SLIT3 — 276 ClinVar variants

All ClinVar germline SLIT3 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 206 flagged for review →

1 Likely pathogenic · 10 Benign · 2 Benign/Likely benign · 38 Likely benign · 225 Uncertain significance

Full SLIT3 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 206

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 lean, ClinVar uncertain 153

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 153

Predictors split 53

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

All SLIT3 variants

Likely pathogenic 1

p.Arg510Cys No assertion criteria Familial congenital diaphragmatic hernia

Benign 10

p.Ser629Asn Multiple submitters
c.2719+9C>T Single submitter
p.Asn289= Single submitter
p.Asn304= Single submitter
p.Asp1365= Single submitter
p.Gly618Ser Single submitter
p.Lys1333= Single submitter
p.Ser1289= Single submitter
p.Val600Met Single submitter
p.Gly1301= No assertion criteria SLIT3-related disorder

Benign/Likely benign 2

p.Cys1011= Multiple submitters
p.Thr1360= Multiple submitters

Likely benign 38

p.Val1169Leu Multiple submitters
p.Ala1180= Single submitter
p.Ala1320= Single submitter
p.Ala179= Single submitter
p.Ala853= Single submitter
p.Arg1479His Single submitter
p.Arg231Gln Single submitter ⚠
p.Arg494Thr Single submitter
p.Asp1032= Single submitter
p.Asp502= Single submitter
p.Cys441= Single submitter
p.Gln146Leu Single submitter
p.Gly1068= Single submitter
p.Ile1306= Single submitter
p.Ile1424Val Single submitter
p.Ile881= Single submitter
p.Leu114= Single submitter
p.Leu1315= Single submitter
p.Leu503= Single submitter
p.Leu90= Single submitter
p.Met299Thr Single submitter
p.Pro1357= Single submitter
p.Pro723= Single submitter
p.Pro935= Single submitter
p.Ser1261= Single submitter
p.Ser268= Single submitter
p.Ser488= Single submitter
p.Thr1099Ile Single submitter
p.Thr1502= Single submitter
p.Thr285= Single submitter
p.Thr595= Single submitter
p.Thr958= Single submitter
p.Val1351= Single submitter
p.Arg233= No assertion criteria SLIT3-related disorder
p.Arg313Cys No assertion criteria SLIT3-related disorder
p.Arg602Cys No assertion criteria SLIT3-related disorder
p.Leu1030= No assertion criteria SLIT3-related disorder
p.Pro997= No assertion criteria SLIT3-related disorder

