NECAP1 — 194 ClinVar variants

All ClinVar germline NECAP1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 95 flagged for review →

3 Pathogenic · 1 Pathogenic/Likely pathogenic · 1 Conflicting · 4 Benign · 1 Benign/Likely benign · 83 Likely benign · 101 Uncertain significance

Full NECAP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 95

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 1

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

Predictors lean, ClinVar uncertain 78

ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.

Predictors split 16

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

All NECAP1 variants

Pathogenic 3

  • p.Asp87fs Single submitter developmental and epileptic encephalopathy, 21
  • c.301+1G>A No assertion criteria developmental and epileptic encephalopathy, 21
  • p.Val13fs No assertion criteria

Pathogenic/Likely pathogenic 1

  • p.Arg48Ter No assertion criteria developmental and epileptic encephalopathy, 21

Conflicting classifications of pathogenicity 1

  • p.Asp224Asn Single submitter developmental and epileptic encephalopathy, 21 ⚠

Benign 4

Benign/Likely benign 1

  • c.492+19A>G Multiple submitters developmental and epileptic encephalopathy, 21

Likely benign 83

  • c.301+15A>C Multiple submitters developmental and epileptic encephalopathy, 21
  • p.Gly172= Multiple submitters developmental and epileptic encephalopathy, 21
  • p.Ile163= Multiple submitters developmental and epileptic encephalopathy, 21
  • p.Leu38= Multiple submitters developmental and epileptic encephalopathy, 21
  • p.Leu60= Multiple submitters developmental and epileptic encephalopathy, 21
  • p.Pro216= Multiple submitters developmental and epileptic encephalopathy, 21
  • p.Thr84= Multiple submitters developmental and epileptic encephalopathy, 21
  • c.196+11C>T Single submitter developmental and epileptic encephalopathy, 21
  • c.196+12G>A Single submitter developmental and epileptic encephalopathy, 21
  • c.196+12G>C Single submitter developmental and epileptic encephalopathy, 21
  • c.196+18C>T Single submitter developmental and epileptic encephalopathy, 21
  • c.196+19C>T Single submitter developmental and epileptic encephalopathy, 21
  • c.196+20C>G Single submitter developmental and epileptic encephalopathy, 21
  • c.196+20C>T Single submitter developmental and epileptic encephalopathy, 21
  • c.197-12C>T Single submitter developmental and epileptic encephalopathy, 21
  • c.197-16T>C Single submitter developmental and epileptic encephalopathy, 21
  • c.197-19T>C Single submitter developmental and epileptic encephalopathy, 21
  • c.197-5G>C Single submitter developmental and epileptic encephalopathy, 21
  • c.197-8T>C Single submitter developmental and epileptic encephalopathy, 21
  • c.301+13G>A Single submitter developmental and epileptic encephalopathy, 21
  • c.301+14G>A Single submitter developmental and epileptic encephalopathy, 21
  • c.302-11G>A Single submitter developmental and epileptic encephalopathy, 21
  • c.302-11G>T Single submitter developmental and epileptic encephalopathy, 21
  • c.302-13A>G Single submitter developmental and epileptic encephalopathy, 21
  • c.302-5C>T Single submitter developmental and epileptic encephalopathy, 21
  • c.383+10G>C Single submitter developmental and epileptic encephalopathy, 21
  • c.383+11dup Single submitter developmental and epileptic encephalopathy, 21
  • c.383+13del Single submitter developmental and epileptic encephalopathy, 21
  • c.383+13T>A Single submitter developmental and epileptic encephalopathy, 21
  • c.383+15T>C Single submitter developmental and epileptic encephalopathy, 21
  • c.383+19T>G Single submitter developmental and epileptic encephalopathy, 21
  • c.384-12G>A Single submitter developmental and epileptic encephalopathy, 21
