SPRED1 — 1197 ClinVar variants

All ClinVar germline SPRED1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 546 flagged for review →

90 Pathogenic · 15 Pathogenic/Likely pathogenic · 47 Likely pathogenic · 65 Conflicting · 43 Benign · 17 Benign/Likely benign · 283 Likely benign · 637 Uncertain significance

Full SPRED1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 546

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 39

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

Predicted LoF vs a conflicting call 2

ClinVar submitters conflict, and it's a predicted loss-of-function change in a gene where LoF causes disease — flagged for review, not resolved (verify NMD-escape for C-terminal truncations). Non-missense.

Predictors lean, ClinVar uncertain 422

ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification. · showing the 150 best-reviewed of 422

Predictors split 83

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

All SPRED1 variants

Pathogenic 90

Pathogenic/Likely pathogenic 15

Likely pathogenic 47

Conflicting classifications of pathogenicity 65

Benign 43

Benign/Likely benign 17

  • c.207+15A>G Multiple submitters Legius syndrome
  • c.207+37A>G Multiple submitters Legius syndrome
  • c.32+20C>T Multiple submitters Legius syndrome
  • c.376+3A>T Multiple submitters Cardiovascular phenotype
  • c.377-10A>G Multiple submitters Legius syndrome
  • c.582+17T>A Multiple submitters Legius syndrome
  • c.583-7A>G Multiple submitters Noonan syndrome and Noonan-related syndrome
  • c.685-8T>C Multiple submitters Noonan syndrome and Noonan-related syndrome
  • c.*256C>T Multiple submitters Noonan syndrome and Noonan-related syndrome
  • p.Ala409Ser Multiple submitters Cardiovascular phenotype ⚠
  • p.Ala409Val Multiple submitters Cardiovascular phenotype ⚠
  • p.Asn10Lys Multiple submitters Legius syndrome
  • p.Asp398Asn Multiple submitters Cardiovascular phenotype
  • p.Asp9Val Multiple submitters Noonan syndrome and Noonan-related syndrome
  • p.Lys97Arg Multiple submitters Legius syndrome
  • p.Ser149Asn Multiple submitters Legius syndrome
  • p.Val212Ile Multiple submitters Noonan syndrome and Noonan-related syndrome

