TUSC3 — 302 ClinVar variants

All ClinVar germline TUSC3 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 80 flagged for review →

8 Pathogenic · 2 Pathogenic/Likely pathogenic · 10 Likely pathogenic · 10 Conflicting · 40 Benign · 4 Benign/Likely benign · 64 Likely benign · 164 Uncertain significance

Full TUSC3 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 80

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 2

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

Predictors lean, ClinVar uncertain 67

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

All TUSC3 variants

Pathogenic 8

  • p.Gln141fs Multiple submitters intellectual disability, autosomal recessive 7
  • p.Gln177Ter Multiple submitters Inborn genetic diseases
  • c.567+1G>C Single submitter intellectual disability, autosomal recessive 7
  • p.Arg67Ter Single submitter
  • p.Arg82Ter Single submitter
  • p.Ser343Thr Single submitter intellectual disability, autosomal recessive 7 ⚠
  • p.Asn263fs No assertion criteria intellectual disability, autosomal recessive 7
  • p.Lys75fs No assertion criteria intellectual disability, autosomal recessive 7

Pathogenic/Likely pathogenic 2

  • p.Gln94fs Multiple submitters intellectual disability, autosomal recessive 7
  • p.Ser331Ter Multiple submitters TUSC3-related disorder

Likely pathogenic 10

  • p.Arg74Ter Multiple submitters intellectual disability, autosomal recessive 7
  • c.568-2A>G Single submitter intellectual disability, autosomal recessive 7
  • c.938-8_939del Single submitter Inborn genetic diseases
  • p.Gln55Ter Single submitter congenital nervous system disorder
  • p.Gln96Ter Single submitter intellectual disability, autosomal recessive 7
  • p.Trp181Ter Single submitter intellectual disability, autosomal recessive 7
  • p.Tyr109Ter Single submitter intellectual disability, autosomal recessive 7
  • p.Tyr19fs Single submitter intellectual disability, autosomal recessive 7
  • p.Gly41fs No assertion criteria intellectual disability, autosomal recessive 7
  • p.Ile238Met No assertion criteria intellectual disability ⚠

Conflicting classifications of pathogenicity 10

  • c.1029-5G>C Single submitter Inborn genetic diseases
  • c.1029-8T>C Single submitter intellectual disability, autosomal recessive 7
  • c.568-15A>G Single submitter intellectual disability, autosomal recessive 7
  • c.937+11G>C Single submitter congenital disorder of glycosylation
  • c.*1531A>G Single submitter congenital disorder of glycosylation
  • c.*1665T>C Single submitter congenital disorder of glycosylation
  • c.*2397G>A Single submitter congenital disorder of glycosylation
  • p.Gly136= Single submitter congenital disorder of glycosylation
  • p.Ile284= Single submitter congenital disorder of glycosylation
  • p.Tyr256= Single submitter Inborn genetic diseases

Benign 40

Benign/Likely benign 4

  • c.1028+11T>C Multiple submitters intellectual disability, autosomal recessive 7
  • p.Ile65Val Multiple submitters Inborn genetic diseases
  • p.Leu29= Multiple submitters Inborn genetic diseases
  • p.Ser304= Multiple submitters Inborn genetic diseases

