NFATC1 — 374 ClinVar variants

All ClinVar germline NFATC1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 216 flagged for review →

6 Conflicting · 36 Benign · 4 Benign/Likely benign · 109 Likely benign · 219 Uncertain significance

Full NFATC1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 216

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 5

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

Predictors lean, ClinVar uncertain 179

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 179

Predictors split 32

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

All NFATC1 variants

Conflicting classifications of pathogenicity 6

p.Ala799Thr Single submitter ⚠
p.Arg690His Single submitter ⚠
p.Gly289Ser Single submitter ⚠
p.Val678Ile Single submitter ⚠
p.Val780Ile Single submitter ⚠
p.Val800Ile Single submitter ⚠

Benign 36

c.1226+17G>A Multiple submitters
c.1589+8G>A Multiple submitters
p.Ala509= Multiple submitters
p.Ala760= Multiple submitters
p.Ala98= Multiple submitters
p.Asn51= Multiple submitters
p.Cys751Gly Multiple submitters
p.Gly35= Multiple submitters
p.Gly763= Multiple submitters
p.Ile79= Multiple submitters
p.Pro262= Multiple submitters
p.Pro285= Multiple submitters
p.Pro352= Multiple submitters
p.Pro368= Multiple submitters
p.Pro413= Multiple submitters
p.Pro661= Multiple submitters
p.Pro662= Multiple submitters
p.Pro68= Multiple submitters
p.Pro68Thr Multiple submitters
p.Pro97= Multiple submitters
p.Ser241= Multiple submitters
p.Ser617= Multiple submitters
p.Tyr688= Multiple submitters
p.Tyr89= Multiple submitters
c.1959+15C>T Single submitter
p.Arg487= Single submitter
p.Gly747Ser Single submitter
p.Gly779= Single submitter
p.His507= Single submitter
p.Leu788= Single submitter
p.Pro791Leu Single submitter
p.Ser299Leu Single submitter
p.Tyr189= Single submitter
p.Tyr442= Single submitter
p.Val764Met Single submitter
c.-16CGC[5] No assertion criteria NFATC1-related disorder

Benign/Likely benign 4

p.Asp482= Multiple submitters
p.Gly795Arg Multiple submitters
p.Leu357Val Multiple submitters
p.Pro212= Multiple submitters