Likely benign 283

  • c.207+10A>G Multiple submitters Legius syndrome
  • c.33-11A>G Multiple submitters Legius syndrome
  • c.582+16A>G Multiple submitters Legius syndrome
  • c.583-9G>T Multiple submitters Legius syndrome
  • c.685-17A>G Multiple submitters Legius syndrome
  • c.*3057A>G Multiple submitters Legius syndrome
  • c.*3561G>A Multiple submitters Legius syndrome
  • c.*3591C>T Multiple submitters Legius syndrome
  • c.*5202C>T Multiple submitters Legius syndrome
  • p.Ala107= Multiple submitters Cardiovascular phenotype
  • p.Ala111= Multiple submitters Cardiovascular phenotype
  • p.Ala134= Multiple submitters Legius syndrome
  • p.Ala142= Multiple submitters Cardiovascular phenotype
  • p.Ala183= Multiple submitters Legius syndrome
  • p.Ala192= Multiple submitters Legius syndrome
  • p.Ala355= Multiple submitters Cardiovascular phenotype
  • p.Ala432= Multiple submitters Legius syndrome
  • p.Ala56= Multiple submitters Cardiovascular phenotype
  • p.Arg18= Multiple submitters Cardiovascular phenotype
  • p.Arg61= Multiple submitters Cardiovascular phenotype
  • p.Asn53= Multiple submitters Cardiovascular phenotype
  • p.Asp146= Multiple submitters Legius syndrome
  • p.Asp382= Multiple submitters Cardiovascular phenotype
  • p.Asp386= Multiple submitters Legius syndrome
  • p.Asp397= Multiple submitters Cardiovascular phenotype
  • p.Asp398= Multiple submitters Legius syndrome
  • p.Asp9= Multiple submitters Cardiovascular phenotype
  • p.Cys127= Multiple submitters Cardiovascular phenotype
  • p.Cys296= Multiple submitters Legius syndrome
  • p.Cys296Arg Multiple submitters Cardiovascular phenotype
  • p.Cys401= Multiple submitters Legius syndrome
  • p.Cys426= Multiple submitters Cardiovascular phenotype
  • p.Cys429= Multiple submitters Legius syndrome
  • p.Cys433= Multiple submitters Cardiovascular phenotype
  • p.Gln215His Multiple submitters Legius syndrome
  • p.Gln281= Multiple submitters Cardiovascular phenotype
  • p.Glu145= Multiple submitters Legius syndrome
  • p.Glu3= Multiple submitters Legius syndrome
  • p.Gly100= Multiple submitters Cardiovascular phenotype
  • p.Gly136= Multiple submitters Cardiovascular phenotype
  • p.Gly198= Multiple submitters Cardiovascular phenotype
  • p.Gly30= Multiple submitters Cardiovascular phenotype
  • p.Gly330= Multiple submitters Legius syndrome
  • p.Ile116= Multiple submitters Cardiovascular phenotype
  • p.Leu293= Multiple submitters Legius syndrome
  • p.Leu302= Multiple submitters Legius syndrome
  • p.Leu318= Multiple submitters Legius syndrome
  • p.Leu370= Multiple submitters Legius syndrome
  • p.Leu39= Multiple submitters Cardiovascular phenotype
  • p.Leu402= Multiple submitters Legius syndrome
  • p.Leu405= Multiple submitters Legius syndrome
  • p.Lys153= Multiple submitters Legius syndrome
  • p.Lys284= Multiple submitters Cardiovascular phenotype
  • p.Lys324= Multiple submitters Cardiovascular phenotype
  • p.Lys360= Multiple submitters Cardiovascular phenotype
  • p.Phe59= Multiple submitters Cardiovascular phenotype
  • p.Pro128= Multiple submitters Cardiovascular phenotype
  • p.Pro390= Multiple submitters Cardiovascular phenotype
  • p.Pro415= Multiple submitters Cardiovascular phenotype
  • p.Ser13= Multiple submitters Cardiovascular phenotype
  • p.Ser190= Multiple submitters Cardiovascular phenotype
  • p.Ser208= Multiple submitters Legius syndrome
  • p.Ser279= Multiple submitters Cardiovascular phenotype
  • p.Ser287= Multiple submitters Cardiovascular phenotype
  • p.Ser295= Multiple submitters Cardiovascular phenotype
  • p.Ser304= Multiple submitters Cardiovascular phenotype
  • p.Ser333= Multiple submitters Legius syndrome
