SPAG1 — 522 ClinVar variants

All ClinVar germline SPAG1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 196 flagged for review →

41 Pathogenic · 5 Pathogenic/Likely pathogenic · 12 Likely pathogenic · 20 Conflicting · 40 Benign · 17 Benign/Likely benign · 181 Likely benign · 206 Uncertain significance

Full SPAG1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 196

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 17

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

Predictors lean, ClinVar uncertain 154

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 154

Predictors split 25

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

All SPAG1 variants

Pathogenic 41

  • c.1097-11C>G Multiple submitters primary ciliary dyskinesia 28
  • p.Ala374fs Multiple submitters primary ciliary dyskinesia 28
  • p.Arg697Ter Multiple submitters primary ciliary dyskinesia 28
  • p.Asp848fs Multiple submitters SPAG1-related disorder
  • p.Gly372fs Multiple submitters primary ciliary dyskinesia 28
  • p.Ile507fs Multiple submitters SPAG1-related disorder
  • c.427-1065_630del Single submitter primary ciliary dyskinesia 28
  • c.595+1G>A Single submitter primary ciliary dyskinesia 28
  • p.Ala676fs Single submitter primary ciliary dyskinesia 28
  • p.Arg248Ter Single submitter primary ciliary dyskinesia
  • p.Arg338fs Single submitter primary ciliary dyskinesia 28
  • p.Arg563fs Single submitter primary ciliary dyskinesia 28
  • p.Arg73fs Single submitter primary ciliary dyskinesia
  • p.Asn859fs Single submitter primary ciliary dyskinesia 28
  • p.Asp713fs Single submitter primary ciliary dyskinesia 28
  • p.Gln333Ter Single submitter primary ciliary dyskinesia 28
  • p.Gln342Ter Single submitter primary ciliary dyskinesia 28
  • p.Gln386Ter Single submitter primary ciliary dyskinesia 28
  • p.Gln555Ter Single submitter primary ciliary dyskinesia 28
  • p.Glu109fs Single submitter primary ciliary dyskinesia 28
  • p.Gly501fs Single submitter primary ciliary dyskinesia 28
  • p.Leu740fs Single submitter primary ciliary dyskinesia 28
  • p.Lys107Ter Single submitter primary ciliary dyskinesia 28
  • p.Lys205fs Single submitter primary ciliary dyskinesia
  • p.Lys254fs Single submitter primary ciliary dyskinesia 28
  • p.Lys366Ter Single submitter primary ciliary dyskinesia 28
  • p.Met529fs Single submitter primary ciliary dyskinesia 28
  • p.Phe87fs Single submitter primary ciliary dyskinesia 28
  • p.Ser104Ter Single submitter primary ciliary dyskinesia 28
  • p.Ser186fs Single submitter primary ciliary dyskinesia 28
  • p.Thr546fs Single submitter primary ciliary dyskinesia 28
  • p.Thr58fs Single submitter primary ciliary dyskinesia 28
  • p.Thr622fs Single submitter primary ciliary dyskinesia 28
  • p.Trp102Ter Single submitter primary ciliary dyskinesia 28
  • p.Trp595Ter Single submitter primary ciliary dyskinesia 28
  • p.Tyr531Ter Single submitter primary ciliary dyskinesia 28
  • p.Tyr695_Arg696delinsTer Single submitter primary ciliary dyskinesia 28
  • p.Val45fs Single submitter primary ciliary dyskinesia 28
  • p.Val734fs Single submitter primary ciliary dyskinesia 28
  • p.Glu227Ter No assertion criteria autosomal dominant nocturnal frontal lobe epilepsy 5
  • p.Met1Arg No assertion criteria primary ciliary dyskinesia 28

Pathogenic/Likely pathogenic 5

  • p.Gln672Ter Multiple submitters SPAG1-related disorder
  • p.Lys301fs Multiple submitters primary ciliary dyskinesia
  • p.Pro80fs Multiple submitters SPAG1-related disorder
  • p.Ser789fs Multiple submitters primary ciliary dyskinesia 28
  • p.Thr201fs Multiple submitters SPAG1-related disorder

Likely pathogenic 12

  • c.939+1G>A Multiple submitters primary ciliary dyskinesia 28
  • c.140+1G>A Single submitter primary ciliary dyskinesia 28
  • c.1988+1G>A Single submitter SPAG1-related disorder
  • c.2116-1G>T Single submitter primary ciliary dyskinesia 28
  • c.2281-1_2281del Single submitter primary ciliary dyskinesia 28
  • c.301-2A>G Single submitter primary ciliary dyskinesia
  • c.488+1G>A Single submitter primary ciliary dyskinesia 28
  • c.702-1G>A Single submitter primary ciliary dyskinesia 28
  • p.Ile854fs Single submitter primary ciliary dyskinesia 28
  • p.Ser134Ter Single submitter primary ciliary dyskinesia
  • p.Ser260Ter Single submitter
  • p.Tyr667Ter Single submitter SPAG1-related disorder