Likely benign 109

c.2092+9A>C Multiple submitters
p.Ala644= Multiple submitters
p.Asp297Asn Multiple submitters ⚠
p.Leu402Pro Multiple submitters
p.Thr603= Multiple submitters
c.1226+14G>A Single submitter
c.1226+15C>T Single submitter
c.1226+7C>T Single submitter
c.1226+8G>A Single submitter
c.127+13C>T Single submitter
c.127+19C>G Single submitter
c.128-12T>A Single submitter
c.128-15T>G Single submitter
c.128-4C>T Single submitter
c.1386+11C>G Single submitter
c.1386+6C>T Single submitter
c.1387-5G>A Single submitter
c.1589+10G>A Single submitter
c.1589+14G>T Single submitter
c.1590-18G>A Single submitter
c.1590-8T>G Single submitter
c.1762+16C>T Single submitter
c.1763-12C>T Single submitter
c.1904-11C>T Single submitter
c.2092+20C>T Single submitter
c.2093-5C>T Single submitter
c.2783-20C>A Single submitter
p.Ala17= Single submitter
p.Ala244Thr Single submitter
p.Ala318= Single submitter
p.Ala347= Single submitter
p.Ala364= Single submitter
p.Ala367= Single submitter
p.Ala388= Single submitter
p.Ala397Val Single submitter
p.Ala450= Single submitter
p.Ala453= Single submitter
p.Ala455= Single submitter
p.Ala61= Single submitter
p.Ala735= Single submitter
p.Ala794= Single submitter
p.Ala867Thr Single submitter
p.Arg243= Single submitter
p.Arg429= Single submitter
p.Arg565= Single submitter
p.Arg727Lys Single submitter
p.Arg915Gln Single submitter
p.Asn513= Single submitter
p.Asp329= Single submitter
p.Glu43= Single submitter
p.Gly330= Single submitter
p.Gly34= Single submitter
p.Gly610= Single submitter
p.Gly891Arg Single submitter
p.Gly902Ser Single submitter
p.Gly95= Single submitter
p.His288= Single submitter
p.His489= Single submitter
p.His567= Single submitter
p.His619= Single submitter
p.His673= Single submitter
p.His769= Single submitter
p.Ile120= Single submitter
p.Leu485= Single submitter
p.Leu65= Single submitter
p.Lys767= Single submitter
p.Phe629= Single submitter
p.Pro208= Single submitter
p.Pro275Leu Single submitter
p.Pro283= Single submitter
p.Pro471= Single submitter
p.Pro54= Single submitter
p.Pro57= Single submitter
p.Pro738= Single submitter
p.Pro749= Single submitter
p.Pro77= Single submitter
p.Pro783= Single submitter
p.Pro791= Single submitter
p.Pro793= Single submitter
p.Pro819= Single submitter
p.Pro82= Single submitter
p.Pro835Ser Single submitter
p.Pro875Gln Single submitter
p.Pro879Leu Single submitter
p.Ser199= Single submitter
p.Ser261= Single submitter
p.Ser269Gly Single submitter
p.Ser299= Single submitter
p.Ser403= Single submitter
p.Ser454= Single submitter
p.Ser542= Single submitter
p.Ser602= Single submitter
p.Ser813= Single submitter
p.Thr215= Single submitter
p.Thr229= Single submitter
p.Thr480= Single submitter
p.Thr809Met Single submitter
p.Tyr193= Single submitter
p.Tyr197= Single submitter
p.Tyr729Cys Single submitter
p.Val331= Single submitter
p.Val530Ile Single submitter
p.Val568Ile Single submitter
p.Val609Met Single submitter
p.Val672= Single submitter
p.Asn71= No assertion criteria NFATC1-related disorder
p.Pro363= No assertion criteria NFATC1-related disorder
p.Ser670= No assertion criteria NFATC1-related disorder
p.Val639= No assertion criteria NFATC1-related disorder

