Sugi Variant

Sugi Variant/BPTF

BPTF — 1153 ClinVar variants

All ClinVar germline BPTF variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 533 flagged for review →

40 Pathogenic · 2 Pathogenic/Likely pathogenic · 35 Likely pathogenic · 45 Conflicting · 52 Benign · 23 Benign/Likely benign · 264 Likely benign · 692 Uncertain significance

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

⚑ Evidence disagreements 533

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 4

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

Predictors agree, ClinVar conflicts 31

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

Predicted LoF vs a conflicting call 3

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 448

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 448

Predictors split 47

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

All BPTF variants

Pathogenic 40

  • p.Arg2858Ter Multiple submitters neurodevelopmental disorder with dysmorphic facies and distal limb anomalies
  • p.Arg841Ter Multiple submitters intellectual disability
  • p.Ser71fs Multiple submitters Inborn genetic diseases
  • p.Thr783fs Multiple submitters Inborn genetic diseases
  • p.Ala1952fs Single submitter neurodevelopmental disorder with dysmorphic facies and distal limb anomalies
  • p.Ala2289fs Single submitter neurodevelopmental disorder with dysmorphic facies and distal limb anomalies
  • p.Arg1393Ter Single submitter
  • p.Arg1738Ter Single submitter
  • p.Arg2208Ter Single submitter
  • p.Arg2593fs Single submitter neurodevelopmental disorder with dysmorphic facies and distal limb anomalies
  • p.Arg68fs Single submitter Inborn genetic diseases
  • p.Arg749fs Single submitter
  • p.Asn1101fs Single submitter
  • p.Asn789fs Single submitter Inborn genetic diseases
  • p.Asp566fs Single submitter neurodevelopmental disorder with dysmorphic facies and distal limb anomalies
  • p.Cys1345_Glu1346delinsTer Single submitter
  • p.Gln1324Ter Single submitter Inborn genetic diseases
  • p.Gln2348fs Single submitter Inborn genetic diseases
  • p.Gln2388Ter Single submitter
  • p.Glu1025fs Single submitter
  • p.Ile1883fs Single submitter
  • p.Leu330fs Single submitter intellectual disability
  • p.Leu687fs Single submitter Inborn genetic diseases
  • p.Leu796fs Single submitter neurodevelopmental disorder with dysmorphic facies and distal limb anomalies
  • p.Lys1053fs Single submitter neurodevelopmental disorder with dysmorphic facies and distal limb anomalies
  • p.Ser1490fs Single submitter
  • p.Ser2883fs Single submitter
  • p.Thr1766_Trp1767insTer Single submitter
  • p.Thr483fs Single submitter Inborn genetic diseases
  • p.Val1613fs Single submitter neurodevelopmental disorder with dysmorphic facies and distal limb anomalies
  • p.Val1780fs Single submitter
  • p.Val2188fs Single submitter neurodevelopmental disorder with dysmorphic facies and distal limb anomalies
  • c.2982_2992+1del No assertion criteria Secondary microcephaly
  • p.Arg1859fs No assertion criteria neurodevelopmental disorder with dysmorphic facies and distal limb anomalies
  • p.Gln667Ter No assertion criteria neurodevelopmental disorder with dysmorphic facies and distal limb anomalies
  • p.Glu18fs No assertion criteria neurodevelopmental disorder with dysmorphic facies and distal limb anomalies
  • p.Glu2654fs No assertion criteria neurodevelopmental disorder with dysmorphic facies and distal limb anomalies
  • p.Glu828fs No assertion criteria Secondary microcephaly
  • p.Lys2901Ter No assertion criteria neurodevelopmental disorder with dysmorphic facies and distal limb anomalies
  • p.Lys866fs No assertion criteria neurodevelopmental disorder with dysmorphic facies and distal limb anomalies

Pathogenic/Likely pathogenic 2

  • p.Arg1322Ter Multiple submitters neurodevelopmental disorder with dysmorphic facies and distal limb anomalies
  • p.Met2870Arg No assertion criteria Secondary microcephaly