Conflicting classifications of pathogenicity 20

Benign 40

Benign/Likely benign 17

  • c.1097-20C>T Multiple submitters primary ciliary dyskinesia 28
  • c.832+9del Multiple submitters primary ciliary dyskinesia 28
  • c.833-20T>C Multiple submitters primary ciliary dyskinesia 28
  • c.939+13T>C Multiple submitters primary ciliary dyskinesia 28
  • p.Ala368Val Multiple submitters primary ciliary dyskinesia 28
  • p.Ala528= Multiple submitters primary ciliary dyskinesia 28
  • p.Arg293Trp Multiple submitters primary ciliary dyskinesia 28
  • p.Asn275= Multiple submitters primary ciliary dyskinesia 28
  • p.Glu331Lys Multiple submitters primary ciliary dyskinesia 28
  • p.Leu514= Multiple submitters primary ciliary dyskinesia 28
  • p.Lys353_Ser354insAsp Multiple submitters primary ciliary dyskinesia 28
  • p.Lys353Glu Multiple submitters primary ciliary dyskinesia 28
  • p.Met529Thr Multiple submitters primary ciliary dyskinesia 28
  • p.Met777Thr Multiple submitters primary ciliary dyskinesia 28
  • p.Ser905= Multiple submitters primary ciliary dyskinesia 28
  • p.Tyr158= Multiple submitters primary ciliary dyskinesia 28
  • p.Val319= Multiple submitters primary ciliary dyskinesia 28

