Sugi Variant

Sugi Variant/KDM5C

KDM5C — 1013 ClinVar variants

All ClinVar germline KDM5C variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 413 flagged for review →

99 Pathogenic · 6 Pathogenic/Likely pathogenic · 84 Likely pathogenic · 36 Conflicting · 80 Benign · 29 Benign/Likely benign · 264 Likely benign · 415 Uncertain significance

Full KDM5C gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 413

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 1

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

Predictors agree, ClinVar conflicts 14

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

Predictors lean, ClinVar uncertain 266

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 266

Predictors split 132

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

All KDM5C variants

Pathogenic 99

  • p.Arg332Ter Multiple submitters syndromic X-linked intellectual disability Claes-Jensen type
  • p.Arg68Ter Multiple submitters Inborn genetic diseases
  • p.Arg778Ter Multiple submitters Spastic paraplegia
  • p.Arg828Ter Multiple submitters syndromic X-linked intellectual disability Claes-Jensen type
  • p.Arg929Ter Multiple submitters Inborn genetic diseases
  • p.Gln1020Ter Multiple submitters Inborn genetic diseases
  • p.Gln199Ter Multiple submitters syndromic X-linked intellectual disability Claes-Jensen type
  • p.Gln588Ter Multiple submitters Spastic paraplegia
  • p.Gln859Ter Multiple submitters Inborn genetic diseases
  • p.Gln970Ter Multiple submitters syndromic X-linked intellectual disability Claes-Jensen type
  • p.Glu1131fs Multiple submitters syndromic X-linked intellectual disability Claes-Jensen type
  • p.Glu810fs Multiple submitters syndromic X-linked intellectual disability Claes-Jensen type
  • p.Leu257fs Multiple submitters syndromic X-linked intellectual disability Claes-Jensen type
  • p.Pro480Leu Multiple submitters Spastic paraplegia
  • c.1402-2A>G Single submitter
  • c.2982-1G>C Single submitter
  • c.351+1G>T Single submitter
  • p.Ala1029fs Single submitter Inborn genetic diseases
  • p.Ala1137fs Single submitter Spastic paraplegia
  • p.Ala138Ter Single submitter
  • p.Ala50fs Single submitter Inborn genetic diseases
  • p.Ala718Pro Single submitter intellectual disability
  • p.Ala887fs Single submitter Spastic paraplegia
  • p.Arg1082fs Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • p.Arg1284fs Single submitter Spastic paraplegia
  • p.Arg390fs Single submitter Spastic paraplegia
  • p.Arg68fs Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • p.Arg694Ter Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • p.Arg909fs Single submitter Spastic paraplegia
  • p.Arg951Ter Single submitter
  • p.Asp1043fs Single submitter
  • p.Asp51fs Single submitter
  • p.Cys1247fs Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • p.Cys488Ter Single submitter intellectual disability
  • p.Cys589fs Single submitter Spastic paraplegia
  • p.Cys738Ter Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • p.Gln1040Ter Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • p.Gln1279Ter Single submitter Inborn genetic diseases
  • p.Gln1294Ter Single submitter
  • p.Gln53Ter Single submitter
  • p.Gln706Ter Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • p.Gln902Ter Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • p.Gln924Ter Single submitter Inborn genetic diseases
  • p.Gln927Ter Single submitter
  • p.Glu1024fs Single submitter Inborn genetic diseases
  • p.Glu1083fs Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • p.Glu1120Ter Single submitter Spastic paraplegia
  • p.Glu1299Ter Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • p.Glu297Ter Single submitter
  • p.Glu433Ter Single submitter intellectual disability
  • p.Glu592fs Single submitter
  • p.Glu852fs Single submitter
  • p.Glu926fs Single submitter Inborn genetic diseases
  • p.Gly1191fs Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • p.Gly333Arg Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • p.Ile1187fs Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • p.Ile689fs Single submitter Spastic paraplegia
  • p.Leu1200fs Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • p.Leu339fs Single submitter
  • p.Leu394fs Single submitter Spastic paraplegia
  • p.Leu502fs Single submitter Spastic paraplegia
  • p.Leu794fs Single submitter intellectual disability
  • p.Lys1156fs Single submitter Inborn genetic diseases
  • p.Met506Val Single submitter
  • p.Met759fs Single submitter Inborn genetic diseases
  • p.Pro1231fs Single submitter Inborn genetic diseases
  • p.Pro27Leu Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • p.Pro49fs Single submitter Spastic paraplegia
  • p.Pro940fs Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • p.Pro998fs Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • p.Ser1136fs Single submitter
  • p.Ser116fs Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • p.Ser1250Ter Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • p.Ser539Ter Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • p.Ser5fs Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • p.Ser941fs Single submitter
  • p.Thr270fs Single submitter Spastic paraplegia
  • p.Trp1118Ter Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • p.Trp1208Ter Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • p.Trp1238Ter Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • p.Trp1288Ter Single submitter Inborn genetic diseases
  • p.Trp501fs Single submitter
  • p.Trp519Ter Single submitter
  • p.Trp622Ter Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • p.Trp773Ter Single submitter
  • p.Tyr162Ter Single submitter
  • p.Tyr167Ter Single submitter Spastic paraplegia
  • p.Tyr30Cys Single submitter
  • p.Tyr601Ter Single submitter
  • p.Val1057fs Single submitter Spastic paraplegia
  • c.2517_2622del No assertion criteria syndromic X-linked intellectual disability Claes-Jensen type
  • c.2622+2dup No assertion criteria syndromic X-linked intellectual disability Claes-Jensen type
  • p.Arg766Trp No assertion criteria syndromic X-linked intellectual disability Claes-Jensen type
  • p.Cys724Ter No assertion criteria syndromic X-linked intellectual disability Claes-Jensen type
  • p.Glu985fs No assertion criteria KDM5C-related disorder
  • p.Leu731Phe No assertion criteria syndromic X-linked intellectual disability Claes-Jensen type
  • p.Pro454fs No assertion criteria syndromic X-linked intellectual disability Claes-Jensen type
  • p.Ser451Arg No assertion criteria syndromic X-linked intellectual disability Claes-Jensen type
  • p.Trp52Cys No assertion criteria syndromic X-linked intellectual disability Claes-Jensen type