Likely pathogenic 35

  • c.1864+712dup Single submitter
  • c.1865-12_1868delinsC Single submitter neurodevelopmental disorder with dysmorphic facies and distal limb anomalies
  • c.8260_8261+2del Single submitter
  • p.Arg1498Ter Single submitter neurodevelopmental disorder with dysmorphic facies and distal limb anomalies
  • p.Arg1863Ter Single submitter neurodevelopmental disorder with dysmorphic facies and distal limb anomalies
  • p.Arg2854fs Single submitter neurodevelopmental disorder with dysmorphic facies and distal limb anomalies
  • p.Arg378Ter Single submitter neurodevelopmental disorder with dysmorphic facies and distal limb anomalies
  • p.Asn2876Ter Single submitter neurodevelopmental disorder with dysmorphic facies and distal limb anomalies
  • p.Asp2583fs Single submitter neurodevelopmental disorder
  • p.Asp269fs Single submitter neurodevelopmental disorder with dysmorphic facies and distal limb anomalies
  • p.Asp2751fs Single submitter neurodevelopmental disorder with dysmorphic facies and distal limb anomalies
  • p.Cys2890fs Single submitter
  • p.Gln1124Ter Single submitter neurodevelopmental disorder with dysmorphic facies and distal limb anomalies
  • p.Gln1611Ter Single submitter neurodevelopmental disorder with dysmorphic facies and distal limb anomalies
  • p.Gln1996Ter Single submitter neurodevelopmental disorder with dysmorphic facies and distal limb anomalies
  • p.Gln2136Ter Single submitter
  • p.Gln2528Ter Single submitter Neurodevelopmental delay
  • p.Glu2895Lys Single submitter neurodevelopmental disorder with dysmorphic facies and distal limb anomalies
  • p.Gly2362fs Single submitter neurodevelopmental disorder with dysmorphic facies and distal limb anomalies
  • p.Gly94fs Single submitter neurodevelopmental disorder with dysmorphic facies and distal limb anomalies
  • p.His1985fs Single submitter neurodevelopmental disorder with dysmorphic facies and distal limb anomalies
  • p.His2820Arg Single submitter
  • p.Ile2639Thr Single submitter ⚠
  • p.Lys933Met Single submitter neurodevelopmental disorder with dysmorphic facies and distal limb anomalies ⚠
  • p.Met2851Arg Single submitter neurodevelopmental disorder with dysmorphic facies and distal limb anomalies
  • p.Pro1761fs Single submitter
  • p.Ser1099Ter Single submitter neurodevelopmental disorder with dysmorphic facies and distal limb anomalies
  • p.Thr1819fs Single submitter neurodevelopmental disorder with dysmorphic facies and distal limb anomalies
  • p.Thr2039Ile Single submitter ⚠
  • p.Thr2227fs Single submitter neurodevelopmental disorder with dysmorphic facies and distal limb anomalies
  • p.Tyr2807Asp Single submitter neurodevelopmental disorder with dysmorphic facies and distal limb anomalies
  • p.Ala1798Thr No assertion criteria Secondary microcephaly ⚠
  • p.Arg378Gln No assertion criteria neurodevelopmental disorder with dysmorphic facies and distal limb anomalies
  • p.Pro1855fs No assertion criteria neurodevelopmental disorder with dysmorphic facies and distal limb anomalies
  • p.Pro2202fs No assertion criteria

Conflicting classifications of pathogenicity 45

Benign 52

Benign/Likely benign 23

  • c.5304-8C>T Multiple submitters
  • p.2676APP[5] Multiple submitters
  • p.2676APP[6] Multiple submitters Inborn genetic diseases
  • p.Ala112Val Multiple submitters Inborn genetic diseases
  • p.Ala1621= Multiple submitters
  • p.Ala1797= Multiple submitters
  • p.Arg1898= Multiple submitters neurodevelopmental disorder with dysmorphic facies and distal limb anomalies
  • p.Asn1576Ser Multiple submitters
  • p.Asp1305Gly Multiple submitters
  • p.Asp1795= Multiple submitters neurodevelopmental disorder with dysmorphic facies and distal limb anomalies
  • p.Asp185del Multiple submitters neurodevelopmental disorder with dysmorphic facies and distal limb anomalies
  • p.Glu163del Multiple submitters
  • p.Glu2625Lys Multiple submitters Inborn genetic diseases
  • p.Gly1641= Multiple submitters neurodevelopmental disorder with dysmorphic facies and distal limb anomalies
  • p.Gly45= Multiple submitters
  • p.Leu1423= Multiple submitters
  • p.Pro12= Multiple submitters neurodevelopmental disorder with dysmorphic facies and distal limb anomalies
  • p.Ser202Gly Multiple submitters Inborn genetic diseases
  • p.Ser2123= Multiple submitters
  • p.Thr1385= Multiple submitters
  • p.Thr1583= Multiple submitters
  • p.Thr1926Ser Multiple submitters Inborn genetic diseases
  • p.Val1431Ala Multiple submitters

Likely benign 264

Uncertain significance 692

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