Likely benign 181

  • c.1097-11C>T Multiple submitters primary ciliary dyskinesia 28
  • c.141-48G>T Multiple submitters
  • c.1435+18del Multiple submitters primary ciliary dyskinesia 28
  • c.1856-118C>T Multiple submitters
  • c.2280+13_2280+16del Multiple submitters primary ciliary dyskinesia 28
  • c.2650-20T>G Multiple submitters primary ciliary dyskinesia 28
  • c.301-8A>G Multiple submitters primary ciliary dyskinesia 28
  • c.939+15T>C Multiple submitters primary ciliary dyskinesia 28
  • c.-2-119C>T Multiple submitters
  • p.Ala376= Multiple submitters primary ciliary dyskinesia 28
  • p.Ala446= Multiple submitters primary ciliary dyskinesia 28
  • p.Ala815Val Multiple submitters primary ciliary dyskinesia 28
  • p.Arg819= Multiple submitters primary ciliary dyskinesia 28
  • p.Asp165= Multiple submitters primary ciliary dyskinesia
  • p.Asp224= Multiple submitters primary ciliary dyskinesia 28
  • p.Asp641= Multiple submitters primary ciliary dyskinesia
  • p.Cys44= Multiple submitters primary ciliary dyskinesia 28
  • p.Gln923= Multiple submitters primary ciliary dyskinesia 28
  • p.Glu500= Multiple submitters primary ciliary dyskinesia 28
  • p.Gly133Asp Multiple submitters primary ciliary dyskinesia 28
  • p.Gly216= Multiple submitters primary ciliary dyskinesia 28
  • p.Gly361= Multiple submitters primary ciliary dyskinesia 28
  • p.His827Tyr Multiple submitters primary ciliary dyskinesia 28
  • p.Leu571= Multiple submitters primary ciliary dyskinesia 28
  • p.Leu670= Multiple submitters primary ciliary dyskinesia 28
  • p.Leu737= Multiple submitters primary ciliary dyskinesia
  • p.Lys213= Multiple submitters primary ciliary dyskinesia 28
  • p.Pro795= Multiple submitters primary ciliary dyskinesia 28
  • p.Pro799= Multiple submitters primary ciliary dyskinesia 28
  • p.Ser867= Multiple submitters primary ciliary dyskinesia 28
  • p.Thr181= Multiple submitters primary ciliary dyskinesia 28
  • p.Thr285= Multiple submitters primary ciliary dyskinesia 28
  • p.Thr887= Multiple submitters primary ciliary dyskinesia
  • p.Tyr875= Multiple submitters primary ciliary dyskinesia 28
  • c.1096+17A>C Single submitter primary ciliary dyskinesia 28
  • c.1096+17A>G Single submitter primary ciliary dyskinesia 28
  • c.1096+75C>T Single submitter
  • c.1096+9T>A Single submitter primary ciliary dyskinesia 28
  • c.1097-4A>G Single submitter primary ciliary dyskinesia 28
  • c.1097-8C>T Single submitter primary ciliary dyskinesia 28
  • c.141-16T>C Single submitter primary ciliary dyskinesia 28
  • c.141-207C>T Single submitter
  • c.1436-20_1436-16del Single submitter primary ciliary dyskinesia 28
  • c.1436-37T>A Single submitter
  • c.1535+16T>C Single submitter primary ciliary dyskinesia 28
  • c.1535+19G>C Single submitter primary ciliary dyskinesia 28
  • c.1536-19A>G Single submitter primary ciliary dyskinesia 28
  • c.1688+118G>A Single submitter
  • c.1688+11del Single submitter primary ciliary dyskinesia 28
  • c.1688+128T>A Single submitter
  • c.1688+13A>T Single submitter primary ciliary dyskinesia 28
  • c.1688+18G>C Single submitter primary ciliary dyskinesia 28
  • c.1688+20T>C Single submitter primary ciliary dyskinesia 28
  • c.1689-10T>C Single submitter primary ciliary dyskinesia 28
  • c.1855+8dup Single submitter primary ciliary dyskinesia 28
  • c.1856-51A>T Single submitter
  • c.1856-5C>T Single submitter
  • c.1856-7C>A Single submitter primary ciliary dyskinesia 28
  • c.1988+11T>G Single submitter primary ciliary dyskinesia 28
  • c.1988+14A>T Single submitter primary ciliary dyskinesia 28
  • c.1988+170C>T Single submitter
  • c.1988+19T>A Single submitter primary ciliary dyskinesia 28
  • c.1988+209C>T Single submitter
  • c.1989-11C>T Single submitter primary ciliary dyskinesia 28
  • c.1989-14T>C Single submitter primary ciliary dyskinesia 28
  • c.1989-15A>G Single submitter primary ciliary dyskinesia 28
  • c.1989-17C>T Single submitter primary ciliary dyskinesia 28
  • c.1989-72C>G Single submitter
  • c.2116-102C>A Single submitter
  • c.2116-11C>T Single submitter primary ciliary dyskinesia 28
  • c.2116-18_2116-17del Single submitter primary ciliary dyskinesia 28
  • c.2116-44C>T Single submitter
  • c.2116-8A>G Single submitter primary ciliary dyskinesia 28
  • c.2280+7G>A Single submitter primary ciliary dyskinesia 28
  • c.2281-12T>C Single submitter primary ciliary dyskinesia 28
  • c.2281-8T>C Single submitter primary ciliary dyskinesia 28
  • c.2649+7G>A Single submitter primary ciliary dyskinesia 28
  • c.2650-18T>G Single submitter primary ciliary dyskinesia 28
  • c.2650-19T>G Single submitter primary ciliary dyskinesia 28
  • c.2650-6T>A Single submitter primary ciliary dyskinesia 28
  • c.300+14C>T Single submitter primary ciliary dyskinesia 28
  • c.300+303dup Single submitter
  • c.301-10C>T Single submitter primary ciliary dyskinesia 28
  • c.426+14A>G Single submitter primary ciliary dyskinesia 28
  • c.427-11T>C Single submitter primary ciliary dyskinesia 28
  • c.427-15A>G Single submitter primary ciliary dyskinesia 28
  • c.427-8T>A Single submitter primary ciliary dyskinesia 28
  • c.488+13dup Single submitter primary ciliary dyskinesia 28
  • c.488+19T>C Single submitter primary ciliary dyskinesia 28
