiency
- c.*406G>A Multiple submitters PSPH deficiency
- c.*490C>T Multiple submitters PSPH deficiency
- p.Arg27Ser Multiple submitters PSPH deficiency
- p.Gly39= Multiple submitters PSPH deficiency
- p.Gly53= Multiple submitters PSPH deficiency
- p.Leu68= Multiple submitters PSPH deficiency
- p.Leu68Pro Multiple submitters PSPH deficiency
- p.Pro57Ser Multiple submitters PSPH deficiency ⚠
- p.Thr63= Multiple submitters PSPH deficiency
- p.Val40= Multiple submitters PSPH deficiency
- c.-429G>T Single submitter PSPH deficiency
- c.*8T>C Single submitter PSPH deficiency
- p.Arg49Trp Single submitter PSPH deficiency
Benign/Likely benign 6
- c.-2C>G Multiple submitters PSPH deficiency
- c.-3G>A Multiple submitters PSPH deficiency
- p.Arg65His Multiple submitters PSPH deficiency
- p.Asp32Gly Multiple submitters PSPH deficiency
- p.Asp42= Multiple submitters PSPH deficiency
- p.Val2Ile Multiple submitters
Likely benign 52
- p.Arg49Gln Multiple submitters PSPH deficiency
- p.Thr24= Multiple submitters PSPH deficiency
- c.276-14A>G Single submitter PSPH deficiency
- c.276-17T>C Single submitter PSPH deficiency
- c.276-20T>G Single submitter PSPH deficiency
- c.276-4G>C Single submitter PSPH deficiency
- c.421+10T>C Single submitter PSPH deficiency
- c.421+12A>T Single submitter PSPH deficiency
- c.421+20A>G Single submitter PSPH deficiency
- c.421+20A>T Single submitter PSPH deficiency
- c.422-14A>C Single submitter PSPH deficiency
- c.422-14A>G Single submitter PSPH deficiency
- c.422-4T>G Single submitter PSPH deficiency
- c.570+12G>C Single submitter PSPH deficiency
- c.570+14G>A Single submitter PSPH deficiency
- c.570+19A>G Single submitter PSPH deficiency
- c.571-14_571-10del Single submitter PSPH deficiency
- c.571-5C>T Single submitter PSPH deficiency
- c.-442A>G Single submitter PSPH deficiency
- c.-456T>C Single submitter PSPH deficiency
- c.*317G>A Single submitter PSPH deficiency
- p.Ala144= Single submitter PSPH deficiency
- p.Ala181Val Single submitter PSPH deficiency
- p.Arg113= Single submitter PSPH deficiency
- p.Arg202= Single submitter PSPH deficiency
- p.Asn124= Single submitter PSPH deficiency
- p.Asn208= Single submitter PSPH deficiency
- p.Asp147= Single submitter PSPH deficiency
- p.Asp183= Single submitter PSPH deficiency
- p.Gln150= Single submitter PSPH deficiency
- p.Gln203= Single submitter PSPH deficiency
- p.Gln83His Single submitter PSPH deficiency
- p.Glu117= Single submitter PSPH deficiency
- p.Glu222= Single submitter
- p.Glu224= Single submitter PSPH deficiency
- p.Gly159= Single submitter PSPH deficiency
- p.Gly180= Single submitter PSPH deficiency
- p.Gly54Arg Single submitter Inborn genetic diseases
- p.Gly90Ser Single submitter
- p.His118= Single submitter PSPH deficiency
- p.Leu123= Single submitter PSPH deficiency
- p.Leu164Phe Single submitter Inborn genetic diseases
- p.Lys136= Single submitter PSPH deficiency
- p.Lys163= Single submitter PSPH deficiency
- p.Phe131= Single submitter PSPH deficiency
- p.Thr149= Single submitter PSPH deficiency
- p.Tyr138= Single submitter PSPH deficiency
- p.Val130= Single submitter PSPH deficiency
- p.Val205= Single submitter PSPH deficiency
- p.Val217= Single submitter PSPH deficiency
- c.140+7A>G No assertion criteria PSPH-related disorder
- c.276-9A>C No assertion criteria PSPH-related disorder
Uncertain significance 95
- c.422-3A>C Multiple submitters PSPH deficiency
- c.570+3A>G Multiple submitters PSPH deficiency
- c.570+5G>C Multiple submitters PSPH deficiency
- c.*341G>A Multiple submitters PSPH deficiency
- p.Asn124Ser Multiple submitters Inborn genetic diseases ⚠
- p.Asp32Asn Multiple submitters PSPH deficiency ⚠
- p.Gln204His Multiple submitters PSPH deficiency ⚠
- p.Glu117Asp Multiple submitters Inborn genetic diseases ⚠
- p.Glu225Lys Multiple submitters Inborn genetic diseases ⚠
- p.His118Arg Multiple submitters PSPH deficiency ⚠
- p.Tyr212Cys Multiple submitters Inborn genetic diseases ⚠
- c.276-2A>G Single submitter PSPH deficiency
- c.-130G>T Single submitter PSPH deficiency
