Sugi Variant

Sugi Variant/PIK3R1

PIK3R1 — 703 ClinVar variants

All ClinVar germline PIK3R1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 260 flagged for review →

40 Pathogenic · 4 Pathogenic/Likely pathogenic · 40 Likely pathogenic · 11 Conflicting · 31 Benign · 17 Benign/Likely benign · 237 Likely benign · 323 Uncertain significance

Full PIK3R1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 260

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 agree, ClinVar conflicts 4

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

Predictors lean, ClinVar uncertain 206

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 206

Predictors split 49

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

All PIK3R1 variants

Pathogenic 40

  • c.1422_1425+1del Expert panel PIK3R1-related immunodeficiency and SHORT syndrome
  • c.1425+1G>A Expert panel PIK3R1-related immunodeficiency and SHORT syndrome
  • c.1425+1G>C Expert panel PIK3R1-related immunodeficiency and SHORT syndrome
  • c.1425+1G>T Expert panel PIK3R1-related immunodeficiency and SHORT syndrome
  • c.1425+2_1425+3del Expert panel PIK3R1-related immunodeficiency and SHORT syndrome
  • c.1425+2T>A Expert panel PIK3R1-related immunodeficiency and SHORT syndrome
  • c.1425+2T>G Expert panel PIK3R1-related immunodeficiency and SHORT syndrome
  • p.Arg649Trp Expert panel PIK3R1-related immunodeficiency and SHORT syndrome
  • p.Asp548fs Expert panel PIK3R1-related immunodeficiency and SHORT syndrome
  • p.Arg301Ter Multiple submitters PIK3R1-related disorder
  • c.1746-2A>T Single submitter vascular malformation
  • c.916+1G>A Single submitter SHORT syndrome
  • p.Arg162Ter Single submitter SHORT syndrome
  • p.Arg348Ter Single submitter
  • p.Arg358Ter Single submitter agammaglobulinemia 7, autosomal recessive
  • p.Arg386Ter Single submitter agammaglobulinemia 7, autosomal recessive
  • p.Arg534Ter Single submitter agammaglobulinemia 7, autosomal recessive
  • p.Asn564Asp Single submitter vascular malformation
  • p.Asp68fs Single submitter
  • p.Gln221Ter Single submitter immunodeficiency 36 with lymphoproliferation
  • p.Gln235Ter Single submitter agammaglobulinemia 7, autosomal recessive
  • p.Gln579delinsLeuMetTer Single submitter vascular malformation
  • p.Gln586Ter Single submitter agammaglobulinemia 7, autosomal recessive
  • p.Gln654Ter Single submitter agammaglobulinemia 7, autosomal recessive
  • p.Glu439fs Single submitter SHORT syndrome
  • p.Ile571fs Single submitter SHORT syndrome
  • p.Leu174fs Single submitter agammaglobulinemia 7, autosomal recessive
  • p.Lys551fs Single submitter SHORT syndrome
  • p.Met322fs Single submitter agammaglobulinemia 7, autosomal recessive
  • p.Trp298Ter Single submitter agammaglobulinemia 7, autosomal recessive
  • p.Tyr150Ter Single submitter immunodeficiency 36 with lymphoproliferation
  • p.Val436fs Single submitter SHORT syndrome
  • c.1746-5_1748del No assertion criteria Vascular Malformations and Overgrowth
  • c.1746-6_1751del No assertion criteria Vascular Malformations and Overgrowth
  • c.1748_1750delGGT No assertion criteria Vascular Malformations and Overgrowth
  • p.Arg649fs No assertion criteria SHORT syndrome
  • p.Asn636fs No assertion criteria SHORT syndrome
  • p.Gly376Arg No assertion criteria Vascular Malformations and Overgrowth
  • p.Ile82fs No assertion criteria agammaglobulinemia 7, autosomal recessive
  • p.Leu573Pro No assertion criteria overgrowth syndrome

Pathogenic/Likely pathogenic 4

  • p.Arg461Ter Multiple submitters agammaglobulinemia 7, autosomal recessive
  • p.Lys448fs Multiple submitters immunodeficiency 36 with lymphoproliferation
  • p.Lys567Glu Multiple submitters CLOVES syndrome
  • p.Gln579_Tyr580del No assertion criteria Vascular Malformations and Overgrowth

