EEFSEC — 116 ClinVar variants

All ClinVar germline EEFSEC variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 102 flagged for review →

2 Pathogenic · 3 Likely pathogenic · 1 Conflicting · 4 Benign · 8 Likely benign · 98 Uncertain significance

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

⚑ Evidence disagreements 102

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.

EEFSEC p.Asp390Ala Likely pathogenic Single submitter
autosomal recessive non-syndromic intellectual disability

Predictors agree, ClinVar conflicts 1

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

EEFSEC p.Pro194Thr Conflicting Single submitter
neurodevelopmental disorder with progressive spasticity and brain abnormalities

Predictors lean, ClinVar uncertain 49

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

Predictors split 51

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

All EEFSEC variants

Pathogenic 2

p.Cys426Ter No assertion criteria neurodevelopmental disorder with progressive spasticity and brain abnormalities
p.Met1Val No assertion criteria neurodevelopmental disorder with progressive spasticity and brain abnormalities

Likely pathogenic 3

p.Asp390Ala Single submitter autosomal recessive non-syndromic intellectual disability ⚠
p.Glu514Ter Single submitter neurodevelopmental disorder with progressive spasticity and brain abnormalities
p.Val585fs Single submitter infantile cerebral and cerebellar atrophy with postnatal progressive microcephaly

Conflicting classifications of pathogenicity 1

p.Pro194Thr Single submitter neurodevelopmental disorder with progressive spasticity and brain abnormalities ⚠

Benign 4

p.Ala435Val Multiple submitters
p.Phe581Cys Multiple submitters
p.Pro180= Multiple submitters
p.Arg591His Single submitter ⚠

Likely benign 8

p.Ala128= Single submitter
p.Ala547Thr Single submitter
p.Ala566Thr Single submitter
p.Asn357Ser Single submitter
p.Ile148Thr Single submitter ⚠
p.Ile363Val Single submitter
p.Thr48= Single submitter
p.Val142Ile Single submitter

Uncertain significance 98

p.Ala193Ser Single submitter ⚠
p.Ala314Val Single submitter ⚠
p.Ala31Thr Single submitter ⚠
p.Ala412Gly Single submitter ⚠
p.Ala460Thr Single submitter ⚠
p.Ala559Thr Single submitter ⚠
p.Arg177Gln Single submitter ⚠
p.Arg285Gln Single submitter neurodevelopmental disorder with progressive spasticity and brain abnormalities ⚠
p.Arg326Trp Single submitter ⚠
p.Arg408Gln Single submitter ⚠
p.Arg424Gln Single submitter ⚠
p.Arg443Gln Single submitter ⚠
p.Arg45Gly Single submitter ⚠
p.Arg491Cys Single submitter ⚠
p.Arg4Trp Single submitter ⚠
p.Arg553Gln Single submitter ⚠
p.Arg556Cys Single submitter ⚠
p.Arg556Leu Single submitter ⚠
p.Arg568Gln Single submitter ⚠
p.Arg568Trp Single submitter ⚠
p.Arg583Pro Single submitter ⚠
p.Arg591Cys Single submitter ⚠
p.Arg63Cys Single submitter ⚠
p.Asp229Glu Single submitter ⚠
p.Asp365Asn Single submitter ⚠
p.Asp365Tyr Single submitter ⚠
p.Asp461Asn Single submitter ⚠
p.Asp587Asn Single submitter ⚠
p.Cys231Tyr Single submitter ⚠
p.Gln108His Single submitter ⚠
p.Gln271Lys Single submitter ⚠
p.Gln360Arg Single submitter ⚠
p.Gln501Leu Single submitter ⚠
p.Gln562Arg Single submitter ⚠
p.Glu307Lys Single submitter ⚠
p.Glu44Gln Single submitter ⚠
p.Glu567Lys Single submitter ⚠
p.Gly190Glu Single submitter ⚠
p.Gly19Ser Single submitter ⚠
p.Gly253Ser Single submitter ⚠
p.Gly301Arg Single submitter ⚠
p.Gly399Ser Single submitter ⚠
p.Gly523Ser Single submitter ⚠
p.Gly82Ser Single submitter ⚠
p.His310Tyr Single submitter ⚠
p.His405Tyr Single submitter ⚠
p.His509Arg Single submitter ⚠
p.Ile104Asn Single submitter ⚠
p.Ile148Val Single submitter ⚠
p.Ile206Thr Single submitter ⚠
p.Ile206Val Single submitter ⚠
p.Ile322Thr Single submitter ⚠
p.Ile489Met Single submitter ⚠
p.Ile543Phe Single submitter ⚠
p.Leu246Pro Single submitter neurodevelopmental disorder with progressive spasticity and brain abnormalities ⚠
p.Leu364Val Single submitter ⚠
p.Leu451Phe Single submitter ⚠
p.Leu493Arg Single submitter ⚠
p.Leu493Val Single submitter ⚠
p.Leu502Phe Single submitter ⚠
p.Leu515Met Single submitter ⚠
p.Leu515Pro Single submitter ⚠
p.Leu99Val Single submitter ⚠
p.Lys169Glu Single submitter ⚠
p.Lys175Asn Single submitter ⚠
p.Lys235Glu Single submitter ⚠
p.Lys265Arg Single submitter ⚠
p.Lys38Arg Single submitter ⚠
p.Lys38Asn Single submitter ⚠
p.Lys396Glu Single submitter ⚠
p.Lys549Asn Single submitter ⚠
p.Met163Arg Single submitter ⚠
p.Met345Ile Single submitter ⚠
p.Met592Thr Single submitter ⚠
p.Phe463Leu Single submitter ⚠
p.Pro152Ser Single submitter ⚠
p.Pro180Leu Single submitter ⚠
p.Pro188Leu Single submitter ⚠
p.Pro259Ser Single submitter ⚠
p.Pro323Leu Single submitter ⚠
p.Pro353Ser Single submitter ⚠
p.Pro362Arg Single submitter ⚠
p.Pro59Gln Single submitter ⚠
p.Pro61Ser Single submitter ⚠
p.Pro84Ser Single submitter ⚠
p.Ser247Thr Single submitter ⚠
p.Ser565Asn Single submitter ⚠
p.Thr217Met Single submitter ⚠
p.Thr441Met Single submitter ⚠
p.Thr441Pro Single submitter ⚠
p.Thr580Ile Single submitter ⚠
p.Val144Leu Single submitter ⚠
p.Val184Leu Single submitter ⚠
p.Val290Ile Single submitter ⚠
p.Val414Leu Single submitter ⚠
p.Val504Met Single submitter ⚠
p.Val58Leu Single submitter ⚠
p.Val6Met Single submitter ⚠