Pathogenic/Likely pathogenic 6

  • c.1243-2A>G Multiple submitters Spastic paraplegia
  • p.Arg681Ter Multiple submitters Spastic paraplegia
  • p.His514Leu Multiple submitters syndromic X-linked intellectual disability Claes-Jensen type
  • p.Pro531Leu Multiple submitters syndromic X-linked intellectual disability Claes-Jensen type
  • p.Tyr325fs Multiple submitters Spastic paraplegia
  • p.Val504Met Multiple submitters KDM5C-related disorder

Likely pathogenic 84

  • p.Arg599Cys Multiple submitters syndromic X-linked intellectual disability Claes-Jensen type
  • p.Arg750Trp Multiple submitters Spastic paraplegia
  • p.Glu698Lys Multiple submitters Inborn genetic diseases
  • p.Gly536Glu Multiple submitters syndromic X-linked intellectual disability Claes-Jensen type
  • p.Val615Phe Multiple submitters syndromic X-linked intellectual disability Claes-Jensen type
  • c.1122+1G>A Single submitter
  • c.1242+26_1747-3685del Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • c.1401+2T>C Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • c.150+1G>A Single submitter Spastic paraplegia
  • c.150+1G>T Single submitter
  • c.1747-2A>T Single submitter Spastic paraplegia
  • c.1866+1G>A Single submitter Spastic paraplegia
  • c.2243+1G>T Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • c.228+1G>C Single submitter
  • c.2981+1G>A Single submitter Spastic paraplegia
  • c.3300+2T>A Single submitter
  • c.3300+71A>G Single submitter
  • c.3301-2A>G Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • c.4038+1G>A Single submitter
  • c.4118-2A>G Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • c.4118-9A>G Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • c.781+1G>A Single submitter Spastic paraplegia
  • c.782-1G>T Single submitter
  • c.964-1G>T Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • p.Ala1078Val Single submitter ⚠
  • p.Ala388Pro Single submitter Inborn genetic diseases
  • p.Ala77Thr Single submitter Inborn genetic diseases
  • p.Arg108Trp Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • p.Arg198Gln Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • p.Arg705Cys Single submitter
  • p.Arg744Trp Single submitter ⚠
  • p.Arg943Ter Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • p.Asn73fs Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • p.Asp1111fs Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • p.Asp402Asn Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • p.Asp517fs Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • p.Asp562Val Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • p.Asp621Gly Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • p.Cys1047fs Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • p.Cys1190fs Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • p.Cys1205fs Single submitter Kabuki syndrome
  • p.Gln1070Ter Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • p.Gln1138Ter Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • p.Glu1122fs Single submitter
  • p.Glu1338fs Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • p.Glu483fs Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • p.Glu546Val Single submitter Inborn genetic diseases
  • p.Glu878Ter Single submitter Inborn genetic diseases
  • p.Gly1349fs Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • p.Gly536Arg Single submitter intellectual disability
  • p.Gly626fs Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • p.Leu1219Arg Single submitter syndromic X-linked intellectual disability Claes-Jensen type ⚠
  • p.Leu197fs Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • p.Leu75fs Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • p.Leu75Pro Single submitter
