UPF1 — 201 ClinVar variants

All ClinVar germline UPF1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 118 flagged for review →

4 Pathogenic · 3 Likely pathogenic · 1 Conflicting · 21 Benign · 2 Benign/Likely benign · 34 Likely benign · 136 Uncertain significance

Full UPF1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 118

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.

UPF1 p.Pro522Leu Conflicting Single submitter
UPF1-related disorder

Predictors lean, ClinVar uncertain 89

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

Predictors split 28

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

All UPF1 variants

Pathogenic 4

p.Asp317del Single submitter Global developmental delay
p.Asp662Asn Single submitter Frontal bossing
p.Glu592Lys Single submitter
p.Tyr935Cys Single submitter ⚠

Likely pathogenic 3

p.Arg858Cys Single submitter
p.Gln830Arg Single submitter intellectual disability
p.Tyr749Cys Single submitter

Conflicting classifications of pathogenicity 1

p.Pro522Leu Single submitter UPF1-related disorder ⚠

Benign 21

c.1266-32T>G Multiple submitters
c.1544+108G>A Multiple submitters
c.2300+75T>C Multiple submitters
c.232-90G>A Multiple submitters
c.2457+89G>A Multiple submitters
c.2458-85G>T Multiple submitters
c.2601-188G>C Multiple submitters
c.2601-47A>G Multiple submitters
c.630-10C>T Multiple submitters
c.-131C>G Multiple submitters
c.*3+10C>G Multiple submitters
c.*3+13G>A Multiple submitters
p.Ala1045Val Multiple submitters
p.Ala620= Multiple submitters
p.Ser417= Multiple submitters
p.Thr46= Multiple submitters
p.Tyr749= Multiple submitters
c.2457+217A>G Single submitter
c.2458-140G>A Single submitter
c.2458-228T>C Single submitter
p.Arg355= Single submitter

Benign/Likely benign 2

p.Cys545= Multiple submitters
p.Pro623= Multiple submitters

Likely benign 34

p.Thr501= Multiple submitters
p.Thr601= Multiple submitters
c.1425+18C>T Single submitter
c.1425+19G>A Single submitter
c.1544+13C>T Single submitter
c.1710-11T>C Single submitter
c.1825-6C>T Single submitter
c.1968+13C>T Single submitter
c.2775+19C>T Single submitter
c.2776-4G>A Single submitter
c.3237+8C>T Single submitter
c.630-11C>T Single submitter
p.Ala1045= Single submitter
p.Ala94= Single submitter
p.Ala978= Single submitter
p.Asn86= Single submitter
p.Asp286= Single submitter
p.Cys186= Single submitter
p.Gly307= Single submitter
p.His129= Single submitter
p.Ile1059= Single submitter
p.Leu293= Single submitter
p.Leu84= Single submitter
p.Pro649= Single submitter
p.Pro742= Single submitter
p.Pro80= Single submitter
p.Pro902= Single submitter
p.Ser227= Single submitter
p.Ser247= Single submitter
p.Ser398= Single submitter
p.Ser713Phe Single submitter Developmental disorder
p.Thr350= Single submitter
p.Tyr796= Single submitter
p.Gln1117= No assertion criteria UPF1-related disorder

