Sugi Variant

Sugi Variant/MCPH1

MCPH1 — 1161 ClinVar variants

All ClinVar germline MCPH1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 320 flagged for review →

36 Pathogenic · 12 Pathogenic/Likely pathogenic · 63 Likely pathogenic · 75 Conflicting · 90 Benign · 15 Benign/Likely benign · 522 Likely benign · 348 Uncertain significance

Full MCPH1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 320

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 30

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

Predictors lean, ClinVar uncertain 236

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 236

Predictors split 54

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

All MCPH1 variants

Pathogenic 36

Pathogenic/Likely pathogenic 12

  • c.322-1G>C Multiple submitters microcephaly 1, primary, autosomal recessive
  • p.Gln386Ter Multiple submitters microcephaly 1, primary, autosomal recessive
  • p.Gly245Ter Multiple submitters microcephaly 1, primary, autosomal recessive
  • p.Leu542Ter Multiple submitters microcephaly 1, primary, autosomal recessive
  • p.Lys105Ter Multiple submitters
  • p.Lys107fs Multiple submitters microcephaly 1, primary, autosomal recessive
  • p.Lys26fs Multiple submitters microcephaly 1, primary, autosomal recessive
  • p.Ser191fs Multiple submitters microcephaly 1, primary, autosomal recessive
  • p.Ser276fs Multiple submitters microcephaly 1, primary, autosomal recessive
  • p.Ser623_Cys624insTer Multiple submitters microcephaly 1, primary, autosomal recessive
  • p.Ser72Leu Multiple submitters autosomal recessive primary microcephaly
  • p.Thr143fs Multiple submitters MCPH1-related disorder

Likely pathogenic 63

  • c.321+2T>C Multiple submitters microcephaly 1, primary, autosomal recessive
  • p.Arg642fs Multiple submitters microcephaly 1, primary, autosomal recessive
  • c.114+1G>C Single submitter microcephaly 1, primary, autosomal recessive
  • c.115-2A>G Single submitter
  • c.1935+1_1935+5del Single submitter microcephaly 1, primary, autosomal recessive
  • c.1973+1G>A Single submitter microcephaly 1, primary, autosomal recessive
  • c.1973+1G>C Single submitter microcephaly 1, primary, autosomal recessive
  • c.22+1G>C Single submitter microcephaly 1, primary, autosomal recessive
  • c.22+2T>A Single submitter microcephaly 1, primary, autosomal recessive
  • c.22+2T>C Single submitter
  • c.2214+1G>A Single submitter microcephaly 1, primary, autosomal recessive
  • c.2215-1G>T Single submitter MCPH1-related disorder
  • c.23-1G>A Single submitter
  • c.23-1G>C Single submitter microcephaly 1, primary, autosomal recessive
  • c.23-829_28del Single submitter
  • c.233+2T>C Single submitter
  • c.2453-1G>A Single submitter microcephaly 1, primary, autosomal recessive
  • c.322-2A>G Single submitter
  • c.436+1G>T Single submitter microcephaly 1, primary, autosomal recessive
  • c.437-2A>G Single submitter
  • c.670+1G>A Single submitter microcephaly 1, primary, autosomal recessive
  • p.Ala93Glu Single submitter microcephaly 1, primary, autosomal recessive
  • p.Arg469fs Single submitter microcephaly 1, primary, autosomal recessive
  • p.Asn117Ter Single submitter microcephaly 1, primary, autosomal recessive
  • p.Asn612fs Single submitter microcephaly 1, primary, autosomal recessive
  • p.Asp392fs Single submitter microcephaly 1, primary, autosomal recessive
  • p.Asp668fs Single submitter microcephaly 1, primary, autosomal recessive
  • p.Asp678fs Single submitter microcephaly 1, primary, autosomal recessive
  • p.Cys444Ter Single submitter microcephaly 1, primary, autosomal recessive
  • p.Cys79Phe Single submitter
  • p.Gln289Ter Single submitter microcephaly 1, primary, autosomal recessive
  • p.Gln441Ter Single submitter microcephaly 1, primary, autosomal recessive
  • p.Gln562Ter Single submitter microcephaly 1, primary, autosomal recessive
  • p.Gln660Ter Single submitter autosomal recessive primary microcephaly
  • p.Glu14Lys Single submitter
  • p.Glu22Lys Single submitter microcephaly 1, primary, autosomal recessive
  • p.Glu299_Ile300insTer Single submitter microcephaly 1, primary, autosomal recessive
  • p.Glu504fs Single submitter microcephaly 1, primary, autosomal recessive
  • p.Glu88Ter Single submitter microcephaly 1, primary, autosomal recessive
  • p.His346fs Single submitter MCPH1-related disorder
  • p.His732fs Single submitter microcephaly 1, primary, autosomal recessive
  • p.Leu209fs Single submitter autosomal recessive primary microcephaly
  • p.Leu650Ter Single submitter microcephaly 1, primary, autosomal recessive
  • p.Leu746Ter Single submitter microcephaly 1, primary, autosomal recessive
  • p.Lys466fs Single submitter microcephaly 1, primary, autosomal recessive
  • p.Lys804Ter Single submitter autosomal recessive primary microcephaly
  • p.Pro436fs Single submitter microcephaly 1, primary, autosomal recessive
  • p.Ser417fs Single submitter microcephaly 1, primary, autosomal recessive
  • p.Ser437Ter Single submitter microcephaly 1, primary, autosomal recessive
  • p.Ser496Ter Single submitter microcephaly 1, primary, autosomal recessive
  • p.Ser560fs Single submitter microcephaly 1, primary, autosomal recessive
  • p.Ser709_Tyr710insTer Single submitter microcephaly 1, primary, autosomal recessive
  • p.Ser89Ter Single submitter microcephaly 1, primary, autosomal recessive
  • p.Thr48Ile Single submitter microcephaly 1, primary, autosomal recessive
  • p.Trp16Ter Single submitter microcephaly 1, primary, autosomal recessive
  • p.Trp60Ter Single submitter microcephaly 1, primary, autosomal recessive
  • p.Trp706Ter Single submitter
  • p.Trp722Ter Single submitter MCPH1-related disorder
  • p.Tyr162fs Single submitter microcephaly 1, primary, autosomal recessive
  • p.Tyr710Ter Single submitter microcephaly 1, primary, autosomal recessive
  • p.Val50_Ile51delinsGlyVal Single submitter
  • p.Val697fs Single submitter microcephaly 1, primary, autosomal recessive
  • c.1_114del No assertion criteria Global developmental delay