  • p.Ser381= Multiple submitters Cardiovascular phenotype
  • p.Ser396= Multiple submitters Legius syndrome
  • p.Ser41= Multiple submitters Cardiovascular phenotype
  • p.Thr196= Multiple submitters Cardiovascular phenotype
  • p.Thr23= Multiple submitters Legius syndrome
  • p.Thr313= Multiple submitters Cardiovascular phenotype
  • p.Thr395= Multiple submitters Legius syndrome
  • p.Thr5= Multiple submitters Cardiovascular phenotype
  • p.Thr7= Multiple submitters Legius syndrome
  • p.Tyr187= Multiple submitters Cardiovascular phenotype
  • p.Tyr211= Multiple submitters Cardiovascular phenotype
  • p.Tyr420= Multiple submitters Cardiovascular phenotype
  • p.Val17= Multiple submitters Cardiovascular phenotype
  • p.Val20= Multiple submitters Cardiovascular phenotype
  • p.Val229= Multiple submitters Cardiovascular phenotype
  • p.Val336= Multiple submitters Legius syndrome
  • p.Val408= Multiple submitters Cardiovascular phenotype
  • c.207+11A>T Single submitter Legius syndrome
  • c.207+12T>C Single submitter Legius syndrome
  • c.207+13G>A Single submitter Legius syndrome
  • c.207+16T>G Single submitter Legius syndrome
  • c.207+19A>G Single submitter Legius syndrome
  • c.208-10C>G Single submitter Legius syndrome
  • c.208-11G>A Single submitter Legius syndrome
  • c.208-12G>C Single submitter Legius syndrome
  • c.32+12A>G Single submitter Legius syndrome
  • c.32+13T>C Single submitter Legius syndrome
  • c.32+14T>C Single submitter Legius syndrome
  • c.32+162G>A Single submitter
  • c.32+16A>G Single submitter Legius syndrome
  • c.32+18C>G Single submitter Legius syndrome
  • c.32+18C>T Single submitter Legius syndrome
  • c.32+3_32+6dup Single submitter Legius syndrome
  • c.32+9C>T Single submitter Legius syndrome
  • c.33-13del Single submitter Legius syndrome
  • c.33-14T>C Single submitter Legius syndrome
  • c.33-7A>G Single submitter Legius syndrome
  • c.376+10C>A Single submitter Legius syndrome
  • c.376+14A>G Single submitter Legius syndrome
  • c.376+17A>G Single submitter Legius syndrome
  • c.376+19T>G Single submitter Legius syndrome
  • c.376+9T>G Single submitter Legius syndrome
  • c.377-12C>T Single submitter Legius syndrome
  • c.377-16T>C Single submitter Legius syndrome
  • c.377-16T>G Single submitter Legius syndrome
  • c.377-19del Single submitter Legius syndrome
  • c.377-201A>G Single submitter
  • c.377-21_377-18del Single submitter Legius syndrome
  • c.423+10G>T Single submitter Legius syndrome
  • c.423+11G>A Single submitter Legius syndrome
  • c.423+17A>G Single submitter Legius syndrome
  • c.423+19G>A Single submitter Legius syndrome
  • c.423+20G>A Single submitter Legius syndrome
  • c.423+8A>G Single submitter Legius syndrome
  • c.424-14G>A Single submitter Legius syndrome
  • c.424-15G>A Single submitter Legius syndrome
  • c.424-16G>A Single submitter Legius syndrome
  • c.424-19T>C Single submitter Legius syndrome
  • c.424-19T>G Single submitter Legius syndrome
  • c.582+18T>C Single submitter Legius syndrome
  • c.583-14T>C Single submitter
  • c.583-15T>C Single submitter Legius syndrome
  • c.583-18A>C Single submitter Legius syndrome
  • c.583-20A>T Single submitter Legius syndrome
  • c.583-8T>C Single submitter Legius syndrome
  • c.684+10G>A Single submitter Legius syndrome
  • c.684+133A>G Single submitter
  • c.684+13A>G Single submitter Legius syndrome
  • c.684+14G>A Single submitter Legius syndrome
  • c.684+20C>G Single submitter Legius syndrome
  • c.685-10T>G Single submitter Legius syndrome
  • c.685-13G>A Single submitter Legius syndrome
  • c.685-15_685-14del Single submitter Legius syndrome
  • c.685-17A>T Single submitter Legius syndrome
  • c.685-19T>C Single submitter
  • c.-191C>T Single submitter Legius syndrome