Uncertain significance 225

p.Arg682Gln Multiple submitters SLIT3-related anomalies of the kidney and urinary tract ⚠
p.Gly1518Ser Multiple submitters ⚠
p.Lys1348Asn Multiple submitters SLIT3-related disorder ⚠
p.Met798Thr Multiple submitters SLIT3-related anomalies of the kidney and urinary tract ⚠
p.Pro1122Gln Multiple submitters ⚠
p.Thr535Asn Multiple submitters SLIT3-related anomalies of the kidney and urinary tract ⚠
c.2483+1967A>G Single submitter SLIT3-related anomalies of the kidney and urinary tract
c.*10_*17del Single submitter SLIT3-related disorder
p.Ala104Gly Single submitter
p.Ala1150Val Single submitter ⚠
p.Ala1320Ser Single submitter ⚠
p.Ala1521Thr Single submitter ⚠
p.Ala254Val Single submitter ⚠
p.Ala275Thr Single submitter ⚠
p.Ala303Gly Single submitter ⚠
p.Ala321Gly Single submitter ⚠
p.Ala324Ser Single submitter ⚠
p.Ala424Thr Single submitter ⚠
p.Ala745Thr Single submitter ⚠
p.Ala773Thr Single submitter ⚠
p.Ala874Val Single submitter ⚠
p.Ala882Thr Single submitter ⚠
p.Arg113Gln Single submitter ⚠
p.Arg113Gly Single submitter ⚠
p.Arg1144His Single submitter ⚠
p.Arg115Cys Single submitter ⚠
p.Arg1344His Single submitter ⚠
p.Arg1356Cys Single submitter ⚠
p.Arg1369Gln Single submitter ⚠
p.Arg1460Cys Single submitter
p.Arg1491Cys Single submitter ⚠
p.Arg1491His Single submitter ⚠
p.Arg1494Gln Single submitter ⚠
p.Arg1494Trp Single submitter ⚠
p.Arg1495Gln Single submitter ⚠
p.Arg15His Single submitter ⚠
p.Arg15Ser Single submitter ⚠
p.Arg231Ter Single submitter SLIT3-related anomalies of the kidney and urinary tract
p.Arg313Pro Single submitter ⚠
p.Arg335Gln Single submitter ⚠
p.Arg463Cys Single submitter ⚠
p.Arg474His Single submitter ⚠
p.Arg484His Single submitter ⚠
p.Arg492His Single submitter ⚠
p.Arg492Leu Single submitter
p.Arg494Ser Single submitter
p.Arg53Cys Single submitter ⚠
p.Arg53Ser Single submitter
p.Arg560Gln Single submitter ⚠
p.Arg560Trp Single submitter ⚠
p.Arg573Gln Single submitter ⚠
p.Arg602His Single submitter ⚠
p.Arg681Lys Single submitter ⚠
p.Arg810Trp Single submitter ⚠
p.Arg88Gln Single submitter ⚠
p.Arg902Cys Single submitter ⚠
p.Arg940Cys Single submitter ⚠
p.Arg940His Single submitter ⚠
p.Arg992Gln Single submitter ⚠
p.Arg992Trp Single submitter ⚠
p.Asn1201Ser Single submitter ⚠
p.Asn1410Ser Single submitter ⚠
p.Asn166Lys Single submitter ⚠
p.Asn304Ser Single submitter ⚠
p.Asn404Lys Single submitter ⚠
p.Asn406Thr Single submitter ⚠
p.Asn520Asp Single submitter ⚠
p.Asn520Ser Single submitter ⚠
p.Asn622Asp Single submitter
p.Asn792Ser Single submitter ⚠
p.Asn962Lys Single submitter ⚠
p.Asp1002Asn Single submitter
p.Asp1013Glu Single submitter ⚠
p.Asp1032Asn Single submitter ⚠
p.Asp1077Gly Single submitter ⚠
p.Asp1124Asn Single submitter ⚠
p.Asp1189Ala Single submitter ⚠
p.Asp158Asn Single submitter ⚠
p.Asp345Asn Single submitter ⚠
p.Asp345His Single submitter ⚠
p.Asp490Gly Single submitter ⚠
p.Asp578Asn Single submitter ⚠
p.Asp862Gly Single submitter ⚠
p.Asp892Glu Single submitter ⚠
p.Asp94Asn Single submitter ⚠
p.Asp999Asn Single submitter ⚠
p.Cys1078Tyr Single submitter ⚠
p.Cys40Tyr Single submitter ⚠
p.Cys511Arg Single submitter ⚠
p.Gln1138Pro Single submitter ⚠
p.Gln122Arg Single submitter ⚠
p.Gln1248Lys Single submitter ⚠
p.Gln1316Leu Single submitter
p.Gln1324Pro Single submitter ⚠
p.Gln1366Arg Single submitter ⚠
p.Gln1445Lys Single submitter ⚠
p.Gln146Arg Single submitter ⚠
p.Gln1485His Single submitter SLIT3-related disorder ⚠
p.Gln163Arg Single submitter ⚠
p.Gln720His Single submitter ⚠
p.Glu1006Ala Single submitter
p.Glu1041Asp Single submitter ⚠
p.Glu1308Val Single submitter
p.Glu1441Lys Single submitter ⚠
p.Glu1512Ala Single submitter ⚠
p.Glu184Gln Single submitter ⚠
p.Glu458Lys Single submitter ⚠
p.Glu498Lys Single submitter ⚠