Conflicting classifications of pathogenicity 75

  • c.115-14C>T Single submitter microcephaly 1, primary, autosomal recessive
  • c.115-6C>G Single submitter Inborn genetic diseases
  • c.1825+14C>G Single submitter microcephaly 1, primary, autosomal recessive
  • c.1935+1G>T Single submitter microcephaly 1, primary, autosomal recessive
  • c.1936-10A>G Single submitter microcephaly 1, primary, autosomal recessive
  • c.1974-2A>G Single submitter microcephaly 1, primary, autosomal recessive
  • c.2136+1G>T Single submitter autosomal recessive primary microcephaly
  • c.2137-7C>T Single submitter microcephaly 1, primary, autosomal recessive
  • c.2214+2T>C Single submitter microcephaly 1, primary, autosomal recessive
  • c.2452+9C>A Single submitter microcephaly 1, primary, autosomal recessive
  • c.2453-14C>T Single submitter microcephaly 1, primary, autosomal recessive
  • c.2453-1G>C Single submitter MCPH1-related disorder
  • p.Ala175Thr Single submitter microcephaly 1, primary, autosomal recessive ⚠
  • p.Ala398Val Single submitter microcephaly 1, primary, autosomal recessive ⚠
  • p.Ala494Thr Single submitter ⚠
  • p.Arg218Cys Single submitter microcephaly 1, primary, autosomal recessive ⚠
  • p.Arg741Ter Single submitter microcephaly 1, primary, autosomal recessive
  • p.Arg752= Single submitter microcephaly 1, primary, autosomal recessive
  • p.Arg785Gln Single submitter Inborn genetic diseases ⚠
  • p.Asn572= Single submitter microcephaly 1, primary, autosomal recessive
  • p.Asn95= Single submitter microcephaly 1, primary, autosomal recessive
  • p.Asp261Glu Single submitter microcephaly 1, primary, autosomal recessive ⚠
  • p.Asp539Gly Single submitter microcephaly 1, primary, autosomal recessive ⚠
  • p.Asp61Gly Single submitter microcephaly 1, primary, autosomal recessive ⚠
  • p.Asp758= Single submitter
  • p.Cys222Arg Single submitter Inborn genetic diseases ⚠
  • p.Cys371= Single submitter microcephaly 1, primary, autosomal recessive
  • p.Cys498= Single submitter
  • p.Gln289= Single submitter microcephaly 1, primary, autosomal recessive
  • p.Gln64= Single submitter microcephaly 1, primary, autosomal recessive
  • p.Gln788Ter Single submitter autosomal recessive primary microcephaly
  • p.Gln822= Single submitter microcephaly 1, primary, autosomal recessive
  • p.Glu457Lys Single submitter microcephaly 1, primary, autosomal recessive ⚠
  • p.Glu521Ter Single submitter microcephaly 1, primary, autosomal recessive
  • p.Gly243= Single submitter microcephaly 1, primary, autosomal recessive
  • p.Gly604Arg Single submitter Inborn genetic diseases ⚠
  • p.Gly626Ser Single submitter Inborn genetic diseases ⚠
  • p.His282fs Single submitter microcephaly 1, primary, autosomal recessive
  • p.His342= Single submitter microcephaly 1, primary, autosomal recessive
  • p.His733Gln Single submitter Inborn genetic diseases ⚠
  • p.His99= Single submitter
  • p.Ile274Thr Single submitter Inborn genetic diseases ⚠
  • p.Ile300Val Single submitter microcephaly 1, primary, autosomal recessive ⚠
  • p.Ile481= Single submitter
  • p.Ile481Phe Single submitter ⚠
  • p.Leu145= Single submitter microcephaly 1, primary, autosomal recessive