Likely benign 64

  • c.1028+8C>G Multiple submitters intellectual disability, autosomal recessive 7
  • c.798+55G>A Multiple submitters
  • c.937+41C>G Multiple submitters
  • c.-108G>A Multiple submitters congenital disorder of glycosylation
  • c.-87C>T Multiple submitters congenital disorder of glycosylation
  • c.-88T>G Multiple submitters congenital disorder of glycosylation
  • c.*2138T>C Multiple submitters congenital disorder of glycosylation
  • c.*83A>C Multiple submitters congenital disorder of glycosylation
  • p.Ser85= Multiple submitters Inborn genetic diseases
  • p.Thr186= Multiple submitters Inborn genetic diseases
  • c.1029-4A>G Single submitter
  • c.1029-5G>A Single submitter intellectual disability, autosomal recessive 7
  • c.138+15C>T Single submitter intellectual disability, autosomal recessive 7
  • c.139-4G>A Single submitter intellectual disability, autosomal recessive 7
  • c.139-6T>C Single submitter intellectual disability, autosomal recessive 7
  • c.309-16C>T Single submitter intellectual disability, autosomal recessive 7
  • c.309-4T>C Single submitter
  • c.309-8C>G Single submitter intellectual disability, autosomal recessive 7
  • c.426+16G>A Single submitter intellectual disability, autosomal recessive 7
  • c.426+171AC[12] Single submitter
  • c.567+14C>T Single submitter intellectual disability, autosomal recessive 7
  • c.568-124C>T Single submitter
  • c.708+16G>T Single submitter intellectual disability, autosomal recessive 7
  • c.708+9A>G Single submitter
  • c.799-18G>C Single submitter intellectual disability, autosomal recessive 7
  • c.862+18C>T Single submitter intellectual disability, autosomal recessive 7
  • c.863-10A>C Single submitter
  • c.938-10C>G Single submitter intellectual disability, autosomal recessive 7
  • c.938-12G>C Single submitter intellectual disability, autosomal recessive 7
  • c.-273G>A Single submitter congenital disorder of glycosylation
  • c.-91G>A Single submitter congenital disorder of glycosylation
  • c.*2100C>A Single submitter congenital disorder of glycosylation
  • c.*2304C>G Single submitter congenital disorder of glycosylation
  • c.*2450A>G Single submitter congenital disorder of glycosylation
  • p.Ala113= Single submitter intellectual disability, autosomal recessive 7
  • p.Ala121= Single submitter intellectual disability, autosomal recessive 7
  • p.Ala13= Single submitter
  • p.Ala179= Single submitter Inborn genetic diseases
  • p.Ala203= Single submitter intellectual disability, autosomal recessive 7
  • p.Ala289= Single submitter intellectual disability, autosomal recessive 7
  • p.Arg82= Single submitter intellectual disability, autosomal recessive 7
  • p.Asp134= Single submitter
  • p.Cys35= Single submitter
  • p.Gln110= Single submitter Inborn genetic diseases
  • p.Ile225= Single submitter intellectual disability, autosomal recessive 7
  • p.Ile283= Single submitter intellectual disability, autosomal recessive 7
  • p.Leu168= Single submitter
  • p.Leu178= Single submitter
  • p.Leu207= Single submitter
  • p.Leu214= Single submitter intellectual disability, autosomal recessive 7
  • p.Leu31= Single submitter intellectual disability, autosomal recessive 7
  • p.Leu316= Single submitter intellectual disability, autosomal recessive 7
  • p.Leu32= Single submitter intellectual disability, autosomal recessive 7
  • p.Leu56= Single submitter Inborn genetic diseases
  • p.Phe154= Single submitter
  • p.Pro195= Single submitter
  • p.Pro21= Single submitter intellectual disability, autosomal recessive 7
  • p.Tyr198= Single submitter Inborn genetic diseases
  • p.Tyr216= Single submitter intellectual disability, autosomal recessive 7
  • p.Val239= Single submitter
  • p.Val308= Single submitter intellectual disability, autosomal recessive 7
  • p.Val317= Single submitter Inborn genetic diseases
  • p.Val53= Single submitter intellectual disability, autosomal recessive 7
  • p.Gly5= No assertion criteria TUSC3-related disorder

