EFTUD2 — 928 ClinVar variants

All ClinVar germline EFTUD2 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 278 flagged for review →

97 Pathogenic · 12 Pathogenic/Likely pathogenic · 77 Likely pathogenic · 31 Conflicting · 87 Benign · 27 Benign/Likely benign · 289 Likely benign · 308 Uncertain significance

Full EFTUD2 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 278

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 lean, ClinVar uncertain 201

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 201

Predictors split 57

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

All EFTUD2 variants

Pathogenic 97

  • c.1058+1G>A Multiple submitters Inborn genetic diseases
  • c.2562-2del Multiple submitters mandibulofacial dysostosis-microcephaly syndrome
  • c.702+1del Multiple submitters mandibulofacial dysostosis-microcephaly syndrome
  • p.Arg262Trp Multiple submitters EFTUD2-related disorders
  • p.Arg569Ter Multiple submitters mandibulofacial dysostosis-microcephaly syndrome
  • p.Arg578Ter Multiple submitters mandibulofacial dysostosis-microcephaly syndrome
  • p.Glu338Ter Multiple submitters
  • p.Leu474fs Multiple submitters mandibulofacial dysostosis-microcephaly syndrome
  • p.Met433fs Multiple submitters mandibulofacial dysostosis-microcephaly syndrome
  • p.Trp733Ter Multiple submitters mandibulofacial dysostosis-microcephaly syndrome
  • p.Tyr114Ter Multiple submitters Global developmental delay
  • p.Val900fs Multiple submitters mandibulofacial dysostosis-microcephaly syndrome
  • c.106-1G>C Single submitter mandibulofacial dysostosis-microcephaly syndrome
  • c.106-2A>G Single submitter Inborn genetic diseases
  • c.1149+1G>C Single submitter mandibulofacial dysostosis-microcephaly syndrome
  • c.1150-1G>T Single submitter
  • c.1150-2A>G Single submitter
  • c.1413+204_1608-909del Single submitter Inborn genetic diseases
  • c.1719+1G>A Single submitter mandibulofacial dysostosis-microcephaly syndrome
  • c.1860+1G>A Single submitter
  • c.1860+2del Single submitter
  • c.1963-1G>T Single submitter
  • c.2045+1G>A Single submitter
  • c.2347+1G>T Single submitter
  • c.2466+1G>A Single submitter
  • c.2561+1G>A Single submitter mandibulofacial dysostosis-microcephaly syndrome
  • c.2562-1G>A Single submitter Inborn genetic diseases
  • c.2565del Single submitter mandibulofacial dysostosis-microcephaly syndrome
  • c.271+2T>A Single submitter mandibulofacial dysostosis-microcephaly syndrome
  • c.351-1G>T Single submitter
  • c.529-2A>G Single submitter cleft lip/palate
  • c.-4-2A>G Single submitter
  • p.Arg785fs Single submitter Inborn genetic diseases
  • p.Asn743fs Single submitter
  • p.Asp295fs Single submitter mandibulofacial dysostosis-microcephaly syndrome
  • p.Asp518fs Single submitter Inborn genetic diseases
  • p.Cys468fs Single submitter
  • p.Gln175Ter Single submitter
  • p.Gln313fs Single submitter mandibulofacial dysostosis-microcephaly syndrome
  • p.Gln366Ter Single submitter
  • p.Gln489fs Single submitter Inborn genetic diseases
  • p.Gln505Ter Single submitter
  • p.Gln523fs Single submitter mandibulofacial dysostosis-microcephaly syndrome
  • p.Gln557Ter Single submitter
  • p.Gln719fs Single submitter mandibulofacial dysostosis-microcephaly syndrome