Uncertain significance 136

c.1156+1G>A Single submitter
c.1157-3C>A Single submitter
c.1157-5C>G Single submitter
c.810+2dup Single submitter
p.Ala1094Val Single submitter ⚠
p.Ala1106Val Single submitter ⚠
p.Ala163Thr Single submitter ⚠
p.Ala214Gly Single submitter ⚠
p.Ala426Ser Single submitter ⚠
p.Ala426Thr Single submitter ⚠
p.Ala465Val Single submitter ⚠
p.Ala560Val Single submitter ⚠
p.Ala597Thr Single submitter ⚠
p.Ala620Pro Single submitter ⚠
p.Ala771Val Single submitter ⚠
p.Ala88Val Single submitter ⚠
p.Arg1017His Single submitter ⚠
p.Arg148Cys Single submitter ⚠
p.Arg189Cys Single submitter ⚠
p.Arg189His Single submitter ⚠
p.Arg236Leu Single submitter ⚠
p.Arg295Gln Single submitter ⚠
p.Arg365Gln Single submitter ⚠
p.Arg365Trp Single submitter ⚠
p.Arg462His Single submitter
p.Arg687His Single submitter ⚠
p.Arg694Gly Single submitter ⚠
p.Arg694Trp Single submitter Mild global developmental delay ⚠
p.Arg697His Single submitter ⚠
p.Arg907His Single submitter
p.Arg917Gln Single submitter ⚠
p.Asn1002Ser Single submitter ⚠
p.Asn185Ser Single submitter ⚠
p.Asn190Lys Single submitter ⚠
p.Asn845Ser Single submitter ⚠
p.Asn905His Single submitter ⚠
p.Asp130Asn Single submitter ⚠
p.Asp334fs Single submitter
p.Asp389Asn Single submitter
p.Asp389Glu Single submitter ⚠
p.Asp591del Single submitter
p.Asp636Asn Single submitter ⚠
p.Asp835Gly Single submitter ⚠
p.Cys183Arg Single submitter ⚠
p.Cys615Tyr Single submitter ⚠
p.Gln1051fs Single submitter
p.Gln1063His Single submitter
p.Gln358Arg Single submitter
p.Gln575Ter Single submitter
p.Glu106Gln Single submitter ⚠
p.Glu22Gln Single submitter
p.Glu22Gly Single submitter
p.Glu288Gln Single submitter ⚠
p.Glu297Lys Single submitter ⚠
p.Glu322Gly Single submitter ⚠
p.Glu532Gly Single submitter ⚠
p.Glu81Lys Single submitter ⚠
p.Gly1018Arg Single submitter ⚠
p.Gly1071Ala Single submitter ⚠
p.Gly1071Ser Single submitter ⚠
p.Gly447Asp Single submitter ⚠
p.Gly52Ser Single submitter ⚠
p.Gly53Ala Single submitter ⚠
p.Gly61Val Single submitter ⚠
p.Gly87Arg Single submitter ⚠
p.Gly901Glu Single submitter ⚠
p.Gly972Ser Single submitter ⚠
p.His847Tyr Single submitter ⚠
p.His887Tyr Single submitter ⚠
p.Ile1091fs Single submitter
p.Ile505Val Single submitter ⚠
p.Ile633Thr Single submitter ⚠
p.Ile635Val Single submitter ⚠
p.Ile923Asn Single submitter ⚠
p.Ile966Leu Single submitter ⚠
p.Leu1035Phe Single submitter ⚠
p.Leu219Phe Single submitter ⚠
p.Leu309Arg Single submitter ⚠
p.Leu708Val Single submitter ⚠
p.Leu884Phe Single submitter ⚠
p.Lys172Asn Single submitter ⚠
p.Lys200Arg Single submitter ⚠
p.Lys264Met Single submitter ⚠
p.Lys367Glu Single submitter ⚠
p.Lys456Glu Single submitter ⚠
p.Lys461Arg Single submitter ⚠
p.Met1061Val Single submitter ⚠
p.Met1067Arg Single submitter ⚠
p.Met608Leu Single submitter ⚠
p.Met807Val Single submitter ⚠
p.Met934Thr Single submitter ⚠
p.Met992Leu Single submitter ⚠
p.Phe420Ser Single submitter Rare genetic intellectual disability ⚠
p.Phe716Leu Single submitter ⚠
p.Pro1004Ser Single submitter ⚠
p.Pro1075Arg Single submitter ⚠
p.Pro283Arg Single submitter ⚠
p.Pro47Leu Single submitter ⚠
p.Pro649Leu Single submitter ⚠
p.Pro876Leu Single submitter ⚠
p.Pro925Thr Single submitter
p.Pro943Ser Single submitter ⚠
p.Pro955Ser Single submitter ⚠
p.Ser124fs Single submitter
p.Ser140Thr Single submitter ⚠
p.Ser227Leu Single submitter ⚠
p.Ser31Thr Single submitter ⚠
p.Ser760Leu Single submitter ⚠
p.Ser810Arg Single submitter ⚠
p.Ser951Cys Single submitter ⚠
p.Ser956Phe Single submitter
p.Thr1113Met Single submitter ⚠
p.Thr112Ala Single submitter ⚠
p.Thr112Ser Single submitter ⚠
p.Thr12Ser Single submitter ⚠
p.Thr258Met Single submitter ⚠
p.Thr496Met Single submitter UPF1-related disorder ⚠
p.Thr601Ala Single submitter ⚠
p.Thr777Ile Single submitter ⚠
p.Thr794Met Single submitter ⚠
p.Thr931Ala Single submitter ⚠
p.Tyr1118His Single submitter ⚠
p.Tyr113Cys Single submitter ⚠
p.Tyr114His Single submitter ⚠
p.Tyr442Cys Single submitter ⚠
p.Tyr507Cys Single submitter ⚠
p.Val135Ile Single submitter ⚠
p.Val399Met Single submitter ⚠
p.Val403Ala Single submitter ⚠
p.Val476Phe Single submitter ⚠
p.Val479Leu Single submitter ⚠
p.Val527Met Single submitter ⚠
p.Val650Met Single submitter ⚠
p.Val731Met Single submitter ⚠
p.Val899Met Single submitter
p.Val946Ile Single submitter ⚠