GTF3C1 — 279 ClinVar variants

All ClinVar germline GTF3C1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 235 flagged for review →

2 Likely pathogenic · 9 Benign · 26 Likely benign · 242 Uncertain significance

Full GTF3C1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 235

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.

GTF3C1 p.Glu1366Lys Likely pathogenic Single submitter
Abnormal brain morphology

Predictors lean, ClinVar uncertain 204

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 204

Predictors split 30

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

All GTF3C1 variants

Likely pathogenic 2

p.Glu1366Lys Single submitter Abnormal brain morphology ⚠
p.Pro2014Thr No assertion criteria esophageal atresia/tracheoesophageal fistula

Benign 9

p.Arg1858Gly Multiple submitters
p.Gln1889Glu Multiple submitters
p.Ile581= Multiple submitters
p.Leu403= Multiple submitters
p.Leu690= Multiple submitters
p.Lys1162= Multiple submitters
p.Phe898= Multiple submitters
c.1127-6T>C Single submitter
p.Leu2021= Single submitter

Likely benign 26

p.Ala1148Ser Single submitter
p.Ala1686Thr Single submitter
p.Ala1693Thr Single submitter
p.Ala1825Thr Single submitter
p.Ala1887Val Single submitter
p.Arg1199Gln Single submitter
p.Arg1399= Single submitter
p.Arg1541His Single submitter
p.Arg1765Gln Single submitter
p.Arg1822Lys Single submitter
p.Arg1973Trp Single submitter
p.Arg2013Lys Single submitter
p.Arg758Lys Single submitter
p.Asn1718Asp Single submitter
p.Cys1055Tyr Single submitter
p.Cys1783Tyr Single submitter
p.Gly1775Glu Single submitter
p.His272Gln Single submitter
p.Ile1519Val Single submitter
p.Ile1591Val Single submitter
p.Ile1749Val Single submitter
p.Ile782Val Single submitter
p.Met1700Val Single submitter
p.Thr1098= Single submitter
p.Val820Met Single submitter
p.Val841Ile Single submitter