  • p.Leu405Pro Single submitter microcephaly 1, primary, autosomal recessive ⚠
  • p.Lys290Ile Single submitter microcephaly 1, primary, autosomal recessive ⚠
  • p.Lys450Thr Single submitter microcephaly 1, primary, autosomal recessive ⚠
  • p.Lys486= Single submitter
  • p.Lys559= Single submitter microcephaly 1, primary, autosomal recessive
  • p.Phe43Ser Single submitter microcephaly 1, primary, autosomal recessive ⚠
  • p.Pro584= Single submitter microcephaly 1, primary, autosomal recessive
  • p.Pro633Leu Single submitter Inborn genetic diseases ⚠
  • p.Pro727Leu Single submitter Inborn genetic diseases
  • p.Pro799Ser Single submitter microcephaly 1, primary, autosomal recessive ⚠
  • p.Ser159= Single submitter microcephaly 1, primary, autosomal recessive
  • p.Ser496Leu Single submitter Inborn genetic diseases ⚠
  • p.Ser595= Single submitter microcephaly 1, primary, autosomal recessive
  • p.Ser72= Single submitter
  • p.Ser765= Single submitter microcephaly 1, primary, autosomal recessive
  • p.Ser801Gly Single submitter microcephaly 1, primary, autosomal recessive ⚠
  • p.Thr163= Single submitter microcephaly 1, primary, autosomal recessive
  • p.Thr30= Single submitter
  • p.Thr468Asn Single submitter microcephaly 1, primary, autosomal recessive ⚠
  • p.Thr594Arg Single submitter ⚠
  • p.Trp715Ter Single submitter microcephaly 1, primary, autosomal recessive
  • p.Tyr415Cys Single submitter Inborn genetic diseases ⚠
  • p.Tyr425Asn Single submitter microcephaly 1, primary, autosomal recessive ⚠
  • p.Tyr606= Single submitter
  • p.Val149Ile Single submitter microcephaly 1, primary, autosomal recessive ⚠
  • p.Val354Ala Single submitter microcephaly 1, primary, autosomal recessive ⚠
  • p.Val464Ile Single submitter microcephaly 1, primary, autosomal recessive ⚠
  • p.Val499Met Single submitter microcephaly 1, primary, autosomal recessive ⚠
  • p.Val651Ile Single submitter microcephaly 1, primary, autosomal recessive ⚠

Benign 90

Benign/Likely benign 15

  • c.23-15A>G Multiple submitters microcephaly 1, primary, autosomal recessive
  • c.2453-13G>A Multiple submitters microcephaly 1, primary, autosomal recessive
  • p.Ala3= Multiple submitters
  • p.Ala761Val Multiple submitters microcephaly 1, primary, autosomal recessive
  • p.Arg752= Multiple submitters
  • p.Asp148Glu Multiple submitters Inborn genetic diseases
  • p.Asp224Gly Multiple submitters Inborn genetic diseases
  • p.Glu451Lys Multiple submitters microcephaly 1, primary, autosomal recessive
  • p.Ser573= Multiple submitters microcephaly 1, primary, autosomal recessive
  • p.Ser580Gly Multiple submitters microcephaly 1, primary, autosomal recessive
  • p.Thr594Met Multiple submitters
  • p.Thr615= Multiple submitters microcephaly 1, primary, autosomal recessive
  • p.Thr682Asn Multiple submitters microcephaly 1, primary, autosomal recessive
  • p.Tyr330Cys Multiple submitters microcephaly 1, primary, autosomal recessive
  • p.Tyr412= Multiple submitters

Likely benign 522

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

Uncertain significance 348

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