  • p.Lys764fs Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • p.Met1Val Single submitter Spastic paraplegia
  • p.Pro538Leu Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • p.Pro554Ser Single submitter
  • p.Pro554Thr Single submitter Inborn genetic diseases
  • p.Pro624fs Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • p.Pro962_Ser963insTer Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • p.Ser522Phe Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • p.Thr1282fs Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • p.Thr393Ile Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • p.Trp134Ter Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • p.Trp426Ter Single submitter KDM5C-related disorder
  • p.Trp534Cys Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • p.Trp622Cys Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • p.Tyr1045Ter Single submitter
  • p.Tyr157Ter Single submitter intellectual disability
  • p.Tyr190Cys Single submitter ⚠
  • p.Tyr190Ter Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • p.Tyr525Cys Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • p.Tyr535Cys Single submitter
  • p.Tyr85Ter Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • p.Val201fs Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • p.Val583Phe Single submitter syndromic X-linked intellectual disability Claes-Jensen type
  • p.Gln237Ter No assertion criteria intellectual disability
  • p.Gln70Ter No assertion criteria syndromic X-linked intellectual disability Claes-Jensen type
  • p.Glu23Ter No assertion criteria plasma cell myeloma
  • p.Gly608Val No assertion criteria syndromic X-linked intellectual disability Claes-Jensen type
  • p.Met1344fs No assertion criteria
  • p.Pro598Leu No assertion criteria

Conflicting classifications of pathogenicity 36

Benign 80

Benign/Likely benign 29

  • c.151-7C>T Multiple submitters Spastic paraplegia
  • c.2517-9_2517-7dup Multiple submitters Inborn genetic diseases
  • c.3439-13C>A Multiple submitters Spastic paraplegia
  • c.4039-4G>A Multiple submitters Inborn genetic diseases
  • c.4317+16A>G Multiple submitters Spastic paraplegia
  • c.523-3C>T Multiple submitters Inborn genetic diseases
  • p.Ala1108= Multiple submitters Spastic paraplegia
  • p.Ala1260Ser Multiple submitters Inborn genetic diseases
  • p.Ala1330= Multiple submitters Inborn genetic diseases
  • p.Ala1529= Multiple submitters Inborn genetic diseases
  • p.Arg136= Multiple submitters Spastic paraplegia
  • p.Arg1546Gln Multiple submitters Spastic paraplegia
  • p.Arg390Gln Multiple submitters Spastic paraplegia ⚠
  • p.Asp443= Multiple submitters Inborn genetic diseases
  • p.Gln588= Multiple submitters Inborn genetic diseases
  • p.Gln628= Multiple submitters Inborn genetic diseases
  • p.Glu1299= Multiple submitters Spastic paraplegia
  • p.Glu704= Multiple submitters Spastic paraplegia
  • p.Gly264= Multiple submitters Spastic paraplegia
  • p.Ile1147= Multiple submitters Spastic paraplegia
  • p.Leu1220= Multiple submitters Spastic paraplegia
  • p.Lys188= Multiple submitters Inborn genetic diseases
  • p.Pro15= Multiple submitters Inborn genetic diseases
  • p.Ser299Asn Multiple submitters Spastic paraplegia ⚠
  • p.Ser578= Multiple submitters Spastic paraplegia
  • p.Thr1180= Multiple submitters Inborn genetic diseases
  • p.Thr1533Pro Multiple submitters Inborn genetic diseases
  • p.Val1148Met Multiple submitters syndromic X-linked intellectual disability Claes-Jensen type
  • p.Val455= Multiple submitters Inborn genetic diseases

Likely benign 264

Uncertain significance 415

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