Uncertain significance 242

p.Ala1092Thr Single submitter ⚠
p.Ala1141Thr Single submitter ⚠
p.Ala1148Thr Single submitter ⚠
p.Ala1398Thr Single submitter ⚠
p.Ala1404Val Single submitter ⚠
p.Ala1558Val Single submitter ⚠
p.Ala1570Ser Single submitter ⚠
p.Ala1638Val Single submitter ⚠
p.Ala1686Ser Single submitter ⚠
p.Ala1741Val Single submitter ⚠
p.Ala1748Thr Single submitter ⚠
p.Ala1768Thr Single submitter ⚠
p.Ala1864Thr Single submitter ⚠
p.Ala1864Val Single submitter ⚠
p.Ala1867Thr Single submitter ⚠
p.Ala1894Val Single submitter ⚠
p.Ala1920Thr Single submitter ⚠
p.Ala1921Val Single submitter ⚠
p.Ala1972Thr Single submitter ⚠
p.Ala23Gly Single submitter ⚠
p.Ala500Val Single submitter ⚠
p.Ala502Val Single submitter ⚠
p.Ala52Thr Single submitter ⚠
p.Ala548Thr Single submitter ⚠
p.Ala839Gly Single submitter ⚠
p.Ala93Val Single submitter ⚠
p.Arg1019Gln Single submitter ⚠
p.Arg1024His Single submitter ⚠
p.Arg1054Cys Single submitter
p.Arg1057His Single submitter ⚠
p.Arg1101Cys Single submitter ⚠
p.Arg1101His Single submitter ⚠
p.Arg115His Single submitter ⚠
p.Arg1205Gln Single submitter ⚠
p.Arg1217Gln Single submitter ⚠
p.Arg1245Cys Single submitter ⚠
p.Arg1245His Single submitter ⚠
p.Arg1260Trp Single submitter ⚠
p.Arg1298Gln Single submitter ⚠
p.Arg135Leu Single submitter ⚠
p.Arg1454Cys Single submitter ⚠
p.Arg1480His Single submitter ⚠
p.Arg1481Gln Single submitter ⚠
p.Arg1509Ser Single submitter ⚠
p.Arg1531Gln Single submitter ⚠
p.Arg1631Gln Single submitter ⚠
p.Arg1687Trp Single submitter ⚠
p.Arg1763Cys Single submitter ⚠
p.Arg1765Trp Single submitter ⚠
p.Arg1818Gln Single submitter ⚠
p.Arg1818Trp Single submitter ⚠
p.Arg183Trp Single submitter ⚠
p.Arg1858Gln Single submitter ⚠
p.Arg1862Lys Single submitter ⚠
p.Arg1862Ser Single submitter ⚠
p.Arg1863His Single submitter ⚠
p.Arg1985Trp Single submitter ⚠
p.Arg2023Cys Single submitter ⚠
p.Arg2050Cys Single submitter ⚠
p.Arg2050His Single submitter ⚠
p.Arg2092Trp Single submitter ⚠
p.Arg2095Cys Single submitter ⚠
p.Arg269Gln Single submitter ⚠
p.Arg292His Single submitter ⚠
p.Arg366Gln Single submitter ⚠
p.Arg378His Single submitter ⚠
p.Arg505Trp Single submitter ⚠
p.Arg542Gly Single submitter ⚠
p.Arg676Gln Single submitter ⚠
p.Arg713Trp Single submitter ⚠
p.Arg763Gln Single submitter ⚠
p.Arg763Trp Single submitter ⚠
p.Arg829Gln Single submitter ⚠
p.Arg842Trp Single submitter ⚠
p.Arg887His Single submitter ⚠
p.Asn1130His Single submitter ⚠
p.Asn1145Lys Single submitter ⚠
p.Asn1549Tyr Single submitter ⚠
p.Asn1665His Single submitter ⚠
p.Asn1671Thr Single submitter ⚠
p.Asn999Thr Single submitter ⚠
p.Asp1009Asn Single submitter ⚠
p.Asp1065Asn Single submitter ⚠
p.Asp1422His Single submitter ⚠
p.Asp1423Gly Single submitter ⚠
p.Asp1528Asn Single submitter ⚠
p.Asp1617Gly Single submitter ⚠
p.Asp1620Tyr Single submitter ⚠
p.Asp1782Gly Single submitter ⚠
p.Asp1826Asn Single submitter ⚠
p.Asp1903Val Single submitter ⚠
p.Asp361Asn Single submitter ⚠
p.Asp438Asn Single submitter ⚠
p.Asp479Glu Single submitter ⚠
p.Asp882Asn Single submitter ⚠
p.Asp936Asn Single submitter ⚠
p.Asp9Asn Single submitter ⚠
p.Cys1681Arg Single submitter ⚠
p.Cys1754Gly Single submitter ⚠
p.Cys431Arg Single submitter ⚠
p.Cys853Tyr Single submitter ⚠
p.Gln1066His Single submitter ⚠
p.Gln1256Arg Single submitter ⚠
p.Gln1448Arg Single submitter ⚠
p.Gln1547Arg Single submitter ⚠
p.Gln165Glu Single submitter ⚠
p.Gln1790Arg Single submitter ⚠
p.Gln1908Leu Single submitter ⚠
p.Gln647Glu Single submitter ⚠
p.Glu1070Lys Single submitter ⚠
p.Glu1186Asp Single submitter ⚠
p.Glu1339Lys Single submitter ⚠
p.Glu1613Gln Single submitter ⚠
p.Glu1624Lys Single submitter ⚠
p.Glu1760Gly Single submitter ⚠
p.Glu282Gly Single submitter
p.Glu282Lys Single submitter ⚠
p.Glu282Val Single submitter
p.Glu623Gln Single submitter ⚠
p.Gly1107Ala Single submitter ⚠