- c.-145-15A>G Single submitter PSPH deficiency
- c.-228C>G Single submitter PSPH deficiency
- c.-22A>G Single submitter PSPH deficiency
- c.-396C>G Single submitter PSPH deficiency
- c.-430T>G Single submitter PSPH deficiency
- c.-461A>G Single submitter PSPH deficiency
- c.-485A>G Single submitter PSPH deficiency
- c.-519C>G Single submitter PSPH deficiency
- c.-94G>A Single submitter PSPH deficiency
- c.*12G>A Single submitter PSPH deficiency
- c.*157C>T Single submitter PSPH deficiency
- c.*203T>C Single submitter PSPH deficiency
- c.*22A>G Single submitter PSPH deficiency
- c.*277G>A Single submitter PSPH deficiency
- c.*278C>T Single submitter PSPH deficiency
- c.*309A>G Single submitter PSPH deficiency
- c.*316C>T Single submitter PSPH deficiency
- c.*371A>G Single submitter PSPH deficiency
- c.*457C>T Single submitter PSPH deficiency
- c.*46A>C Single submitter PSPH deficiency
- c.*588G>A Single submitter PSPH deficiency
- c.*649A>C Single submitter PSPH deficiency
- p.Ala120Ser Single submitter PSPH deficiency ⚠
- p.Ala127Thr Single submitter PSPH deficiency ⚠
- p.Ala190Pro Single submitter PSPH deficiency ⚠
- p.Ala192Thr Single submitter Inborn genetic diseases ⚠
- p.Ala209Thr Single submitter Inborn genetic diseases ⚠
- p.Ala43Val Single submitter Inborn genetic diseases ⚠
- p.Ala67Asp Single submitter Inborn genetic diseases ⚠
- p.Arg101Gln Single submitter PSPH deficiency ⚠
- p.Arg134Ser Single submitter PSPH deficiency ⚠
- p.Arg8Ser Single submitter Inborn genetic diseases
- p.Arg92= Single submitter PSPH deficiency
- p.Arg97Cys Single submitter PSPH deficiency ⚠
- p.Asn102_Val103insPhe Single submitter PSPH deficiency
- p.Asn102Ser Single submitter PSPH deficiency ⚠
- p.Asn124His Single submitter Inborn genetic diseases ⚠
- p.Asn129Ser Single submitter PSPH deficiency ⚠
- p.Asn133His Single submitter Inborn genetic diseases ⚠
- p.Asn133Ser Single submitter PSPH deficiency ⚠
- p.Asn140= Single submitter PSPH deficiency
- p.Asn199His Single submitter PSPH deficiency ⚠
- p.Asn199Ile Single submitter PSPH deficiency ⚠
- p.Asn199Lys Single submitter PSPH deficiency ⚠
- p.Asp191His Single submitter Inborn genetic diseases ⚠
- p.Asp20= Single submitter PSPH deficiency
- p.Asp42Val Single submitter Inborn genetic diseases ⚠
- p.Cys18Arg Single submitter ⚠
- p.Glu142Lys Single submitter PSPH deficiency ⚠
- p.Glu225Ala Single submitter PSPH deficiency ⚠
- p.Glu225Gln Single submitter PSPH deficiency ⚠
- p.Glu28Gln Single submitter Inborn genetic diseases
- p.Glu64Gly Single submitter Inborn genetic diseases ⚠
- p.Glu6Val Single submitter Inborn genetic diseases ⚠
- p.Gly141Ser Single submitter PSPH deficiency ⚠
- p.Gly156Asp Single submitter PSPH deficiency ⚠
- p.Gly157Ter Single submitter PSPH deficiency
- p.Gly198Glu Single submitter PSPH deficiency ⚠
- p.His170Arg Single submitter PSPH deficiency ⚠
- p.Ile162Val Single submitter PSPH deficiency ⚠
- p.Ile175Leu Single submitter Inborn genetic diseases ⚠
- p.Leu62Pro Single submitter Inborn genetic diseases ⚠
- p.Leu79Phe Single submitter PSPH deficiency ⚠
- p.Lys122Asn Single submitter PSPH deficiency ⚠
- p.Lys160Arg Single submitter PSPH deficiency ⚠
- p.Met184Arg Single submitter Inborn genetic diseases
- p.Phe106Leu Single submitter PSPH deficiency ⚠
- p.Phe169Ser Single submitter PSPH deficiency
- p.Phe216Cys Single submitter PSPH deficiency ⚠
- p.Phe58Leu Single submitter Inborn genetic diseases ⚠
- p.Pro84His Single submitter Inborn genetic diseases
- p.Ser114Ile Single submitter PSPH deficiency ⚠
- p.Ser155Phe Single submitter PSPH deficiency ⚠
- p.Thr149Met Single submitter PSPH deficiency ⚠
- p.Thr214Pro Single submitter PSPH deficiency ⚠
- p.Thr214Ser Single submitter PSPH deficiency ⚠
- p.Thr48Ile Single submitter Inborn genetic diseases ⚠
- p.Tyr12Asn Single submitter Inborn genetic diseases ⚠
- p.Val116Ile Single submitter PSPH deficiency ⚠
- p.Val161Met Single submitter PSPH deficiency ⚠
- p.Val40Phe Single submitter
- p.Gly90fs No assertion criteria