  • c.488+9del Single submitter primary ciliary dyskinesia 28
  • c.489-7A>G Single submitter primary ciliary dyskinesia 28
  • c.489-7A>T Single submitter primary ciliary dyskinesia 28
  • c.595+15AAT[2] Single submitter primary ciliary dyskinesia 28
  • c.596-12A>T Single submitter primary ciliary dyskinesia 28
  • c.596-6T>C Single submitter primary ciliary dyskinesia 28
  • c.701+10T>A Single submitter primary ciliary dyskinesia 28
  • c.701+11G>A Single submitter primary ciliary dyskinesia 28
  • c.701+16T>C Single submitter
  • c.701+17T>C Single submitter primary ciliary dyskinesia 28
  • c.701+3G>T Single submitter primary ciliary dyskinesia 28
  • c.702-15C>T Single submitter primary ciliary dyskinesia 28
  • c.832+13A>G Single submitter primary ciliary dyskinesia 28
  • c.832+14T>C Single submitter primary ciliary dyskinesia 28
  • c.833-15T>C Single submitter primary ciliary dyskinesia 28
  • c.939+8T>C Single submitter primary ciliary dyskinesia 28
  • c.940-19T>C Single submitter primary ciliary dyskinesia 28
  • c.940-7G>A Single submitter primary ciliary dyskinesia 28
  • c.-2C>T Single submitter
  • c.*124C>G Single submitter
  • p.Ala159= Single submitter primary ciliary dyskinesia 28
  • p.Ala228= Single submitter
  • p.Ala238= Single submitter primary ciliary dyskinesia 28
  • p.Ala283= Single submitter primary ciliary dyskinesia 28
  • p.Ala373= Single submitter primary ciliary dyskinesia 28
  • p.Ala377= Single submitter primary ciliary dyskinesia 28
  • p.Ala483= Single submitter
  • p.Ala588= Single submitter primary ciliary dyskinesia
  • p.Ala625= Single submitter primary ciliary dyskinesia 28
  • p.Ala625Thr Single submitter primary ciliary dyskinesia
  • p.Ala693= Single submitter primary ciliary dyskinesia 28
  • p.Ala772Ser Single submitter primary ciliary dyskinesia
  • p.Ala806= Single submitter primary ciliary dyskinesia 28
  • p.Ala826= Single submitter primary ciliary dyskinesia 28
  • p.Arg321= Single submitter
  • p.Arg375= Single submitter primary ciliary dyskinesia 28
  • p.Arg613His Single submitter primary ciliary dyskinesia
  • p.Arg76= Single submitter primary ciliary dyskinesia 28
  • p.Arg922= Single submitter primary ciliary dyskinesia 28
  • p.Asn259= Single submitter primary ciliary dyskinesia 28
  • p.Asn638= Single submitter primary ciliary dyskinesia 28
  • p.Asn690= Single submitter primary ciliary dyskinesia 28
  • p.Asn804= Single submitter
  • p.Asn910= Single submitter primary ciliary dyskinesia 28
  • p.Asp264= Single submitter primary ciliary dyskinesia 28
  • p.Asp35= Single submitter primary ciliary dyskinesia 28
  • p.Asp96= Single submitter primary ciliary dyskinesia
  • p.Cys265= Single submitter primary ciliary dyskinesia 28
  • p.Gln536= Single submitter primary ciliary dyskinesia 28
  • p.Glu535= Single submitter primary ciliary dyskinesia 28
  • p.Glu733= Single submitter primary ciliary dyskinesia 28
  • p.Gly274= Single submitter primary ciliary dyskinesia 28
  • p.Gly352= Single submitter primary ciliary dyskinesia
  • p.Gly438= Single submitter primary ciliary dyskinesia 28
  • p.Gly466= Single submitter primary ciliary dyskinesia 28
  • p.Gly607= Single submitter primary ciliary dyskinesia 28
  • p.Gly630= Single submitter primary ciliary dyskinesia 28
  • p.Gly786Asp Single submitter primary ciliary dyskinesia
  • p.Ile173= Single submitter primary ciliary dyskinesia 28
  • p.Ile385= Single submitter primary ciliary dyskinesia 28
  • p.Ile488= Single submitter primary ciliary dyskinesia 28
  • p.Ile583= Single submitter primary ciliary dyskinesia 28
  • p.Leu292= Single submitter
  • p.Leu564= Single submitter primary ciliary dyskinesia 28
  • p.Leu816= Single submitter primary ciliary dyskinesia 28
  • p.Leu868= Single submitter primary ciliary dyskinesia 28
  • p.Leu888= Single submitter
  • p.Leu9= Single submitter primary ciliary dyskinesia 28
  • p.Lys215= Single submitter primary ciliary dyskinesia 28
  • p.Lys820= Single submitter primary ciliary dyskinesia 28
  • p.Lys891= Single submitter primary ciliary dyskinesia 28
  • p.Met777Ile Single submitter primary ciliary dyskinesia
  • p.Phe164= Single submitter
  • p.Phe262Leu Single submitter
  • p.Pro307= Single submitter primary ciliary dyskinesia 28
  • p.Pro746Ser Single submitter primary ciliary dyskinesia
  • p.Pro792= Single submitter primary ciliary dyskinesia 28
  • p.Pro838= Single submitter primary ciliary dyskinesia 28
  • p.Pro866= Single submitter primary ciliary dyskinesia 28
  • p.Ser260= Single submitter primary ciliary dyskinesia 28
  • p.Ser347= Single submitter primary ciliary dyskinesia 28
  • p.Ser610= Single submitter primary ciliary dyskinesia
  • p.Ser647= Single submitter primary ciliary dyskinesia 28
  • p.Ser86= Single submitter primary ciliary dyskinesia 28
  • p.Thr832= Single submitter primary ciliary dyskinesia 28
  • p.Thr907= Single submitter primary ciliary dyskinesia 28
  • p.Tyr245= Single submitter primary ciliary dyskinesia 28
  • p.Tyr286= Single submitter primary ciliary dyskinesia 28
  • p.Tyr537= Single submitter primary ciliary dyskinesia 28
  • p.Tyr639= Single submitter primary ciliary dyskinesia 28
  • p.Val761= Single submitter primary ciliary dyskinesia 28
  • p.Leu704= No assertion criteria SPAG1-related disorder

Uncertain significance 206