  • c.384-14C>A Single submitter developmental and epileptic encephalopathy, 21
  • c.384-14C>T Single submitter developmental and epileptic encephalopathy, 21
  • c.384-15G>A Single submitter developmental and epileptic encephalopathy, 21
  • c.384-19A>G Single submitter developmental and epileptic encephalopathy, 21
  • c.492+15T>C Single submitter developmental and epileptic encephalopathy, 21
  • c.492+18A>T Single submitter developmental and epileptic encephalopathy, 21
  • c.492+7A>G Single submitter developmental and epileptic encephalopathy, 21
  • c.493-6T>C Single submitter developmental and epileptic encephalopathy, 21
  • c.676+10G>A Single submitter developmental and epileptic encephalopathy, 21
  • c.676+15T>C Single submitter developmental and epileptic encephalopathy, 21
  • c.676+16C>G Single submitter developmental and epileptic encephalopathy, 21
  • c.676+18A>G Single submitter developmental and epileptic encephalopathy, 21
  • c.676+9A>G Single submitter developmental and epileptic encephalopathy, 21
  • c.677-12C>T Single submitter developmental and epileptic encephalopathy, 21
  • c.779+12A>G Single submitter developmental and epileptic encephalopathy, 21
  • c.779+19C>T Single submitter developmental and epileptic encephalopathy, 21
  • c.780-12_780-10del Single submitter developmental and epileptic encephalopathy, 21
  • c.780-13T>C Single submitter developmental and epileptic encephalopathy, 21
  • c.780-6T>C Single submitter
  • c.780-7C>G Single submitter developmental and epileptic encephalopathy, 21
  • c.95+16C>T Single submitter developmental and epileptic encephalopathy, 21
  • c.95+9C>T Single submitter developmental and epileptic encephalopathy, 21
  • c.96-15C>T Single submitter developmental and epileptic encephalopathy, 21
  • p.Ala241= Single submitter developmental and epileptic encephalopathy, 21
  • p.Ala70= Single submitter developmental and epileptic encephalopathy, 21
  • p.Arg177= Single submitter developmental and epileptic encephalopathy, 21
  • p.Asn264= Single submitter
  • p.Asp39= Single submitter developmental and epileptic encephalopathy, 21
  • p.Asp42= Single submitter developmental and epileptic encephalopathy, 21
  • p.Gln124= Single submitter developmental and epileptic encephalopathy, 21
  • p.Gln268= Single submitter developmental and epileptic encephalopathy, 21
  • p.Gln76= Single submitter developmental and epileptic encephalopathy, 21
  • p.Glu139= Single submitter developmental and epileptic encephalopathy, 21
  • p.Gly152= Single submitter
  • p.Gly182= Single submitter developmental and epileptic encephalopathy, 21
  • p.Gly193= Single submitter developmental and epileptic encephalopathy, 21
  • p.Ile227= Single submitter developmental and epileptic encephalopathy, 21
  • p.Lys131= Single submitter developmental and epileptic encephalopathy, 21
  • p.Phe105= Single submitter developmental and epileptic encephalopathy, 21
  • p.Phe117= Single submitter developmental and epileptic encephalopathy, 21
  • p.Pro190= Single submitter developmental and epileptic encephalopathy, 21
  • p.Pro191= Single submitter developmental and epileptic encephalopathy, 21
  • p.Pro198= Single submitter developmental and epileptic encephalopathy, 21
  • p.Pro41= Single submitter
  • p.Ser140= Single submitter developmental and epileptic encephalopathy, 21
  • p.Ser185= Single submitter developmental and epileptic encephalopathy, 21
  • p.Ser270= Single submitter developmental and epileptic encephalopathy, 21
  • p.Thr238= Single submitter developmental and epileptic encephalopathy, 21
  • p.Thr239= Single submitter
  • p.Val130= Single submitter
  • p.Val237Leu Single submitter developmental and epileptic encephalopathy, 21