Likely pathogenic 40

Conflicting classifications of pathogenicity 11

Benign 31

Benign/Likely benign 17

  • c.1118+11G>A Multiple submitters SHORT syndrome
  • c.334+12T>C Multiple submitters agammaglobulinemia 7, autosomal recessive
  • c.334+14A>C Multiple submitters immunodeficiency 36 with lymphoproliferation
  • c.634+6T>C Multiple submitters agammaglobulinemia 7, autosomal recessive
  • c.837-7C>T Multiple submitters immunodeficiency 36 with lymphoproliferation
  • c.*3C>T Multiple submitters
  • p.Glu65= Multiple submitters immunodeficiency 36 with lymphoproliferation
  • p.Gly640= Multiple submitters SHORT syndrome
  • p.Ile207= Multiple submitters SHORT syndrome
  • p.Leu191= Multiple submitters immunodeficiency 36 with lymphoproliferation
  • p.Leu703= Multiple submitters SHORT syndrome
  • p.Phe392= Multiple submitters immunodeficiency 36 with lymphoproliferation
  • p.Ser102= Multiple submitters agammaglobulinemia 7, autosomal recessive
  • p.Ser229= Multiple submitters immunodeficiency 36 with lymphoproliferation
  • p.Thr350= Multiple submitters agammaglobulinemia 7, autosomal recessive
  • p.Tyr390= Multiple submitters agammaglobulinemia 7, autosomal recessive
  • p.Tyr73= Multiple submitters immunodeficiency 36 with lymphoproliferation