Uncertain significance 164

  • c.*1197G>A Multiple submitters congenital disorder of glycosylation
  • c.*1957A>G Multiple submitters congenital disorder of glycosylation
  • c.*46+1G>A Multiple submitters
  • p.Ala13Val Multiple submitters congenital disorder of glycosylation ⚠
  • p.Arg159Lys Multiple submitters Inborn genetic diseases ⚠
  • p.Arg15Gln Multiple submitters Inborn genetic diseases ⚠
  • p.Arg15Pro Multiple submitters Inborn genetic diseases ⚠
  • p.Arg312Trp Multiple submitters Inborn genetic diseases ⚠
  • p.Arg9Gly Multiple submitters congenital disorder of glycosylation ⚠
  • p.Leu217Met Multiple submitters Inborn genetic diseases ⚠
  • p.Pro7Ser Multiple submitters intellectual disability, autosomal recessive 7 ⚠
  • p.Ser8Leu Multiple submitters congenital disorder of glycosylation ⚠
  • c.139-17del Single submitter
  • c.308+3A>G Single submitter intellectual disability, autosomal recessive 7
  • c.309-10T>C Single submitter intellectual disability, autosomal recessive 7
  • c.309-3C>G Single submitter intellectual disability, autosomal recessive 7
  • c.426+13A>T Single submitter congenital disorder of glycosylation
  • c.426+15C>T Single submitter congenital disorder of glycosylation
  • c.568-4_568-3delinsAT Single submitter Inborn genetic diseases
  • c.863-2A>G Single submitter
  • c.-111C>A Single submitter congenital disorder of glycosylation
  • c.-130C>G Single submitter congenital disorder of glycosylation
  • c.-159C>T Single submitter congenital disorder of glycosylation
  • c.-167G>A Single submitter congenital disorder of glycosylation
  • c.-190C>T Single submitter congenital disorder of glycosylation
  • c.-191C>T Single submitter congenital disorder of glycosylation
  • c.-206C>T Single submitter congenital disorder of glycosylation
  • c.-254C>A Single submitter congenital disorder of glycosylation
  • c.-289A>G Single submitter congenital disorder of glycosylation
  • c.-303C>G Single submitter congenital disorder of glycosylation
  • c.-304G>T Single submitter congenital disorder of glycosylation
  • c.-358A>G Single submitter congenital disorder of glycosylation
  • c.-46G>C Single submitter congenital disorder of glycosylation
  • c.-48C>T Single submitter congenital disorder of glycosylation
  • c.-4C>T Single submitter
  • c.-51G>A Single submitter congenital disorder of glycosylation
  • c.-82A>G Single submitter congenital disorder of glycosylation
  • c.*1009C>A Single submitter congenital disorder of glycosylation
  • c.*1024T>C Single submitter congenital disorder of glycosylation
  • c.*1078C>G Single submitter congenital disorder of glycosylation
  • c.*111G>A Single submitter congenital disorder of glycosylation
  • c.*1191C>T Single submitter congenital disorder of glycosylation
  • c.*128A>G Single submitter congenital disorder of glycosylation
  • c.*1313G>A Single submitter congenital disorder of glycosylation
  • c.*1371T>G Single submitter congenital disorder of glycosylation
  • c.*1391T>C Single submitter congenital disorder of glycosylation
  • c.*1581C>T Single submitter congenital disorder of glycosylation
  • c.*1607T>C Single submitter congenital disorder of glycosylation
  • c.*1723T>G Single submitter congenital disorder of glycosylation
  • c.*1737C>T Single submitter congenital disorder of glycosylation
  • c.*1861A>G Single submitter congenital disorder of glycosylation
  • c.*188C>T Single submitter congenital disorder of glycosylation
  • c.*1973T>A Single submitter congenital disorder of glycosylation