Uncertain significance 219

p.Ala164Gly Multiple submitters ⚠
p.Ala260Thr Multiple submitters ⚠
p.Ala318Thr Multiple submitters ⚠
p.Ala735Thr Multiple submitters ⚠
p.Ala760Val Multiple submitters ⚠
p.Arg243His Multiple submitters ⚠
p.Asp138Asn Multiple submitters ⚠
p.Asp483Asn Multiple submitters
p.Gly224Arg Multiple submitters ⚠
p.Leu744Phe Multiple submitters ⚠
p.Leu790Phe Multiple submitters ⚠
p.Met408Val Multiple submitters NFATC1-related disorder ⚠
p.Met527Leu Multiple submitters ⚠
p.Pro285Leu Multiple submitters ⚠
p.Pro363Leu Multiple submitters ⚠
p.Pro401Thr Multiple submitters ⚠
p.Pro752Leu Multiple submitters ⚠
p.Pro783Leu Multiple submitters ⚠
p.Ser373del Multiple submitters
p.Ser87Leu Multiple submitters ⚠
p.Thr60Met Multiple submitters ⚠
p.Tyr195His Multiple submitters ⚠
p.Val803Met Multiple submitters ⚠
c.2092+5C>T Single submitter
p.Ala155Thr Single submitter ⚠
p.Ala174Thr Single submitter
p.Ala17Thr Single submitter ⚠
p.Ala227Ser Single submitter ⚠
p.Ala30Val Single submitter ⚠
p.Ala367Thr Single submitter ⚠
p.Ala40Thr Single submitter ⚠
p.Ala481Val Single submitter ⚠
p.Ala55Ser Single submitter ⚠
p.Ala55Thr Single submitter ⚠
p.Ala735Val Single submitter ⚠
p.Ala797Asp Single submitter ⚠
p.Ala797Gly Single submitter ⚠
p.Ala83Val Single submitter ⚠
p.Ala92Pro Single submitter ⚠
p.Ala98Val Single submitter ⚠
p.Arg150Gln Single submitter ⚠
p.Arg180Gln Single submitter ⚠
p.Arg235Gln Single submitter ⚠
p.Arg235Trp Single submitter ⚠
p.Arg243Cys Single submitter ⚠
p.Arg255Cys Single submitter ⚠
p.Arg255His Single submitter ⚠
p.Arg273Trp Single submitter ⚠
p.Arg292Gln Single submitter ⚠
p.Arg292Trp Single submitter ⚠
p.Arg32Leu Single submitter ⚠
p.Arg429Gln Single submitter ⚠
p.Arg565Cys Single submitter ⚠
p.Arg590His Single submitter ⚠
p.Arg648Gln Single submitter ⚠
p.Arg648Trp Single submitter ⚠
p.Arg664Trp Single submitter ⚠
p.Arg685Leu Single submitter ⚠
p.Arg883His Single submitter ⚠
p.Arg893Trp Single submitter ⚠
p.Arg933Gln Single submitter ⚠
p.Arg933Gly Single submitter ⚠
p.Asn264Ser Single submitter ⚠
p.Asn469Thr Single submitter ⚠
p.Asn51Lys Single submitter ⚠
p.Asn525Lys Single submitter ⚠
p.Asn680Asp Single submitter ⚠
p.Asn929Ser Single submitter ⚠
p.Asp143Ala Single submitter ⚠
p.Asp322Asn Single submitter ⚠
p.Asp365Asn Single submitter ⚠
p.Asp707Asn Single submitter ⚠
p.Asp708_Tyr709insSerAspAsp Single submitter
p.Asp739Asn Single submitter ⚠
p.Asp770Tyr Single submitter ⚠
p.Asp901Gly Single submitter ⚠
p.Cys263Gly Single submitter ⚠
p.Cys69Arg Single submitter ⚠
p.Cys843Tyr Single submitter ⚠
p.Cys868Tyr Single submitter ⚠
p.Gln201His Single submitter ⚠
p.Gln206Pro Single submitter
p.Gln306Glu Single submitter ⚠
p.Gln825Ter Single submitter
p.Glu249Lys Single submitter ⚠
p.Glu25Lys Single submitter ⚠
p.Glu42Lys Single submitter ⚠
p.Gly22Arg Single submitter ⚠
p.Gly24Glu Single submitter ⚠
p.Gly272Ser Single submitter ⚠
p.Gly354Arg Single submitter ⚠
p.Gly35Asp Single submitter
p.Gly573Ser Single submitter ⚠
p.Gly611Arg Single submitter
p.Gly747Arg Single submitter ⚠
p.Gly815Arg Single submitter ⚠
p.Gly90Arg Single submitter ⚠
p.Gly90Val Single submitter ⚠
p.His422Arg Single submitter ⚠
p.His458Tyr Single submitter ⚠
p.His507Arg Single submitter ⚠
p.His62Gln Single submitter ⚠
p.His62Pro Single submitter ⚠
p.His785Tyr Single submitter ⚠
p.His85Gln Single submitter ⚠
p.Ile377Val Single submitter ⚠
p.Ile460Leu Single submitter ⚠
p.Ile478Thr Single submitter ⚠
p.Ile478Val Single submitter ⚠