  • p.Gln837Ter Single submitter EFTUD2-related disorders
  • p.Gln87Ter Single submitter mandibulofacial dysostosis-microcephaly syndrome
  • p.Gln892fs Single submitter
  • p.Gln894fs Single submitter mandibulofacial dysostosis-microcephaly syndrome
  • p.Gln924Ter Single submitter mandibulofacial dysostosis-microcephaly syndrome
  • p.Glu127fs Single submitter mandibulofacial dysostosis-microcephaly syndrome
  • p.Glu35Ter Single submitter
  • p.Glu517Ter Single submitter mandibulofacial dysostosis-microcephaly syndrome
  • p.Glu91fs Single submitter mandibulofacial dysostosis-microcephaly syndrome
  • p.Gly195fs Single submitter
  • p.Gly224Val Single submitter
  • p.Gly444fs Single submitter mandibulofacial dysostosis-microcephaly syndrome
  • p.Gly777Val Single submitter
  • p.His208fs Single submitter
  • p.His642fs Single submitter
  • p.Ile157fs Single submitter mandibulofacial dysostosis-microcephaly syndrome
  • p.Ile170fs Single submitter mandibulofacial dysostosis-microcephaly syndrome
  • p.Ile552fs Single submitter mandibulofacial dysostosis-microcephaly syndrome
  • p.Leu630fs Single submitter
  • p.Leu635fs Single submitter
  • p.Lys142fs Single submitter mandibulofacial dysostosis-microcephaly syndrome
  • p.Lys244fs Single submitter Inborn genetic diseases
  • p.Lys98Ter Single submitter
  • p.Met465fs Single submitter
  • p.Met603fs Single submitter mandibulofacial dysostosis-microcephaly syndrome
  • p.Phe349fs Single submitter
  • p.Phe718fs Single submitter
  • p.Phe833fs Single submitter mandibulofacial dysostosis-microcephaly syndrome
  • p.Phe881fs Single submitter mandibulofacial dysostosis-microcephaly syndrome
  • p.Pro376Arg Single submitter
  • p.Pro53fs Single submitter
  • p.Pro867fs Single submitter mandibulofacial dysostosis-microcephaly syndrome
  • p.Ser183fs Single submitter mandibulofacial dysostosis-microcephaly syndrome
  • p.Ser866fs Single submitter Inborn genetic diseases
  • p.Thr661fs Single submitter
  • p.Tyr198Ter Single submitter mandibulofacial dysostosis-microcephaly syndrome
  • p.Tyr336fs Single submitter
  • p.Tyr614Ter Single submitter mandibulofacial dysostosis-microcephaly syndrome
  • p.Tyr636fs Single submitter mandibulofacial dysostosis-microcephaly syndrome
  • p.Val592fs Single submitter mandibulofacial dysostosis-microcephaly syndrome
  • p.Val667fs Single submitter
  • p.Val836fs Single submitter Inborn genetic diseases
  • p.Val849fs Single submitter
  • c.2823+1del No assertion criteria mandibulofacial dysostosis-microcephaly syndrome
  • p.Cys256fs No assertion criteria mandibulofacial dysostosis-microcephaly syndrome
  • p.Gln807fs No assertion criteria esophageal atresia/tracheoesophageal fistula
  • p.His208Arg No assertion criteria mandibulofacial dysostosis-microcephaly syndrome
  • p.Leu637Arg No assertion criteria mandibulofacial dysostosis-microcephaly syndrome
  • p.Met1Ile No assertion criteria mandibulofacial dysostosis-microcephaly syndrome
  • p.Tyr831Ter No assertion criteria mandibulofacial dysostosis-microcephaly syndrome
  • p.Tyr832Ter No assertion criteria mandibulofacial dysostosis-microcephaly syndrome
  • p.Val587fs No assertion criteria mandibulofacial dysostosis-microcephaly syndrome

