Sugi Variant

Sugi Variant/CIITA

CIITA — 1679 ClinVar variants

All ClinVar germline CIITA variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 585 flagged for review →

52 Pathogenic · 10 Pathogenic/Likely pathogenic · 41 Likely pathogenic · 45 Conflicting · 47 Benign · 11 Benign/Likely benign · 826 Likely benign · 647 Uncertain significance

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

⚑ Evidence disagreements 585

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 10

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

Predictors lean, ClinVar uncertain 349

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 349

Predictors split 226

The independent predictors disagree with each other — read with care. · showing the 150 best-reviewed of 226

All CIITA variants

Pathogenic 52

  • p.Gln228Ter Multiple submitters MHC class II deficiency
  • p.Ala196fs Single submitter MHC class II deficiency
  • p.Ala388fs Single submitter MHC class II deficiency
  • p.Ala616fs Single submitter MHC class II deficiency
  • p.Ala702fs Single submitter MHC class II deficiency
  • p.Ala803fs Single submitter MHC class II deficiency
  • p.Ala855fs Single submitter MHC class II deficiency
  • p.Arg414Ter Single submitter MHC class II deficiency
  • p.Arg864fs Single submitter MHC class II deficiency
  • p.Asp467fs Single submitter MHC class II deficiency
  • p.Cys523fs Single submitter MHC class II deficiency
  • p.Cys812Ter Single submitter MHC class II deficiency
  • p.Gln1121Ter Single submitter MHC class II deficiency
  • p.Gln367Ter Single submitter MHC class II deficiency
  • p.Gln475Ter Single submitter MHC class II deficiency
  • p.Gln573Ter Single submitter MHC class II deficiency
  • p.Gln672Ter Single submitter MHC class II deficiency
  • p.Gln676Ter Single submitter MHC class II deficiency
  • p.Gln735Ter Single submitter MHC class II deficiency
  • p.Gln827Ter Single submitter MHC class II deficiency
  • p.Glu126Ter Single submitter MHC class II deficiency
  • p.Glu352fs Single submitter MHC class II deficiency
  • p.Glu622fs Single submitter MHC class II deficiency
  • p.Glu815fs Single submitter MHC class II deficiency
  • p.Gly350fs Single submitter MHC class II deficiency
  • p.Gly831fs Single submitter MHC class II deficiency
  • p.Gly856fs Single submitter MHC class II deficiency
  • p.Leu397fs Single submitter MHC class II deficiency
  • p.Lys914Ter Single submitter MHC class II deficiency
  • p.Lys926fs Single submitter MHC class II deficiency
  • p.Met210fs Single submitter MHC class II deficiency
  • p.Phe501fs Single submitter MHC class II deficiency
  • p.Pro268fs Single submitter MHC class II deficiency
  • p.Pro269fs Single submitter MHC class II deficiency
  • p.Pro843fs Single submitter MHC class II deficiency
  • p.Ser213fs Single submitter MHC class II deficiency
  • p.Ser513fs Single submitter MHC class II deficiency
  • p.Ser942fs Single submitter MHC class II deficiency
  • p.Ser944fs Single submitter MHC class II deficiency
  • p.Trp688Ter Single submitter MHC class II deficiency
  • p.Trp721Ter Single submitter MHC class II deficiency
  • p.Trp750Ter Single submitter MHC class II deficiency
  • p.Trp822Ter Single submitter MHC class II deficiency
  • p.Tyr1033fs Single submitter MHC class II deficiency
  • p.Tyr12Ter Single submitter MHC class II deficiency
  • p.Tyr463Ter Single submitter MHC class II deficiency
  • p.Tyr641fs Single submitter MHC class II deficiency
  • p.Val338fs Single submitter MHC class II deficiency
  • c.2890_2969+1del No assertion criteria MHC class II deficiency 1
  • p.Asn310fs No assertion criteria MHC class II deficiency 1
  • p.Glu381Ter No assertion criteria MHC class II deficiency 1
  • p.Ile1027del No assertion criteria MHC class II deficiency 1

Pathogenic/Likely pathogenic 10

  • c.2888+1G>A Multiple submitters MHC class II deficiency
  • c.2889-1G>T Multiple submitters MHC class II deficiency
  • p.Ala462fs Multiple submitters MHC class II deficiency
  • p.Ala656fs Multiple submitters MHC class II deficiency
  • p.Arg308Ter Multiple submitters MHC class II deficiency
  • p.Arg539Ter Multiple submitters MHC class II deficiency
  • p.Gln507fs Multiple submitters MHC class II deficiency
  • p.Gln764fs Multiple submitters MHC class II deficiency 1
  • p.Gly655fs Multiple submitters MHC class II deficiency
  • p.Pro211fs Multiple submitters MHC class II deficiency 1