  • c.*2037G>C Single submitter congenital disorder of glycosylation
  • c.*2057T>C Single submitter congenital disorder of glycosylation
  • c.*2101A>G Single submitter congenital disorder of glycosylation
  • c.*2131G>T Single submitter congenital disorder of glycosylation
  • c.*2146A>T Single submitter congenital disorder of glycosylation
  • c.*217C>T Single submitter congenital disorder of glycosylation
  • c.*2183G>A Single submitter congenital disorder of glycosylation
  • c.*222A>G Single submitter congenital disorder of glycosylation
  • c.*2241T>C Single submitter congenital disorder of glycosylation
  • c.*2277A>G Single submitter congenital disorder of glycosylation
  • c.*2283T>C Single submitter congenital disorder of glycosylation
  • c.*2316A>G Single submitter congenital disorder of glycosylation
  • c.*2363G>T Single submitter congenital disorder of glycosylation
  • c.*2371C>T Single submitter congenital disorder of glycosylation
  • c.*2393A>G Single submitter congenital disorder of glycosylation
  • c.*2407G>A Single submitter congenital disorder of glycosylation
  • c.*286C>G Single submitter congenital disorder of glycosylation
  • c.*288G>A Single submitter congenital disorder of glycosylation
  • c.*341A>G Single submitter congenital disorder of glycosylation
  • c.*364G>C Single submitter congenital disorder of glycosylation
  • c.*36T>G Single submitter congenital disorder of glycosylation
  • c.*499G>A Single submitter congenital disorder of glycosylation
  • c.*510C>A Single submitter congenital disorder of glycosylation
  • c.*566G>A Single submitter congenital disorder of glycosylation
  • c.*589G>A Single submitter congenital disorder of glycosylation
  • c.*686A>C Single submitter congenital disorder of glycosylation
  • c.*732G>A Single submitter congenital disorder of glycosylation
  • c.*763A>C Single submitter congenital disorder of glycosylation
  • c.*869A>C Single submitter congenital disorder of glycosylation
  • c.*947A>G Single submitter congenital disorder of glycosylation
  • c.*98A>G Single submitter congenital disorder of glycosylation
  • p.Ala113Val Single submitter Inborn genetic diseases ⚠
  • p.Ala174Thr Single submitter Inborn genetic diseases ⚠
  • p.Ala175Pro Single submitter Inborn genetic diseases ⚠
  • p.Ala179Thr Single submitter intellectual disability, autosomal recessive 7 ⚠
  • p.Ala179Val Single submitter ⚠
  • p.Ala232Ser Single submitter Inborn genetic diseases ⚠
  • p.Ala275Ser Single submitter Inborn genetic diseases ⚠
  • p.Ala290Ser Single submitter Inborn genetic diseases ⚠
  • p.Ala290Thr Single submitter intellectual disability, autosomal recessive 7
  • p.Ala6Ser Single submitter Inborn genetic diseases ⚠
  • p.Ala6Val Single submitter congenital disorder of glycosylation ⚠
  • p.Arg11Gly Single submitter intellectual disability, autosomal recessive 7 ⚠
  • p.Arg162Gly Single submitter ⚠
  • p.Arg18Gln Single submitter intellectual disability, autosomal recessive 7 ⚠
  • p.Arg194Thr Single submitter intellectual disability, autosomal recessive 7 ⚠
  • p.Arg62Ile Single submitter Inborn genetic diseases ⚠
  • p.Arg63= Single submitter congenital disorder of glycosylation
  • p.Arg63Cys Single submitter intellectual disability, autosomal recessive 7 ⚠
  • p.Arg63Gly Single submitter Inborn genetic diseases ⚠
  • p.Arg63Pro Single submitter Inborn genetic diseases ⚠
  • p.Arg67Gln Single submitter Inborn genetic diseases
  • p.Arg74Gln Single submitter intellectual disability, autosomal recessive 7 ⚠