Likely benign 237

  • c.1300-15T>A Expert panel PIK3R1-related immunodeficiency and SHORT syndrome
  • c.1300-15T>C Expert panel PIK3R1-related immunodeficiency and SHORT syndrome
  • c.1300-3T>C Expert panel PIK3R1-related immunodeficiency and SHORT syndrome
  • c.1425+12A>G Expert panel PIK3R1-related immunodeficiency and SHORT syndrome
  • c.1426-20T>G Expert panel PIK3R1-related immunodeficiency and SHORT syndrome
  • p.Ala318Val Expert panel PIK3R1-related immunodeficiency and SHORT syndrome
  • p.Ala444= Expert panel PIK3R1-related immunodeficiency and SHORT syndrome
  • p.Asp117= Expert panel PIK3R1-related immunodeficiency and SHORT syndrome
  • p.Gln435= Expert panel PIK3R1-related immunodeficiency and SHORT syndrome
  • p.Leu56= Expert panel PIK3R1-related immunodeficiency and SHORT syndrome
  • p.Lys34= Expert panel PIK3R1-related immunodeficiency and SHORT syndrome
  • p.Thr104= Expert panel PIK3R1-related immunodeficiency and SHORT syndrome
  • c.1020-19T>C Multiple submitters immunodeficiency 36 with lymphoproliferation
  • c.1020-19T>G Multiple submitters
  • c.1118+11del Multiple submitters SHORT syndrome
  • c.1300-10A>C Multiple submitters SHORT syndrome
  • c.1569-17G>A Multiple submitters immunodeficiency 36 with lymphoproliferation
  • c.1985+19C>A Multiple submitters SHORT syndrome
  • c.1985+38A>C Multiple submitters
  • c.1985+7A>G Multiple submitters agammaglobulinemia 7, autosomal recessive
  • c.334+18G>A Multiple submitters agammaglobulinemia 7, autosomal recessive
  • c.335-17G>T Multiple submitters immunodeficiency 36 with lymphoproliferation
  • c.427+174A>G Multiple submitters
  • c.427+32T>C Multiple submitters
  • c.634+8T>C Multiple submitters agammaglobulinemia 7, autosomal recessive
  • c.837-13C>A Multiple submitters agammaglobulinemia 7, autosomal recessive
  • c.917-3348G>A Multiple submitters
  • c.917-3877G>C Multiple submitters
  • p.Ala10= Multiple submitters SHORT syndrome
  • p.Ala201= Multiple submitters SHORT syndrome
  • p.Ala3= Multiple submitters SHORT syndrome
  • p.Ala682= Multiple submitters SHORT syndrome
  • p.Arg9= Multiple submitters SHORT syndrome
  • p.Asp352= Multiple submitters SHORT syndrome
  • p.Asp664= Multiple submitters SHORT syndrome
  • p.Glu75= Multiple submitters SHORT syndrome
  • p.Gly665= Multiple submitters agammaglobulinemia 7, autosomal recessive
  • p.Gly71= Multiple submitters immunodeficiency 36 with lymphoproliferation
  • p.Leu118= Multiple submitters SHORT syndrome
  • p.Leu149= Multiple submitters immunodeficiency 36 with lymphoproliferation
  • p.Leu286= Multiple submitters SHORT syndrome
  • p.Pro70= Multiple submitters agammaglobulinemia 7, autosomal recessive
  • p.Ser156= Multiple submitters SHORT syndrome
  • p.Ser251= Multiple submitters immunodeficiency 36 with lymphoproliferation
  • p.Ser339= Multiple submitters immunodeficiency 36 with lymphoproliferation
  • p.Ser83= Multiple submitters SHORT syndrome
  • p.Thr296= Multiple submitters SHORT syndrome
  • p.Thr576= Multiple submitters SHORT syndrome
  • c.1019+16C>G Single submitter SHORT syndrome
  • c.1019+19_1019+20insTGAAAC Single submitter agammaglobulinemia 7, autosomal recessive
  • c.1019+19C>T Single submitter SHORT syndrome
  • c.1020-18T>A Single submitter agammaglobulinemia 7, autosomal recessive
  • c.1119-13A>T Single submitter SHORT syndrome
  • c.1119-15A>G Single submitter
  • c.1119-9T>C Single submitter agammaglobulinemia 7, autosomal recessive
  • c.1299+9_1299+19del Single submitter SHORT syndrome
  • c.1300-10A>T Single submitter agammaglobulinemia 7, autosomal recessive
  • c.1300-11A>C Single submitter agammaglobulinemia 7, autosomal recessive
  • c.1300-13T>G Single submitter SHORT syndrome
  • c.1300-9T>C Single submitter agammaglobulinemia 7, autosomal recessive
  • c.1425+11T>A Single submitter SHORT syndrome
  • c.1425+19T>C Single submitter SHORT syndrome
  • c.1426-10T>C Single submitter agammaglobulinemia 7, autosomal recessive
  • c.1426-224C>A Single submitter
  • c.1568+10_1568+18del Single submitter SHORT syndrome
  • c.1568+10dup Single submitter SHORT syndrome
  • c.1568+10T>C Single submitter agammaglobulinemia 7, autosomal recessive
  • c.1568+13C>G Single submitter SHORT syndrome
  • c.1568+18T>G Single submitter SHORT syndrome
  • c.1568+7del Single submitter SHORT syndrome
  • c.1569-129del Single submitter
  • c.1569-13C>A Single submitter agammaglobulinemia 7, autosomal recessive
  • c.1569-14T>C Single submitter immunodeficiency 36 with lymphoproliferation