Likely pathogenic 41

  • c.199+1G>A Multiple submitters MHC class II deficiency
  • c.628+1G>A Multiple submitters rheumatoid arthritis
  • p.Leu114fs Multiple submitters MHC class II deficiency
  • c.200-1G>C Single submitter MHC class II deficiency
  • c.2657+1G>A Single submitter MHC class II deficiency
  • c.3062+2T>C Single submitter MHC class II deficiency
  • c.3147_3149+2del Single submitter MHC class II deficiency
  • c.3317+1G>A Single submitter MHC class II deficiency
  • c.3317+2dup Single submitter
  • c.359-2A>G Single submitter MHC class II deficiency
  • c.436+1G>A Single submitter MHC class II deficiency
  • c.436+1G>C Single submitter MHC class II deficiency
  • c.436+2T>C Single submitter MHC class II deficiency
  • c.481+1G>A Single submitter MHC class II deficiency
  • c.482-1G>C Single submitter MHC class II deficiency
  • c.52+1del Single submitter MHC class II deficiency
  • c.772+1G>T Single submitter MHC class II deficiency
  • c.937+1G>A Single submitter MHC class II deficiency
  • c.937+2T>C Single submitter MHC class II deficiency
  • c.938-2A>G Single submitter MHC class II deficiency
  • p.Ala5fs Single submitter MHC class II deficiency
  • p.Ala94fs Single submitter MHC class II deficiency
  • p.Arg552fs Single submitter MHC class II deficiency
  • p.Asp492fs Single submitter MHC class II deficiency
  • p.Gln107Ter Single submitter MHC class II deficiency
  • p.Gln242Ter Single submitter MHC class II deficiency
  • p.Gln444Ter Single submitter MHC class II deficiency
  • p.Gln900Ter Single submitter MHC class II deficiency 1
  • p.Gln936Ter Single submitter MHC class II deficiency
  • p.Gln987Ter Single submitter MHC class II deficiency
  • p.Glu379fs Single submitter MHC class II deficiency
  • p.Leu240fs Single submitter MHC class II deficiency
  • p.Leu392fs Single submitter MHC class II deficiency
  • p.Leu472fs Single submitter MHC class II deficiency 1
  • p.Leu960fs Single submitter MHC class II deficiency
  • p.Lys116fs Single submitter MHC class II deficiency
  • p.Lys794fs Single submitter rheumatoid arthritis
  • p.Pro476fs Single submitter MHC class II deficiency
  • p.Thr165fs Single submitter rheumatoid arthritis
  • p.Tyr445Ter Single submitter MHC class II deficiency 1
  • p.Val1004fs Single submitter MHC class II deficiency

Conflicting classifications of pathogenicity 45

Benign 47

  • c.199+89C>T Multiple submitters MHC class II deficiency
  • c.200-10T>C Multiple submitters MHC class II deficiency
  • c.2816+57G>A Multiple submitters MHC class II deficiency
  • c.2888+34C>T Multiple submitters MHC class II deficiency
  • c.296-20G>A Multiple submitters MHC class II deficiency
  • c.2969+80C>A Multiple submitters MHC class II deficiency
  • c.2970-74G>T Multiple submitters MHC class II deficiency
  • c.3318-27G>A Multiple submitters MHC class II deficiency
  • c.358+11G>A Multiple submitters rheumatoid arthritis
  • c.359-67T>G Multiple submitters MHC class II deficiency
  • c.482-45G>T Multiple submitters MHC class II deficiency
  • c.629-116C>A Multiple submitters MHC class II deficiency
  • c.772+24G>A Multiple submitters MHC class II deficiency
  • c.773-18T>G Multiple submitters MHC class II deficiency
  • c.938-119T>C Multiple submitters MHC class II deficiency
  • c.-46G>A Multiple submitters MHC class II deficiency
  • c.*158G>A Multiple submitters MHC class II deficiency
  • c.*23-7G>C Multiple submitters MHC class II deficiency
  • c.*690C>T Multiple submitters MHC class II deficiency
  • c.*735G>A Multiple submitters MHC class II deficiency
  • c.*910T>C Multiple submitters MHC class II deficiency
  • c.*911G>A Multiple submitters MHC class II deficiency
  • p.Cys1057= Multiple submitters MHC class II deficiency
  • p.Cys75= Multiple submitters MHC class II deficiency
  • p.Gln900Arg Multiple submitters MHC class II deficiency
  • p.Gly174= Multiple submitters MHC class II deficiency
  • p.His824= Multiple submitters MHC class II deficiency
  • p.Ile762= Multiple submitters MHC class II deficiency
  • p.Lys975Arg Multiple submitters MHC class II deficiency
  • p.Pro124Thr Multiple submitters MHC class II deficiency
  • p.Thr1085= Multiple submitters MHC class II deficiency
  • p.Thr892= Multiple submitters MHC class II deficiency
  • c.3062+14G>T Single submitter MHC class II deficiency
  • c.3149+10del Single submitter MHC class II deficiency
  • c.3149+14del Single submitter MHC class II deficiency
  • c.3150-6C>T Single submitter MHC class II deficiency
  • c.3233+8_3233+9del Single submitter MHC class II deficiency
  • c.3318-7del Single submitter MHC class II deficiency
  • c.772+12del Single submitter MHC class II deficiency
  • c.772+12G>A Single submitter MHC class II deficiency
  • c.773-8del Single submitter MHC class II deficiency
  • c.937+20G>A Single submitter MHC class II deficiency
  • c.*1126T>G Single submitter MHC class II deficiency
  • c.*644C>G Single submitter MHC class II deficiency
  • p.Gly174Arg Single submitter MHC class II deficiency
  • p.Pro231Ser Single submitter MHC class II deficiency
  • p.Ser177= Single submitter MHC class II deficiency

Benign/Likely benign 11

  • c.53-12C>T Multiple submitters MHC class II deficiency
  • p.Ala658Gly Multiple submitters MHC class II deficiency
  • p.Ala691Asp Multiple submitters MHC class II deficiency
  • p.Gly500Ala Multiple submitters MHC class II deficiency ⚠
  • p.Ile497= Multiple submitters MHC class II deficiency
  • p.Leu45Val Multiple submitters MHC class II deficiency
  • p.Leu477Ile Multiple submitters MHC class II deficiency ⚠
  • p.Pro410= Multiple submitters MHC class II deficiency
  • p.Ser781Leu Multiple submitters MHC class II deficiency
  • p.Thr165Ser Multiple submitters MHC class II deficiency
  • p.Val782Ala Multiple submitters MHC class II deficiency

Likely benign 826

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

Uncertain significance 647

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