p.Glu507Lys Single submitter ⚠
p.Glu594Lys Single submitter ⚠
p.Glu698Ala Single submitter ⚠
p.Gly1086Arg Single submitter ⚠
p.Gly1106Ala Single submitter ⚠
p.Gly1287Ser Single submitter ⚠
p.Gly1358Ser Single submitter ⚠
p.Gly1374Ser Single submitter ⚠
p.Gly1399Glu Single submitter ⚠
p.Gly1420Glu Single submitter ⚠
p.Gly1437Ser Single submitter ⚠
p.Gly147Arg Single submitter ⚠
p.Gly1518Asp Single submitter ⚠
p.Gly175Arg Single submitter ⚠
p.Gly250Ala Single submitter ⚠
p.Gly28Trp Single submitter ⚠
p.Gly461Arg Single submitter ⚠
p.Gly461Val Single submitter ⚠
p.Gly49Trp Single submitter ⚠
p.Gly513Ser Single submitter ⚠
p.Gly51Cys Single submitter ⚠
p.Gly58Val Single submitter ⚠
p.Gly627Ser Single submitter ⚠
p.Gly675Cys Single submitter ⚠
p.Gly7Glu Single submitter ⚠
p.Gly83Arg Single submitter ⚠
p.Gly83Val Single submitter ⚠
p.His1111Gln Single submitter ⚠
p.His1340Tyr Single submitter ⚠
p.His267Tyr Single submitter ⚠
p.His597Tyr Single submitter ⚠
p.His901Gln Single submitter ⚠
p.Ile1424Leu Single submitter ⚠
p.Ile319Phe Single submitter ⚠
p.Ile343Val Single submitter
p.Ile956Phe Single submitter ⚠
p.Leu1196Phe Single submitter ⚠
p.Leu127Met Single submitter ⚠
p.Leu1363Val Single submitter ⚠
p.Leu1520Phe Single submitter ⚠
p.Leu18Val Single submitter ⚠
p.Leu241Phe Single submitter ⚠
p.Leu26Pro Single submitter ⚠
p.Leu357Pro Single submitter ⚠
p.Leu415Met Single submitter
p.Leu448Val Single submitter ⚠
p.Leu607Ile Single submitter ⚠
p.Leu660Ile Single submitter ⚠
p.Leu671Val Single submitter
p.Lys120Glu Single submitter ⚠
p.Lys1256Arg Single submitter ⚠
p.Lys1416Arg Single submitter ⚠
p.Lys680Met Single submitter ⚠
p.Met1476Leu Single submitter ⚠
p.Met299Val Single submitter ⚠
p.Met798Ile Single submitter ⚠
p.Phe423Leu Single submitter ⚠
p.Phe81Leu Single submitter ⚠
p.Pro1023Leu Single submitter ⚠
p.Pro1107Ala Single submitter ⚠
p.Pro1152Leu Single submitter ⚠
p.Pro1152Ser Single submitter ⚠
p.Pro1430Leu Single submitter ⚠
p.Pro1448Leu Single submitter ⚠
p.Pro149Arg Single submitter ⚠
p.Pro29Leu Single submitter ⚠
p.Pro557Ala Single submitter ⚠
p.Pro664Thr Single submitter
p.Pro985Ser Single submitter ⚠
p.Ser1067Arg Single submitter ⚠
p.Ser1345Pro Single submitter ⚠
p.Ser170Asn Single submitter ⚠
p.Ser282Leu Single submitter ⚠
p.Ser318Phe Single submitter ⚠
p.Ser488Thr Single submitter ⚠
p.Ser493Gly Single submitter ⚠
p.Ser528Gly Single submitter ⚠
p.Ser630Leu Single submitter ⚠
p.Ser885Asn Single submitter ⚠
p.Thr132Met Single submitter ⚠
p.Thr1385Asn Single submitter ⚠
p.Thr285Met Single submitter ⚠
p.Thr398Met Single submitter ⚠
p.Thr459Arg Single submitter ⚠
p.Thr645Asn Single submitter ⚠
p.Thr651Met Single submitter ⚠
p.Thr710Ile Single submitter ⚠
p.Thr778Met Single submitter ⚠
p.Thr856Asn Single submitter ⚠
p.Tyr1018Phe Single submitter ⚠
p.Tyr1389His Single submitter ⚠
p.Val1012Met Single submitter ⚠
p.Val1019Met Single submitter ⚠
p.Val1090Met Single submitter ⚠
p.Val1160Ile Single submitter ⚠
p.Val1186Leu Single submitter ⚠
p.Val1186Met Single submitter
p.Val1213Met Single submitter ⚠
p.Val1253Ile Single submitter ⚠
p.Val1351Met Single submitter ⚠
p.Val1454Gly Single submitter ⚠
p.Val1498Ile Single submitter ⚠
p.Val159Met Single submitter ⚠
p.Val262Met Single submitter ⚠
p.Val291Met Single submitter ⚠
p.Val32Leu Single submitter ⚠
p.Val45Met Single submitter ⚠
p.Val583Met Single submitter
p.Val736Met Single submitter ⚠
p.Val767Met Single submitter ⚠
p.Val816Ala Single submitter ⚠
p.Val909Gly Single submitter ⚠
p.Val954Met Single submitter ⚠
p.Ala347Ser No assertion criteria SLIT3-related disorder ⚠
p.Asp638Gly No assertion criteria SLIT3-related disorder ⚠
p.Thr398fs No assertion criteria
p.Thr778Lys No assertion criteria SLIT3-related disorder ⚠