Uncertain significance 101

  • p.Ala173Val Multiple submitters Inborn genetic diseases ⚠
  • p.Arg102His Multiple submitters developmental and epileptic encephalopathy, 21 ⚠
  • p.Arg146His Multiple submitters developmental and epileptic encephalopathy, 21 ⚠
  • p.Arg46Cys Multiple submitters developmental and epileptic encephalopathy, 21 ⚠
  • p.Asp118Asn Multiple submitters developmental and epileptic encephalopathy, 21 ⚠
  • p.Gly253Glu Multiple submitters Inborn genetic diseases ⚠
  • p.Gly45Ala Multiple submitters developmental and epileptic encephalopathy, 21 ⚠
  • p.His126Tyr Multiple submitters Inborn genetic diseases ⚠
  • p.Ile163Val Multiple submitters developmental and epileptic encephalopathy, 21 ⚠
  • p.Lys194Arg Multiple submitters developmental and epileptic encephalopathy, 21 ⚠
  • p.Pro190Leu Multiple submitters developmental and epileptic encephalopathy, 21 ⚠
  • p.Pro214Ser Multiple submitters Inborn genetic diseases ⚠
  • p.Pro216Leu Multiple submitters Inborn genetic diseases ⚠
  • p.Pro236Ser Multiple submitters Inborn genetic diseases ⚠
  • p.Thr111Ala Multiple submitters Inborn genetic diseases ⚠
  • p.Thr84Met Multiple submitters Inborn genetic diseases ⚠
  • c.302-12C>G Single submitter developmental and epileptic encephalopathy, 21
  • c.383+3G>T Single submitter developmental and epileptic encephalopathy, 21
  • c.492+3G>A Single submitter developmental and epileptic encephalopathy, 21
  • c.96-4C>T Single submitter
  • p.Ala116Ser Single submitter developmental and epileptic encephalopathy, 21 ⚠
  • p.Ala145Gly Single submitter Inborn genetic diseases ⚠
  • p.Ala225Gly Single submitter developmental and epileptic encephalopathy, 21 ⚠
  • p.Ala258Thr Single submitter developmental and epileptic encephalopathy, 21 ⚠
  • p.Ala266Val Single submitter developmental and epileptic encephalopathy, 21 ⚠
  • p.Ala26Val Single submitter developmental and epileptic encephalopathy, 21 ⚠
  • p.Ala72Ser Single submitter developmental and epileptic encephalopathy, 21 ⚠
  • p.Ala81Ser Single submitter developmental and epileptic encephalopathy, 21 ⚠
  • p.Arg113Gln Single submitter developmental and epileptic encephalopathy, 21 ⚠
  • p.Arg113Trp Single submitter developmental and epileptic encephalopathy, 21 ⚠
  • p.Arg146Cys Single submitter developmental and epileptic encephalopathy, 21 ⚠
  • p.Arg146Leu Single submitter developmental and epileptic encephalopathy, 21 ⚠
  • p.Arg180Lys Single submitter developmental and epileptic encephalopathy, 21 ⚠
  • p.Arg46His Single submitter developmental and epileptic encephalopathy, 21 ⚠
  • p.Arg48Gln Single submitter Inborn genetic diseases ⚠
  • p.Arg90Cys Single submitter developmental and epileptic encephalopathy, 21 ⚠
  • p.Arg95Gln Single submitter Inborn genetic diseases ⚠
  • p.Arg95Trp Single submitter ⚠
  • p.Asn249Ser Single submitter developmental and epileptic encephalopathy, 21 ⚠
  • p.Asn264Asp Single submitter developmental and epileptic encephalopathy, 21 ⚠
  • p.Asn264Ser Single submitter developmental and epileptic encephalopathy, 21 ⚠
  • p.Asn271Ser Single submitter developmental and epileptic encephalopathy, 21 ⚠
  • p.Asp115Glu Single submitter Inborn genetic diseases ⚠
  • p.Asp144Asn Single submitter developmental and epileptic encephalopathy, 21 ⚠
  • p.Asp150Gly Single submitter developmental and epileptic encephalopathy, 21 ⚠
  • p.Gln141Arg Single submitter developmental and epileptic encephalopathy, 21 ⚠
  • p.Gln265Leu Single submitter developmental and epileptic encephalopathy, 21 ⚠
  • p.Gln274His Single submitter developmental and epileptic encephalopathy, 21 ⚠
  • p.Gln97His Single submitter ⚠
  • p.Glu133Gly Single submitter developmental and epileptic encephalopathy, 21
