SRPK3 — 160 ClinVar variants

All ClinVar germline SRPK3 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 125 flagged for review →

3 Pathogenic · 2 Likely pathogenic · 5 Conflicting · 5 Benign · 1 Benign/Likely benign · 12 Likely benign · 132 Uncertain significance

Full SRPK3 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 125

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 3

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

SRPK3 p.Arg101Cys Conflicting Single submitter
SRPK3 p.His159Tyr Conflicting Single submitter
autosomal recessive limb-girdle muscular dystrophy type 2J
SRPK3 p.Val40Glu Conflicting Single submitter

Predictors lean, ClinVar uncertain 96

ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.

Predictors split 26

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

All SRPK3 variants

Pathogenic 3

p.Pro68fs Single submitter congenital myopathy
p.His159Asp No assertion criteria intellectual developmental disorder, X-linked 114
p.Thr458Asn No assertion criteria intellectual developmental disorder, X-linked 114 ⚠

Likely pathogenic 2

p.Gly340fs Single submitter
p.Ile71fs Single submitter intellectual developmental disorder, X-linked 114

Conflicting classifications of pathogenicity 5

p.Arg101Cys Single submitter ⚠
p.Arg131Gln Single submitter ⚠
p.His159Tyr Single submitter autosomal recessive limb-girdle muscular dystrophy type 2J ⚠
p.Ser335Tyr Single submitter ⚠
p.Val40Glu Single submitter ⚠

Benign 5

c.907+15A>G Multiple submitters
c.907+6G>A Multiple submitters
p.Gly340Val Multiple submitters
p.Lys205= Multiple submitters
p.Phe492= Single submitter

Benign/Likely benign 1

p.Ala35= Multiple submitters

Likely benign 12

p.Ala23_Ser30del Single submitter
p.Ala535= Single submitter
p.Asp51= Single submitter
p.Asp52Asn Single submitter ⚠
p.Gly15Ser Single submitter
p.Gly324= Single submitter
p.His197= Single submitter
p.Ser112= Single submitter
p.Ser248= Single submitter
p.Thr299Ala Single submitter
p.Val40Ala Single submitter
p.Ser539= No assertion criteria SRPK3-related disorder