p.Ile585Val Single submitter ⚠
p.Leu126Phe Single submitter ⚠
p.Leu231Val Single submitter ⚠
p.Leu327Val Single submitter ⚠
p.Leu357Met Single submitter ⚠
p.Leu402Val Single submitter ⚠
p.Leu65Arg Single submitter ⚠
p.Leu757Val Single submitter ⚠
p.Leu842Phe Single submitter ⚠
p.Lys11Arg Single submitter ⚠
p.Lys613Gln Single submitter ⚠
p.Lys645Thr Single submitter ⚠
p.Met37Thr Single submitter ⚠
p.Met642Ile Single submitter ⚠
p.Phe12Leu Single submitter ⚠
p.Phe366Leu Single submitter ⚠
p.Phe663Leu Single submitter ⚠
p.Pro113Ala Single submitter ⚠
p.Pro13Ala Single submitter ⚠
p.Pro13Leu Single submitter ⚠
p.Pro146Leu Single submitter ⚠
p.Pro152Ala Single submitter ⚠
p.Pro152Leu Single submitter ⚠
p.Pro16Ser Single submitter ⚠
p.Pro196Leu Single submitter ⚠
p.Pro276Arg Single submitter ⚠
p.Pro287Leu Single submitter ⚠
p.Pro343Arg Single submitter ⚠
p.Pro352His Single submitter ⚠
p.Pro361Leu Single submitter ⚠
p.Pro390Leu Single submitter ⚠
p.Pro404Ser Single submitter ⚠
p.Pro410Arg Single submitter ⚠
p.Pro425Arg Single submitter ⚠
p.Pro425Leu Single submitter ⚠
p.Pro425Ser Single submitter ⚠
p.Pro459Arg Single submitter ⚠
p.Pro523Leu Single submitter ⚠
p.Pro607Ala Single submitter ⚠
p.Pro653Leu Single submitter ⚠
p.Pro66Leu Single submitter ⚠
p.Pro68Leu Single submitter ⚠
p.Pro699Ser Single submitter ⚠
p.Pro713Ser Single submitter ⚠
p.Pro717Leu Single submitter ⚠
p.Pro738His Single submitter ⚠
p.Pro759Thr Single submitter ⚠
p.Pro762Leu Single submitter ⚠
p.Pro773Arg Single submitter ⚠
p.Pro793Leu Single submitter ⚠
p.Pro829Leu Single submitter ⚠
p.Pro858Ser Single submitter ⚠
p.Pro858Thr Single submitter ⚠
p.Pro888Leu Single submitter ⚠
p.Pro908Ser Single submitter ⚠
p.Ser151Cys Single submitter ⚠
p.Ser161Arg Single submitter ⚠
p.Ser175Thr Single submitter ⚠
p.Ser194Leu Single submitter ⚠
p.Ser245Gly Single submitter ⚠
p.Ser257Cys Single submitter ⚠
p.Ser282Leu Single submitter ⚠
p.Ser294Thr Single submitter ⚠
p.Ser309Arg Single submitter ⚠
p.Ser372Tyr Single submitter ⚠
p.Ser50Phe Single submitter ⚠
p.Ser577Phe Single submitter ⚠
p.Ser686Gly Single submitter ⚠
p.Ser755Arg Single submitter ⚠
p.Ser755Ile Single submitter ⚠
p.Ser75Ala Single submitter ⚠
p.Ser765Arg Single submitter ⚠
p.Ser813Leu Single submitter ⚠
p.Thr202Met Single submitter ⚠
p.Thr215Met Single submitter ⚠
p.Thr305Ser Single submitter ⚠
p.Thr308Ala Single submitter ⚠
p.Thr405Arg Single submitter ⚠
p.Thr405Met Single submitter ⚠
p.Thr498Arg Single submitter ⚠
p.Thr504Ala Single submitter ⚠
p.Thr881Met Single submitter ⚠
p.Thr912Met Single submitter ⚠
p.Tyr129Phe Single submitter ⚠
p.Tyr371Asp Single submitter ⚠
p.Tyr394Cys Single submitter ⚠
p.Tyr466Ser Single submitter ⚠
p.Tyr47Cys Single submitter ⚠
p.Tyr606Cys Single submitter ⚠
p.Tyr709Asp Single submitter ⚠
p.Tyr729His Single submitter ⚠
p.Val210Met Single submitter ⚠
p.Val246Ile Single submitter ⚠
p.Val246Leu Single submitter ⚠
p.Val295Met Single submitter ⚠
p.Val313Met Single submitter ⚠
p.Val331Ile Single submitter ⚠
p.Val353Leu Single submitter ⚠
p.Val432Ala Single submitter ⚠
p.Val461Met Single submitter ⚠
p.Val566Ile Single submitter ⚠
p.Val615Ala Single submitter ⚠
p.Val627Ile Single submitter ⚠
p.Val658Ile Single submitter ⚠
p.Val672Ile Single submitter ⚠
p.Val780Phe Single submitter ⚠
p.Val882Phe Single submitter ⚠
p.Val8Ile Single submitter ⚠
p.Ala98Ser No assertion criteria NFATC1-related disorder ⚠
p.Pro68fs No assertion criteria NFATC1-related disorder