  • p.Glu61Val Single submitter ⚠
  • p.Gly107Val Single submitter ⚠
  • p.Gly172Asp Single submitter developmental and epileptic encephalopathy, 21 ⚠
  • p.Gly172Val Single submitter developmental and epileptic encephalopathy, 21 ⚠
  • p.Gly181Ala Single submitter developmental and epileptic encephalopathy, 21 ⚠
  • p.Gly222Ser Single submitter developmental and epileptic encephalopathy, 21 ⚠
  • p.Gly253Arg Single submitter ⚠
  • p.Gly53Ala Single submitter Inborn genetic diseases ⚠
  • p.Gly79Asp Single submitter developmental and epileptic encephalopathy, 21 ⚠
  • p.Leu229Ser Single submitter Inborn genetic diseases ⚠
  • p.Leu251Phe Single submitter developmental and epileptic encephalopathy, 21 ⚠
  • p.Leu251Val Single submitter Inborn genetic diseases ⚠
  • p.Leu60Phe Single submitter developmental and epileptic encephalopathy, 21 ⚠
  • p.Leu60Pro Single submitter Inborn genetic diseases ⚠
  • p.Lys148Glu Single submitter developmental and epileptic encephalopathy, 21 ⚠
  • p.Lys160Thr Single submitter developmental and epileptic encephalopathy, 21 ⚠
  • p.Lys194Ile Single submitter developmental and epileptic encephalopathy, 21 ⚠
  • p.Lys54Thr Single submitter developmental and epileptic encephalopathy, 21 ⚠
  • p.Lys59Arg Single submitter Inborn genetic diseases ⚠
  • p.Met143Val Single submitter developmental and epileptic encephalopathy, 21 ⚠
  • p.Phe255= Single submitter developmental and epileptic encephalopathy, 21
  • p.Phe69Leu Single submitter Inborn genetic diseases ⚠
  • p.Pro188Leu Single submitter ⚠
  • p.Pro188Thr Single submitter developmental and epileptic encephalopathy, 21 ⚠
  • p.Pro189Thr Single submitter NECAP1-related disorder ⚠
  • p.Pro190Arg Single submitter developmental and epileptic encephalopathy, 21 ⚠
  • p.Pro199Ser Single submitter developmental and epileptic encephalopathy, 21 ⚠
  • p.Pro213Ser Single submitter Inborn genetic diseases ⚠
  • p.Pro234Ser Single submitter developmental and epileptic encephalopathy, 21 ⚠
  • p.Pro23Leu Single submitter developmental and epileptic encephalopathy, 21 ⚠
  • p.Pro73Ser Single submitter developmental and epileptic encephalopathy, 21 ⚠
  • p.Ser122Cys Single submitter Inborn genetic diseases ⚠
  • p.Ser202Phe Single submitter Inborn genetic diseases ⚠
  • p.Ser218Phe Single submitter developmental and epileptic encephalopathy, 21 ⚠
  • p.Ser218Tyr Single submitter developmental and epileptic encephalopathy, 21 ⚠
  • p.Ser260Asn Single submitter developmental and epileptic encephalopathy, 21 ⚠
  • p.Ser261Cys Single submitter developmental and epileptic encephalopathy, 21 ⚠
  • p.Ser34Thr Single submitter developmental and epileptic encephalopathy, 21 ⚠
  • p.Ser65= Single submitter developmental and epileptic encephalopathy, 21
  • p.Thr196Pro Single submitter developmental and epileptic encephalopathy, 21 ⚠
  • p.Thr238Met Single submitter developmental and epileptic encephalopathy, 21 ⚠
  • p.Thr239Ser Single submitter developmental and epileptic encephalopathy, 21 ⚠
  • p.Thr243Ala Single submitter developmental and epileptic encephalopathy, 21 ⚠
  • p.Thr44Asn Single submitter developmental and epileptic encephalopathy, 21 ⚠
  • p.Thr86Ile Single submitter developmental and epileptic encephalopathy, 21 ⚠
  • p.Tyr57Cys Single submitter Inborn genetic diseases ⚠
  • p.Val210Ala Single submitter developmental and epileptic encephalopathy, 21 ⚠
  • p.Val237Ile Single submitter developmental and epileptic encephalopathy, 21 ⚠
  • p.Val245Ala Single submitter developmental and epileptic encephalopathy, 21 ⚠
  • p.Val273Ala Single submitter developmental and epileptic encephalopathy, 21 ⚠
  • p.Val82Met Single submitter developmental and epileptic encephalopathy, 21 ⚠