  • p.Arg82Gly Single submitter intellectual disability, autosomal recessive 7 ⚠
  • p.Arg97Gln Single submitter ⚠
  • p.Arg9Leu Single submitter Inborn genetic diseases ⚠
  • p.Asn114Lys Single submitter Inborn genetic diseases ⚠
  • p.Asn144Ser Single submitter Inborn genetic diseases ⚠
  • p.Asn220Asp Single submitter Inborn genetic diseases
  • p.Asn220Lys Single submitter Inborn genetic diseases ⚠
  • p.Asn260Lys Single submitter Inborn genetic diseases ⚠
  • p.Asn263Ser Single submitter Inborn genetic diseases ⚠
  • p.Asn288Ile Single submitter intellectual disability, autosomal recessive 7 ⚠
  • p.Asp138Glu Single submitter Inborn genetic diseases ⚠
  • p.Asp346His Single submitter Inborn genetic diseases ⚠
  • p.Cys102Arg Single submitter Inborn genetic diseases ⚠
  • p.Gln94Leu Single submitter Inborn genetic diseases ⚠
  • p.Glu280Lys Single submitter congenital disorder of glycosylation ⚠
  • p.Glu348Ter Single submitter Inborn genetic diseases
  • p.Glu54Asp Single submitter Inborn genetic diseases ⚠
  • p.Gly23Arg Single submitter intellectual disability, autosomal recessive 7 ⚠
  • p.Gly271Arg Single submitter Inborn genetic diseases ⚠
  • p.Gly39Ala Single submitter Inborn genetic diseases ⚠
  • p.Gly39Arg Single submitter Inborn genetic diseases ⚠
  • p.Gly39Val Single submitter intellectual disability, autosomal recessive 7 ⚠
  • p.His153Arg Single submitter Inborn genetic diseases ⚠
  • p.Ile111Met Single submitter Inborn genetic diseases ⚠
  • p.Ile190Val Single submitter Inborn genetic diseases ⚠
  • p.Ile225Met Single submitter Inborn genetic diseases ⚠
  • p.Ile225Val Single submitter Inborn genetic diseases ⚠
  • p.Ile238Val Single submitter Inborn genetic diseases ⚠
  • p.Ile283Val Single submitter Inborn genetic diseases ⚠
  • p.Ile332Thr Single submitter Inborn genetic diseases ⚠
  • p.Ile77Leu Single submitter Inborn genetic diseases ⚠
  • p.Ile87Val Single submitter congenital disorder of glycosylation ⚠
  • p.Leu29Phe Single submitter intellectual disability, autosomal recessive 7 ⚠
  • p.Leu345Val Single submitter Inborn genetic diseases ⚠
  • p.Leu34del Single submitter intellectual disability, autosomal recessive 7
  • p.Leu34dup Single submitter
  • p.Leu48Ile Single submitter intellectual disability, autosomal recessive 7 ⚠
  • p.Lys161Arg Single submitter congenital disorder of glycosylation ⚠
  • p.Met1Ile Single submitter congenital disorder of glycosylation
  • p.Met233Val Single submitter Inborn genetic diseases ⚠
  • p.Met89Thr Single submitter Inborn genetic diseases ⚠
  • p.Phe224Val Single submitter intellectual disability, autosomal recessive 7 ⚠
  • p.Pro156Arg Single submitter Inborn genetic diseases ⚠
  • p.Pro21Arg Single submitter congenital disorder of glycosylation ⚠
  • p.Pro21Ser Single submitter Inborn genetic diseases ⚠
  • p.Pro80Ala Single submitter intellectual disability, autosomal recessive 7 ⚠
  • p.Pro80Leu Single submitter Inborn genetic diseases ⚠
  • p.Pro80Ser Single submitter Inborn genetic diseases ⚠
  • p.Pro95Ala Single submitter ⚠
  • p.Ser281= Single submitter congenital disorder of glycosylation
  • p.Thr165Ala Single submitter Inborn genetic diseases ⚠
  • p.Thr186Met Single submitter intellectual disability, autosomal recessive 7 ⚠
  • p.Thr229Ala Single submitter Inborn genetic diseases ⚠
  • p.Thr303Ser Single submitter ⚠
  • p.Tyr226Cys Single submitter Inborn genetic diseases ⚠
  • p.Val139Ile Single submitter Inborn genetic diseases ⚠
  • p.Val266= Single submitter Inborn genetic diseases
  • p.Val323Leu Single submitter Inborn genetic diseases