p.Gly1211Ala Single submitter ⚠
p.Gly1289Asp Single submitter ⚠
p.Gly1348Arg Single submitter ⚠
p.Gly1355Val Single submitter ⚠
p.Gly1563Ser Single submitter ⚠
p.Gly1655Ser Single submitter ⚠
p.Gly1775Arg Single submitter ⚠
p.Gly1877Cys Single submitter ⚠
p.Gly1945Ser Single submitter ⚠
p.Gly1964Arg Single submitter ⚠
p.Gly301Arg Single submitter ⚠
p.Gly519Arg Single submitter ⚠
p.Gly741Arg Single submitter ⚠
p.Gly744Asp Single submitter ⚠
p.Gly899Ser Single submitter ⚠
p.His1815Gln Single submitter ⚠
p.Ile110Met Single submitter ⚠
p.Ile1177Met Single submitter ⚠
p.Ile1405Met Single submitter ⚠
p.Ile1656Met Single submitter ⚠
p.Ile1668Leu Single submitter ⚠
p.Ile2047Val Single submitter ⚠
p.Ile273Met Single submitter ⚠
p.Ile273Thr Single submitter ⚠
p.Ile707Val Single submitter ⚠
p.Ile892Val Single submitter ⚠
p.Leu1175Ser Single submitter ⚠
p.Leu1393Val Single submitter ⚠
p.Leu1464Phe Single submitter ⚠
p.Leu1705Phe Single submitter ⚠
p.Leu1739Gln Single submitter ⚠
p.Leu1788Val Single submitter ⚠
p.Leu1888Phe Single submitter ⚠
p.Leu1897His Single submitter ⚠
p.Leu1996Pro Single submitter ⚠
p.Leu528Met Single submitter ⚠
p.Leu547Arg Single submitter ⚠
p.Leu753= Single submitter
p.Leu7Trp Single submitter ⚠
p.Leu909Phe Single submitter
p.Lys1535Asn Single submitter ⚠
p.Lys304Met Single submitter ⚠
p.Lys411Arg Single submitter ⚠
p.Lys411Thr Single submitter ⚠
p.Lys765Glu Single submitter ⚠
p.Met1165Val Single submitter ⚠
p.Met138Val Single submitter ⚠
p.Met1444Val Single submitter ⚠
p.Met157Ile Single submitter ⚠
p.Met1700Thr Single submitter ⚠
p.Met1806Val Single submitter ⚠
p.Met2080Leu Single submitter ⚠
p.Met461Thr Single submitter ⚠
p.Met886Ile Single submitter ⚠
p.Phe1021Leu Single submitter ⚠
p.Phe1039fs Single submitter
p.Phe1370Leu Single submitter ⚠
p.Phe1544Ser Single submitter ⚠
p.Phe2061Leu Single submitter ⚠
p.Phe806Leu Single submitter ⚠
p.Pro1637Ser Single submitter ⚠
p.Pro1664Ser Single submitter ⚠
p.Pro1886Ser Single submitter ⚠
p.Pro1910Ser Single submitter ⚠
p.Pro1913Leu Single submitter ⚠
p.Pro2055Leu Single submitter ⚠
p.Pro2064Leu Single submitter ⚠
p.Pro41Leu Single submitter ⚠
p.Pro41Ser Single submitter ⚠
p.Pro533Arg Single submitter ⚠
p.Pro536Leu Single submitter ⚠
p.Pro67Ala Single submitter ⚠
p.Pro775Leu Single submitter ⚠
p.Pro843Leu Single submitter ⚠
p.Pro890Ser Single submitter ⚠
p.Ser1315Cys Single submitter ⚠
p.Ser1379Asn Single submitter ⚠
p.Ser1672Ala Single submitter ⚠
p.Ser1842Thr Single submitter ⚠
p.Ser1854Pro Single submitter ⚠
p.Ser354Phe Single submitter ⚠
p.Ser534Thr Single submitter ⚠
p.Ser546Asn Single submitter ⚠
p.Ser549Asn Single submitter ⚠
p.Ser557Gly Single submitter ⚠
p.Ser726Phe Single submitter ⚠
p.Ser726Tyr Single submitter ⚠
p.Ser884Ala Single submitter ⚠
p.Thr1146Ala Single submitter ⚠
p.Thr1259Met Single submitter ⚠
p.Thr1553Ser Single submitter ⚠
p.Thr1708= Single submitter
p.Thr1708Met Single submitter ⚠
p.Thr1878Asn Single submitter ⚠
p.Thr2063Ala Single submitter ⚠
p.Thr2063Ile Single submitter ⚠
p.Thr43Met Single submitter ⚠
p.Thr498Ile Single submitter ⚠
p.Thr556Ile Single submitter ⚠
p.Thr774Ile Single submitter ⚠
p.Tyr1026Cys Single submitter ⚠
p.Tyr2025His Single submitter ⚠
p.Tyr957His Single submitter ⚠
p.Val1003Gly Single submitter
p.Val1052Met Single submitter ⚠
p.Val1058Ile Single submitter ⚠
p.Val1316Ile Single submitter ⚠
p.Val1465Met Single submitter ⚠
p.Val1497Met Single submitter ⚠
p.Val1571Ile Single submitter ⚠
p.Val1932Ile Single submitter ⚠
p.Val1989Gly Single submitter ⚠
p.Val1990Met Single submitter ⚠
p.Val2066Gly Single submitter ⚠
p.Val2096Met Single submitter ⚠
p.Val2101Ala Single submitter ⚠
p.Val363Leu Single submitter ⚠
p.Val559Ile Single submitter ⚠
p.Val564Ala Single submitter ⚠
p.Val803Phe Single submitter ⚠
p.Val865Ile Single submitter ⚠
p.Val905Ile Single submitter ⚠