  • c.-294CT[2] Single submitter RASopathy
  • c.-332G>A Single submitter
  • c.*1040G>A Single submitter Legius syndrome
  • c.*2018T>G Single submitter Legius syndrome
  • c.*2247A>G Single submitter Legius syndrome
  • c.*2570T>C Single submitter Legius syndrome
  • c.*2611C>T Single submitter Legius syndrome
  • c.*2885G>A Single submitter Legius syndrome
  • c.*3623G>T Single submitter Legius syndrome
  • c.*4372A>G Single submitter Legius syndrome
  • c.*4697G>A Single submitter Legius syndrome
  • c.*581T>C Single submitter Legius syndrome
  • c.*633A>G Single submitter Legius syndrome
  • p.Ala109= Single submitter Cardiovascular phenotype
  • p.Ala119= Single submitter Cardiovascular phenotype
  • p.Ala15= Single submitter
  • p.Ala259= Single submitter Legius syndrome
  • p.Ala276= Single submitter Cardiovascular phenotype
  • p.Ala406= Single submitter Legius syndrome
  • p.Ala443= Single submitter Legius syndrome
  • p.Ala6= Single submitter Legius syndrome
  • p.Arg184= Single submitter Legius syndrome
  • p.Arg207= Single submitter Legius syndrome
  • p.Arg214= Single submitter Cardiovascular phenotype
  • p.Arg235= Single submitter Cardiovascular phenotype
  • p.Arg24= Single submitter Cardiovascular phenotype
  • p.Arg251= Single submitter Legius syndrome
  • p.Arg325= Single submitter Cardiovascular phenotype
  • p.Arg326= Single submitter Cardiovascular phenotype
  • p.Arg341= Single submitter Legius syndrome
  • p.Arg349= Single submitter Cardiovascular phenotype
  • p.Arg428= Single submitter Cardiovascular phenotype
  • p.Asn182= Single submitter Legius syndrome
  • p.Asn227= Single submitter Cardiovascular phenotype
  • p.Asn347= Single submitter Cardiovascular phenotype
  • p.Asp11= Single submitter Cardiovascular phenotype
  • p.Asp113= Single submitter Legius syndrome
  • p.Asp26= Single submitter Cardiovascular phenotype
  • p.Asp260= Single submitter Cardiovascular phenotype
  • p.Asp275= Single submitter Cardiovascular phenotype
  • p.Asp277= Single submitter Cardiovascular phenotype
  • p.Asp329Gly Single submitter Cardiovascular phenotype ⚠
  • p.Asp389= Single submitter Cardiovascular phenotype
  • p.Asp57= Single submitter Cardiovascular phenotype
  • p.Asp96= Single submitter Legius syndrome
  • p.Cys220= Single submitter Cardiovascular phenotype
  • p.Cys338= Single submitter Cardiovascular phenotype
  • p.Cys362= Single submitter Cardiovascular phenotype
  • p.Cys371= Single submitter Cardiovascular phenotype
  • p.Cys418= Single submitter Legius syndrome
  • p.Cys419= Single submitter Legius syndrome
  • p.Cys435= Single submitter Cardiovascular phenotype
  • p.Gln191= Single submitter Cardiovascular phenotype
  • p.Gln215= Single submitter Cardiovascular phenotype
  • p.Gln281His Single submitter Cardiovascular phenotype
  • p.Gln353= Single submitter Cardiovascular phenotype
  • p.Glu121= Single submitter Legius syndrome
  • p.Glu129= Single submitter Cardiovascular phenotype
  • p.Glu135= Single submitter Cardiovascular phenotype
  • p.Glu242= Single submitter Cardiovascular phenotype
  • p.Glu244= Single submitter Cardiovascular phenotype
  • p.Glu272= Single submitter Cardiovascular phenotype
  • p.Glu299= Single submitter Cardiovascular phenotype
  • p.Glu328= Single submitter Cardiovascular phenotype
  • p.Glu63= Single submitter Cardiovascular phenotype
  • p.Glu73= Single submitter Cardiovascular phenotype
  • p.Gly126= Single submitter Cardiovascular phenotype
  • p.Gly221= Single submitter Cardiovascular phenotype
  • p.Gly297= Single submitter Cardiovascular phenotype
  • p.Gly36= Single submitter Legius syndrome
  • p.Gly434= Single submitter Cardiovascular phenotype