  • c.1569-189A>G Single submitter
  • c.1569-62A>G Single submitter
  • c.1569-6C>T Single submitter agammaglobulinemia 7, autosomal recessive
  • c.1745+14A>G Single submitter SHORT syndrome
  • c.1745+18A>G Single submitter SHORT syndrome
  • c.1746-9G>C Single submitter SHORT syndrome
  • c.1814+21del Single submitter agammaglobulinemia 7, autosomal recessive
  • c.1814+3A>G Single submitter
  • c.1814+8G>T Single submitter agammaglobulinemia 7, autosomal recessive
  • c.1815-10G>A Single submitter SHORT syndrome
  • c.1815-17_1815-16del Single submitter SHORT syndrome
  • c.1815-39G>A Single submitter
  • c.1815-6_1815-3del Single submitter SHORT syndrome
  • c.1815-99C>T Single submitter
  • c.1985+11C>T Single submitter SHORT syndrome
  • c.1985+19C>T Single submitter agammaglobulinemia 7, autosomal recessive
  • c.1986-11C>T Single submitter SHORT syndrome
  • c.1986-17T>C Single submitter SHORT syndrome
  • c.1986-19T>C Single submitter SHORT syndrome
  • c.1986-31_1986-19del Single submitter SHORT syndrome
  • c.1986-8CT[2] Single submitter agammaglobulinemia 7, autosomal recessive
  • c.334+14_334+15delinsCA Single submitter immunodeficiency 36 with lymphoproliferation
  • c.334+18G>C Single submitter SHORT syndrome
  • c.334+7A>G Single submitter SHORT syndrome
  • c.335-198C>G Single submitter
  • c.335-8G>A Single submitter
  • c.427+15A>G Single submitter agammaglobulinemia 7, autosomal recessive
  • c.427+20G>A Single submitter agammaglobulinemia 7, autosomal recessive
  • c.428-18G>A Single submitter agammaglobulinemia 7, autosomal recessive
  • c.502+128T>C Single submitter
  • c.503-5C>T Single submitter SHORT syndrome
  • c.634+11T>C Single submitter SHORT syndrome
  • c.634+11T>G Single submitter SHORT syndrome
  • c.634+14C>A Single submitter agammaglobulinemia 7, autosomal recessive
  • c.634+256T>C Single submitter
  • c.634+82A>G Single submitter agammaglobulinemia 7, autosomal recessive
  • c.635-10A>T Single submitter SHORT syndrome
  • c.635-11T>A Single submitter SHORT syndrome
  • c.635-14T>C Single submitter agammaglobulinemia 7, autosomal recessive
  • c.635-4G>A Single submitter SHORT syndrome
  • c.635-4G>T Single submitter
  • c.635-5T>G Single submitter agammaglobulinemia 7, autosomal recessive
  • c.836+14G>A Single submitter SHORT syndrome
  • c.836+8A>G Single submitter SHORT syndrome
  • c.837-11C>T Single submitter SHORT syndrome
  • c.837-13C>T Single submitter immunodeficiency 36 with lymphoproliferation
  • c.916+15G>T Single submitter SHORT syndrome
  • c.916+16C>G Single submitter agammaglobulinemia 7, autosomal recessive
  • c.916+18T>G Single submitter SHORT syndrome
  • c.916+8T>C Single submitter agammaglobulinemia 7, autosomal recessive
  • c.917-11T>A Single submitter agammaglobulinemia 7, autosomal recessive
  • c.917-1492A>G Single submitter
  • c.917-1501C>T Single submitter
  • c.917-17T>G Single submitter
  • c.917-3491T>C Single submitter
  • c.917-3524A>G Single submitter
  • c.917-3C>T Single submitter immunodeficiency 36 with lymphoproliferation
  • c.-280A>G Single submitter
  • c.-386-183C>T Single submitter
  • p.Ala106= Single submitter SHORT syndrome
  • p.Ala123= Single submitter SHORT syndrome
  • p.Ala138= Single submitter SHORT syndrome
  • p.Ala183= Single submitter agammaglobulinemia 7, autosomal recessive
  • p.Ala306= Single submitter SHORT syndrome
  • p.Ala360= Single submitter SHORT syndrome
  • p.Ala98= Single submitter agammaglobulinemia 7, autosomal recessive
  • p.Arg228= Single submitter SHORT syndrome
  • p.Arg503= Single submitter agammaglobulinemia 7, autosomal recessive
  • p.Arg631= Single submitter SHORT syndrome
  • p.Arg66= Single submitter agammaglobulinemia 7, autosomal recessive
  • p.Asn320= Single submitter SHORT syndrome
  • p.Asn323= Single submitter SHORT syndrome
  • p.Asn325= Single submitter agammaglobulinemia 7, autosomal recessive
  • p.Asn406= Single submitter SHORT syndrome
  • p.Asn453= Single submitter agammaglobulinemia 7, autosomal recessive
  • p.Asn488= Single submitter SHORT syndrome
  • p.Asn595= Single submitter SHORT syndrome
  • p.Asn625= Single submitter SHORT syndrome
  • p.Asn673= Single submitter
  • p.Asp178= Single submitter SHORT syndrome
  • p.Asp529= Single submitter agammaglobulinemia 7, autosomal recessive
  • p.Asp643= Single submitter agammaglobulinemia 7, autosomal recessive
  • p.Gln110= Single submitter SHORT syndrome
  • p.Gln241= Single submitter SHORT syndrome