Pathogenic/Likely pathogenic 12

  • c.1414-2A>G Multiple submitters neurodevelopmental disorder
  • c.1962+1G>A Multiple submitters
  • c.2133-2A>G Multiple submitters mandibulofacial dysostosis-microcephaly syndrome
  • c.2562-2_2562-1del Multiple submitters mandibulofacial dysostosis-microcephaly syndrome
  • c.2562-2A>G Multiple submitters mandibulofacial dysostosis-microcephaly syndrome
  • c.702+1G>T Multiple submitters Inborn genetic diseases
  • c.703-2A>G Multiple submitters mandibulofacial dysostosis-microcephaly syndrome
  • p.Arg354Ter Multiple submitters Inborn genetic diseases
  • p.Arg938His Multiple submitters mandibulofacial dysostosis-microcephaly syndrome
  • p.Asn286Ser Multiple submitters mandibulofacial dysostosis-microcephaly syndrome
  • p.Leu190fs Multiple submitters mandibulofacial dysostosis-microcephaly syndrome
  • p.Tyr514Ter Multiple submitters mandibulofacial dysostosis-microcephaly syndrome

Likely pathogenic 77

  • c.1607+1G>T Multiple submitters mandibulofacial dysostosis-microcephaly syndrome
  • p.Gly494Asp Multiple submitters EFTUD2-related disorder
  • p.Gly769Asp Multiple submitters mandibulofacial dysostosis-microcephaly syndrome
  • c.105+2T>G Single submitter Inborn genetic diseases
  • c.1149+1G>A Single submitter
  • c.1150-1G>A Single submitter EFTUD2-related disorders
  • c.1286-2A>C Single submitter mandibulofacial dysostosis-microcephaly syndrome
  • c.1286-2A>G Single submitter mandibulofacial dysostosis-microcephaly syndrome
  • c.1607+3A>G Single submitter mandibulofacial dysostosis-microcephaly syndrome
  • c.2045+2T>G Single submitter mandibulofacial dysostosis-microcephaly syndrome
  • c.2561+1G>T Single submitter mandibulofacial dysostosis-microcephaly syndrome
  • c.2562-2_2562del Single submitter
  • c.(350+1_351-1 Single submitter mandibulofacial dysostosis-microcephaly syndrome
  • c.351-2A>G Single submitter mandibulofacial dysostosis-microcephaly syndrome
  • c.427-1G>A Single submitter mandibulofacial dysostosis-microcephaly syndrome
  • c.619+1del Single submitter EFTUD2-related disorders
  • c.702+1G>C Single submitter mandibulofacial dysostosis-microcephaly syndrome
  • c.702+2T>C Single submitter mandibulofacial dysostosis-microcephaly syndrome
  • c.870-1G>T Single submitter mandibulofacial dysostosis-microcephaly syndrome
  • c.995-10T>A Single submitter esophageal atresia
  • c.995-1G>C Single submitter
  • p.Ala676fs Single submitter mandibulofacial dysostosis-microcephaly syndrome
  • p.Ala851fs Single submitter mandibulofacial dysostosis-microcephaly syndrome
  • p.Arg730His Single submitter EFTUD2-related disorders
  • p.Arg919fs Single submitter
  • p.Arg939fs Single submitter mandibulofacial dysostosis-microcephaly syndrome
  • p.Asn548fs Single submitter
  • p.Asn683Tyr Single submitter Global developmental delay
  • p.Asp725Gly Single submitter
  • p.Asp747fs Single submitter mandibulofacial dysostosis-microcephaly syndrome
  • p.Cys135Arg Single submitter EFTUD2-related disorders
  • p.Gln248Ter Single submitter
  • p.Gln313Ter Single submitter EFTUD2-related disorders
  • p.Gln436Ter Single submitter mandibulofacial dysostosis-microcephaly syndrome
  • p.Gln575Ter Single submitter mandibulofacial dysostosis-microcephaly syndrome
  • p.Glu16fs Single submitter
  • p.Glu240fs Single submitter mandibulofacial dysostosis-microcephaly syndrome
  • p.Glu35= Single submitter
  • p.Gly141Asp Single submitter
  • p.Gly180Val Single submitter
  • p.Gly570= Single submitter EFTUD2-related disorders
  • p.Gly633Arg Single submitter
  • p.Ile875fs Single submitter
  • p.Leu149Ter Single submitter mandibulofacial dysostosis-microcephaly syndrome
  • p.Leu265fs Single submitter mandibulofacial dysostosis-microcephaly syndrome
  • p.Leu779Phe Single submitter mandibulofacial dysostosis-microcephaly syndrome
  • p.Leu801fs Single submitter EFTUD2-related disorders
  • p.Lys379Asn Single submitter mandibulofacial dysostosis-microcephaly syndrome
  • p.Lys581fs Single submitter mandibulofacial dysostosis-microcephaly syndrome
  • p.Phe770Ser Single submitter mandibulofacial dysostosis-microcephaly syndrome
  • p.Pro778His Single submitter
  • p.Pro778Thr Single submitter mandibulofacial dysostosis-microcephaly syndrome
  • p.Ser183Arg Single submitter mandibulofacial dysostosis-microcephaly syndrome
  • p.Ser290Asn Single submitter mandibulofacial dysostosis-microcephaly syndrome ⚠
  • p.Ser649Ter Single submitter mandibulofacial dysostosis-microcephaly syndrome
  • p.Ser670fs Single submitter mandibulofacial dysostosis-microcephaly syndrome
  • p.Ser897fs Single submitter
  • p.Ter973Ser Single submitter
  • p.Thr143fs Single submitter
  • p.Thr678Met Single submitter mandibulofacial dysostosis-microcephaly syndrome
  • p.Trp709Ter Single submitter mandibulofacial dysostosis-microcephaly syndrome
  • p.Trp724Ter Single submitter mandibulofacial dysostosis-microcephaly syndrome
  • p.Tyr722Ter Single submitter mandibulofacial dysostosis-microcephaly syndrome
  • p.Val431fs Single submitter mandibulofacial dysostosis-microcephaly syndrome
  • p.Val550Asp Single submitter mandibulofacial dysostosis-microcephaly syndrome
  • p.Val843fs Single submitter mandibulofacial dysostosis-microcephaly syndrome
  • c.1149+5G>C No assertion criteria
  • c.1286-2del No assertion criteria mandibulofacial dysostosis-microcephaly syndrome
  • c.2133-1G>T No assertion criteria
  • c.350+5G>A No assertion criteria
  • c.426+1dup No assertion criteria mandibulofacial dysostosis-microcephaly syndrome
  • c.870-5_870-4del No assertion criteria mandibulofacial dysostosis-microcephaly syndrome
  • p.Ala445fs No assertion criteria mandibulofacial dysostosis-microcephaly syndrome
  • p.Glu650fs No assertion criteria Chromatinopathy
  • p.Thr112fs No assertion criteria mandibulofacial dysostosis-microcephaly syndrome
  • p.Tyr276Ter No assertion criteria mandibulofacial dysostosis-microcephaly syndrome
  • p.Tyr847fs No assertion criteria EFTUD2-related disorder

Conflicting classifications of pathogenicity 31

Benign 87

Benign/Likely benign 27

Likely benign 289

Uncertain significance 308

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