Uncertain significance 132

p.Ala106Val Multiple submitters ⚠
p.Glu455Lys Multiple submitters familial dilated cardiomyopathy ⚠
p.Gly8Asp Multiple submitters ⚠
c.1356+3A>C Single submitter
c.1519+1G>A Single submitter intellectual developmental disorder, X-linked 114
c.387+1G>A Single submitter
c.388-2A>G Single submitter
c.583-5T>A Single submitter
c.749-2A>G Single submitter multiminicore myopathy
c.775-2A>G Single submitter
p.Ala225Thr Single submitter ⚠
p.Ala298Val Single submitter ⚠
p.Ala346Thr Single submitter ⚠
p.Ala346Val Single submitter ⚠
p.Ala413Thr Single submitter ⚠
p.Ala540Thr Single submitter ⚠
p.Ala557Thr Single submitter ⚠
p.Arg101His Single submitter ⚠
p.Arg151Lys Single submitter ⚠
p.Arg229His Single submitter ⚠
p.Arg247Cys Single submitter ⚠
p.Arg247His Single submitter ⚠
p.Arg280Gln Single submitter ⚠
p.Arg280Trp Single submitter ⚠
p.Arg285Gln Single submitter ⚠
p.Arg285Trp Single submitter ⚠
p.Arg287Gln Single submitter ⚠
p.Arg287Trp Single submitter ⚠
p.Arg342Cys Single submitter ⚠
p.Arg342His Single submitter ⚠
p.Arg373Gln Single submitter ⚠
p.Arg373Ter Single submitter
p.Arg427Gln Single submitter ⚠
p.Arg427Trp Single submitter ⚠
p.Arg430Trp Single submitter ⚠
p.Arg473His Single submitter ⚠
p.Arg473Pro Single submitter ⚠
p.Arg497His Single submitter
p.Arg500Gln Single submitter ⚠
p.Arg505Trp Single submitter ⚠
p.Arg78Gln Single submitter ⚠
p.Asn504Asp Single submitter ⚠
p.Asn514Ser Single submitter ⚠
p.Asp401Val Single submitter ⚠
p.Asp423Asn Single submitter ⚠
p.Asp60Asn Single submitter ⚠
p.Asp60Gly Single submitter ⚠
p.Cys129Arg Single submitter ⚠
p.Cys206Phe Single submitter ⚠
p.Cys62Ser Single submitter ⚠
p.Cys96Tyr Single submitter ⚠
p.Gln100Pro Single submitter intellectual developmental disorder, X-linked 114 ⚠
p.Gln277His Single submitter ⚠
p.Gln42His Single submitter ⚠
p.Gln537Glu Single submitter ⚠
p.Glu141Gln Single submitter ⚠
p.Glu216Gln Single submitter ⚠
p.Glu233Asp Single submitter ⚠
p.Glu233Lys Single submitter ⚠
p.Glu256Val Single submitter ⚠
p.Glu28Asp Single submitter ⚠
p.Glu28Gln Single submitter ⚠
p.Glu28Lys Single submitter ⚠
p.Glu33Asp Single submitter ⚠
p.Glu33Lys Single submitter ⚠
p.Glu422Ala Single submitter ⚠
p.Glu439Lys Single submitter ⚠
p.Glu522Lys Single submitter intellectual developmental disorder, X-linked 114 ⚠
p.Glu529Ala Single submitter ⚠
p.Glu53Lys Single submitter ⚠
p.Glu54fs Single submitter
p.Glu551Lys Single submitter ⚠
p.Gly13Ser Single submitter ⚠
p.Gly154Glu Single submitter ⚠
p.Gly198Ser Single submitter ⚠
p.Gly223Trp Single submitter ⚠
p.Gly261Ser Single submitter ⚠
p.Gly26Arg Single submitter ⚠
p.Gly26Glu Single submitter ⚠
p.Gly311Asp Single submitter ⚠
p.Gly319Ser Single submitter ⚠
p.Gly323Arg Single submitter ⚠
p.Gly328Val Single submitter ⚠
p.Gly347Asp Single submitter ⚠
p.Gly352Asp Single submitter ⚠
p.Gly376Arg Single submitter ⚠
p.Gly459Val Single submitter ⚠
p.Gly519Ser Single submitter ⚠
p.Gly6Ala Single submitter ⚠
p.Gly72Asp Single submitter ⚠
p.Gly86Asp Single submitter ⚠
p.Gly86Cys Single submitter intellectual developmental disorder, X-linked 114 ⚠
p.Ile403Val Single submitter ⚠
p.Ile446Ser Single submitter ⚠
p.Ile481Thr Single submitter ⚠
p.Ile71Thr Single submitter
p.Ile99Ser Single submitter ⚠
p.Leu220Gln Single submitter ⚠
p.Lys269Thr Single submitter neurodevelopmental disorder ⚠
p.Lys63fs Single submitter
p.Phe503Leu Single submitter ⚠
p.Phe541Leu Single submitter ⚠
p.Pro135His Single submitter ⚠
p.Pro186Ser Single submitter ⚠
p.Pro215Leu Single submitter ⚠
p.Pro243Leu Single submitter ⚠
p.Pro244Ser Single submitter ⚠
p.Pro245His Single submitter ⚠
p.Pro336fs Single submitter
p.Pro394Leu Single submitter ⚠
p.Pro397Ala Single submitter ⚠
p.Pro465Leu Single submitter ⚠
p.Pro490Gln Single submitter ⚠
p.Pro58His Single submitter ⚠
p.Ser136Asn Single submitter ⚠
p.Ser317Ala Single submitter ⚠
p.Thr235Ala Single submitter ⚠
p.Thr252Ser Single submitter ⚠
p.Thr350Ile Single submitter ⚠
p.Thr421Lys Single submitter ⚠
p.Thr449Ala Single submitter ⚠
p.Trp174Cys Single submitter ⚠
p.Trp237Ter Single submitter
p.Tyr528Cys Single submitter ⚠
p.Val105Ala Single submitter ⚠
p.Val158Ala Single submitter ⚠
p.Val158Ile Single submitter ⚠
p.Val163Met Single submitter ⚠
p.Val257Ile Single submitter ⚠
p.Val432Ile Single submitter ⚠
p.Val74Met Single submitter ⚠
p.Val82Met Single submitter ⚠