PTPN22 — 123 ClinVar variants

All ClinVar germline PTPN22 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 81 flagged for review →

3 Conflicting · 9 Benign · 1 Benign/Likely benign · 19 Likely benign · 91 Uncertain significance

Full PTPN22 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 81

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.

PTPN22 p.His370Asn Conflicting Single submitter

Predictors lean, ClinVar uncertain 69

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

Predictors split 11

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

All PTPN22 variants

Conflicting classifications of pathogenicity 3

p.His370Asn Single submitter ⚠
p.Lys750Asn Single submitter ⚠
p.Trp620= Single submitter chronic fatigue syndrome with infection-triggered onset

Benign 9

c.2135-4del Multiple submitters
p.Ala49= Multiple submitters
p.Ser505Cys Multiple submitters
p.Ser692Cys Multiple submitters
c.2134+1G>T Single submitter
c.2135-5_2135-4del Single submitter
p.Gly657= Single submitter
p.Trp620Arg Single submitter
p.Arg263Gln No assertion criteria PTPN22-related disorder

Benign/Likely benign 1

c.197-4A>G Multiple submitters

Likely benign 19

p.Gln456Glu Multiple submitters
p.Ser543Gly Multiple submitters
c.2359+11T>C Single submitter
p.Glu27= Single submitter
p.Gly154= Single submitter
p.His477= Single submitter
p.Lys516= Single submitter
p.Phe469= Single submitter
p.Phe481Leu Single submitter
p.Phe665Ser Single submitter
p.Ser107Pro Single submitter
p.Ser228= Single submitter
p.Ser74= Single submitter
p.Tyr142= Single submitter
p.Val286= Single submitter
c.273+4C>T No assertion criteria PTPN22-related disorder
c.828+4T>G No assertion criteria
p.Asn192= No assertion criteria PTPN22-related disorder
p.Leu567= No assertion criteria

Uncertain significance 91

c.1894+2T>C Single submitter rheumatoid arthritis
c.916-3A>C Single submitter
c.992+3G>A Single submitter
p.Ala434Glu Single submitter ⚠
p.Ala512Asp Single submitter ⚠
p.Arg141His Single submitter ⚠
p.Arg165Thr Single submitter ⚠
p.Arg183Gln Single submitter ⚠
p.Arg233Ser Single submitter ⚠
p.Arg263Trp Single submitter ⚠
p.Arg266Trp Single submitter ⚠
p.Arg33Ser Single submitter ⚠
p.Arg510His Single submitter ⚠
p.Arg672Gly Single submitter ⚠
p.Arg680Ter Single submitter
p.Arg690His Single submitter ⚠
p.Arg70Trp Single submitter
p.Arg756Gln Single submitter ⚠
p.Asn284Lys Single submitter ⚠
p.Asn340His Single submitter ⚠
p.Asp195Tyr Single submitter ⚠
p.Asp197Gly Single submitter
p.Asp218Asn Single submitter ⚠
p.Asp41Asn Single submitter ⚠
p.Asp79Ala Single submitter ⚠
p.Asp79Asn Single submitter ⚠
p.Cys139Tyr Single submitter ⚠
p.Cys214Tyr Single submitter ⚠
p.Cys238Tyr Single submitter ⚠
p.Gln15Pro Single submitter ⚠
p.Glu207Asp Single submitter ⚠
p.Glu360Asp Single submitter ⚠
p.Glu360Lys Single submitter ⚠
p.Glu633Lys Single submitter ⚠
p.Glu719Lys Single submitter ⚠
p.Glu72Lys Single submitter ⚠
p.His189Arg Single submitter ⚠
p.His517Asn Single submitter ⚠
p.His518Arg Single submitter ⚠
p.His687Leu Single submitter ⚠
p.Ile171Leu Single submitter ⚠
p.Ile202Val Single submitter ⚠
p.Ile240Val Single submitter ⚠
p.Ile529Val Single submitter ⚠
p.Leu281fs Single submitter rheumatoid arthritis
p.Leu287Ser Single submitter ⚠
p.Leu31Met Single submitter ⚠
p.Leu31Val Single submitter systemic lupus erythematosus
p.Leu686Pro Single submitter ⚠
p.Lys166Gln Single submitter ⚠
p.Lys411Asn Single submitter ⚠
p.Lys664Ile Single submitter ⚠
p.Met245Ile Single submitter ⚠
p.Met758Val Single submitter ⚠
p.Phe380Leu Single submitter ⚠
p.Phe562_Pro563delinsLeuThr Single submitter type 1 diabetes mellitus
p.Phe562Val Single submitter ⚠
p.Phe89Val Single submitter ⚠
p.Pro194Leu Single submitter ⚠
p.Pro199Ser Single submitter ⚠
p.Pro270Ser Single submitter ⚠
p.Pro326Leu Single submitter ⚠
p.Pro329Thr Single submitter ⚠
p.Pro451Ala Single submitter ⚠
p.Pro614Ala Single submitter ⚠
p.Pro614Leu Single submitter ⚠
p.Pro615Leu Single submitter ⚠
p.Pro694Arg Single submitter
p.Pro694Gln Single submitter
p.Ser200Pro Single submitter ⚠
p.Ser362Asn Single submitter ⚠
p.Ser377Phe Single submitter ⚠
p.Ser470Pro Single submitter ⚠
p.Ser474Pro Single submitter ⚠
p.Ser520Cys Single submitter ⚠
p.Ser546Cys Single submitter ⚠
p.Ser547Pro Single submitter ⚠
p.Ser624Leu Single submitter ⚠
p.Ser641Pro Single submitter ⚠
p.Ser676Thr Single submitter ⚠
p.Ser691Pro Single submitter ⚠
p.Ser704Ala Single submitter ⚠
p.Ser724Thr Single submitter ⚠
p.Ser734Phe Single submitter ⚠
p.Ser793Leu Single submitter ⚠
p.Thr275Lys Single submitter ⚠
p.Thr728Ile Single submitter type 1 diabetes mellitus ⚠
p.Trp244Arg Single submitter
p.Tyr471Asn Single submitter ⚠
p.Tyr528Cys Single submitter ⚠
p.Val525Ile Single submitter ⚠