  • p.Gln478= Single submitter SHORT syndrome
  • p.Gln522= Single submitter SHORT syndrome
  • p.Gln579= Single submitter agammaglobulinemia 7, autosomal recessive
  • p.Gln586= Single submitter immunodeficiency 36 with lymphoproliferation
  • p.Gln705= Single submitter SHORT syndrome
  • p.Gln722= Single submitter SHORT syndrome
  • p.Glu451= Single submitter agammaglobulinemia 7, autosomal recessive
  • p.Glu555= Single submitter agammaglobulinemia 7, autosomal recessive
  • p.Gly321= Single submitter agammaglobulinemia 7, autosomal recessive
  • p.Gly35= Single submitter SHORT syndrome
  • p.Gly446= Single submitter agammaglobulinemia 7, autosomal recessive
  • p.Gly54= Single submitter SHORT syndrome
  • p.Gly588= Single submitter agammaglobulinemia 7, autosomal recessive
  • p.Gly680= Single submitter SHORT syndrome
  • p.His180= Single submitter SHORT syndrome
  • p.His25= Single submitter agammaglobulinemia 7, autosomal recessive
  • p.His619= Single submitter agammaglobulinemia 7, autosomal recessive
  • p.His700= Single submitter SHORT syndrome
  • p.Ile177= Single submitter agammaglobulinemia 7, autosomal recessive
  • p.Ile535= Single submitter SHORT syndrome
  • p.Leu11= Single submitter SHORT syndrome
  • p.Leu135= Single submitter SHORT syndrome
  • p.Leu250= Single submitter agammaglobulinemia 7, autosomal recessive
  • p.Leu258= Single submitter agammaglobulinemia 7, autosomal recessive
  • p.Leu30= Single submitter SHORT syndrome
  • p.Leu396= Single submitter agammaglobulinemia 7, autosomal recessive
  • p.Leu466= Single submitter SHORT syndrome
  • p.Leu531= Single submitter agammaglobulinemia 7, autosomal recessive
  • p.Leu545= Single submitter immunodeficiency 36 with lymphoproliferation
  • p.Leu573= Single submitter SHORT syndrome
  • p.Leu609= Single submitter agammaglobulinemia 7, autosomal recessive
  • p.Leu638= Single submitter SHORT syndrome
  • p.Leu710= Single submitter agammaglobulinemia 7, autosomal recessive
  • p.Lys256= Single submitter SHORT syndrome
  • p.Lys551= Single submitter SHORT syndrome
  • p.Lys561= Single submitter SHORT syndrome
  • p.Lys88= Single submitter SHORT syndrome
  • p.Phe186= Single submitter agammaglobulinemia 7, autosomal recessive
  • p.Phe247= Single submitter agammaglobulinemia 7, autosomal recessive
  • p.Phe398= Single submitter SHORT syndrome
  • p.Phe494= Single submitter SHORT syndrome
  • p.Phe646= Single submitter agammaglobulinemia 7, autosomal recessive
  • p.Phe69= Single submitter SHORT syndrome
  • p.Pro129= Single submitter SHORT syndrome
  • p.Pro170= Single submitter agammaglobulinemia 7, autosomal recessive
  • p.Pro233= Single submitter SHORT syndrome
  • p.Pro303= Single submitter SHORT syndrome
  • p.Pro312= Single submitter SHORT syndrome
  • p.Pro395= Single submitter agammaglobulinemia 7, autosomal recessive
  • p.Pro50= Single submitter agammaglobulinemia 7, autosomal recessive
  • p.Pro568= Single submitter agammaglobulinemia 7, autosomal recessive
  • p.Pro89= Single submitter SHORT syndrome
  • p.Ser171= Single submitter SHORT syndrome
  • p.Ser216= Single submitter
  • p.Ser36= Single submitter SHORT syndrome
  • p.Ser474= Single submitter SHORT syndrome
  • p.Ser565= Single submitter SHORT syndrome
  • p.Ser702= Single submitter agammaglobulinemia 7, autosomal recessive
  • p.Thr239= Single submitter SHORT syndrome
  • p.Thr253= Single submitter SHORT syndrome
  • p.Thr471= Single submitter agammaglobulinemia 7, autosomal recessive
  • p.Thr490= Single submitter agammaglobulinemia 7, autosomal recessive
  • p.Thr500= Single submitter
  • p.Thr623= Single submitter agammaglobulinemia 7, autosomal recessive
  • p.Thr675= Single submitter
  • p.Thr713= Single submitter SHORT syndrome
  • p.Tyr150= Single submitter SHORT syndrome
  • p.Tyr189= Single submitter immunodeficiency 36 with lymphoproliferation
  • p.Tyr203= Single submitter SHORT syndrome
  • p.Tyr219= Single submitter SHORT syndrome
  • p.Tyr236= Single submitter SHORT syndrome
  • p.Tyr408= Single submitter SHORT syndrome
  • p.Tyr452= Single submitter agammaglobulinemia 7, autosomal recessive
  • p.Tyr504= Single submitter SHORT syndrome
  • p.Tyr508= Single submitter SHORT syndrome
  • p.Tyr657= Single submitter
  • p.Val343= Single submitter SHORT syndrome
  • p.Val661= Single submitter agammaglobulinemia 7, autosomal recessive
  • p.Val712= Single submitter SHORT syndrome
  • p.Val97= Single submitter

Uncertain significance 323

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