  • p.Gly444= Single submitter Legius syndrome
  • p.Gly62= Single submitter Cardiovascular phenotype
  • p.His236= Single submitter Cardiovascular phenotype
  • p.His263= Single submitter Cardiovascular phenotype
  • p.His344= Single submitter Cardiovascular phenotype
  • p.His90= Single submitter Cardiovascular phenotype
  • p.Ile234= Single submitter Cardiovascular phenotype
  • p.Ile253= Single submitter Cardiovascular phenotype
  • p.Ile363= Single submitter Cardiovascular phenotype
  • p.Ile413= Single submitter Cardiovascular phenotype
  • p.Leu140= Single submitter Cardiovascular phenotype
  • p.Leu151= Single submitter Cardiovascular phenotype
  • p.Leu223= Single submitter Cardiovascular phenotype
  • p.Leu271= Single submitter Cardiovascular phenotype
  • p.Leu34= Single submitter Legius syndrome
  • p.Leu407= Single submitter Cardiovascular phenotype
  • p.Leu76= Single submitter Legius syndrome
  • p.Lys322= Single submitter Cardiovascular phenotype
  • p.Lys399= Single submitter Cardiovascular phenotype
  • p.Lys439= Single submitter Legius syndrome
  • p.Lys46= Single submitter Cardiovascular phenotype
  • p.Lys93= Single submitter Legius syndrome
  • p.Lys98= Single submitter Cardiovascular phenotype
  • p.Phe282= Single submitter Cardiovascular phenotype
  • p.Phe311= Single submitter
  • p.Phe342= Single submitter Legius syndrome
  • p.Phe387= Single submitter Cardiovascular phenotype
  • p.Phe400= Single submitter Legius syndrome
  • p.Phe58= Single submitter Legius syndrome
  • p.Pro167= Single submitter Cardiovascular phenotype
  • p.Pro177= Single submitter Legius syndrome
  • p.Pro285= Single submitter Legius syndrome
  • p.Pro305= Single submitter Legius syndrome
  • p.Pro305Leu Single submitter Cardiovascular phenotype
  • p.Ser124= Single submitter Cardiovascular phenotype
  • p.Ser148= Single submitter Legius syndrome
  • p.Ser149= Single submitter Cardiovascular phenotype
  • p.Ser170= Single submitter Legius syndrome
  • p.Ser225= Single submitter Legius syndrome
  • p.Ser278= Single submitter Cardiovascular phenotype
  • p.Ser316= Single submitter Legius syndrome
  • p.Ser367= Single submitter Cardiovascular phenotype
  • p.Ser383= Single submitter Cardiovascular phenotype
  • p.Ser392= Single submitter Cardiovascular phenotype
  • p.Ser40= Single submitter Cardiovascular phenotype
  • p.Ser41Cys Single submitter Cardiovascular phenotype
  • p.Thr102= Single submitter Cardiovascular phenotype
  • p.Thr161= Single submitter Cardiovascular phenotype
  • p.Thr86= Single submitter Cardiovascular phenotype
  • p.Thr88= Single submitter Cardiovascular phenotype
  • p.Tyr168= Single submitter Cardiovascular phenotype
  • p.Tyr294= Single submitter Cardiovascular phenotype
  • p.Tyr337= Single submitter Legius syndrome
  • p.Tyr377= Single submitter Cardiovascular phenotype
  • p.Tyr82= Single submitter Cardiovascular phenotype
  • p.Val152= Single submitter Cardiovascular phenotype
  • p.Val162= Single submitter Legius syndrome
  • p.Val21= Single submitter Cardiovascular phenotype
  • p.Val212= Single submitter
  • p.Val237= Single submitter Legius syndrome
  • p.Val246= Single submitter Cardiovascular phenotype
  • p.Val310= Single submitter Legius syndrome
  • p.Val348Gly Single submitter Cardiovascular phenotype
  • p.Val414= Single submitter Cardiovascular phenotype
  • p.Val42= Single submitter Cardiovascular phenotype
  • p.Val421= Single submitter Cardiovascular phenotype
  • p.Val47= Single submitter Cardiovascular phenotype
  • p.Val85= Single submitter Cardiovascular phenotype
  • p.Cys429Arg No assertion criteria Noonan syndrome

Uncertain significance 637

Showing the top 300 by review status; the full set is in the sitemap.