INTS11 — 159 ClinVar variants

All ClinVar germline INTS11 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 114 flagged for review →

4 Pathogenic · 5 Likely pathogenic · 2 Conflicting · 5 Benign · 20 Likely benign · 123 Uncertain significance

Full INTS11 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 114

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.

INTS11 p.Ala473Val Conflicting Single submitter

Predictors lean, ClinVar uncertain 95

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

Predictors split 18

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

INTS11 p.Arg231Cys Uncertain significance Multiple submitters
neurodevelopmental disorder with motor and language delay, ocular defects, and brain abnormalities
INTS11 p.Ala25Val Uncertain significance Single submitter
INTS11 p.Ala498Thr Uncertain significance Single submitter
INTS11 p.Arg196Cys Uncertain significance Single submitter
INTS11 p.Arg477Trp Uncertain significance Single submitter
INTS11 p.Asp212Glu Uncertain significance Single submitter
INTS11 p.Glu371Lys Uncertain significance Single submitter
INTS11 p.Gly26Ser Uncertain significance Single submitter
INTS11 p.Gly503Arg Uncertain significance Single submitter
INTS11 p.Gly55Ser Uncertain significance Single submitter
neurodevelopmental disorder with motor and language delay, ocular defects, and brain abnormalities
INTS11 p.Lys303Glu Uncertain significance Single submitter
INTS11 p.Met399Thr Uncertain significance Single submitter
neurodevelopmental disorder with motor and language delay, ocular defects, and brain abnormalities
INTS11 p.Met437Ile Uncertain significance Single submitter
INTS11 p.Ser172Cys Uncertain significance Single submitter
INTS11 p.Thr141Met Uncertain significance Single submitter
INTS11 p.Thr443Met Uncertain significance Single submitter
INTS11 p.Val515Met Uncertain significance Single submitter
neurodevelopmental disorder with motor and language delay, ocular defects, and brain abnormalities
INTS11 p.Val553Met Uncertain significance Single submitter

All INTS11 variants

Pathogenic 4

p.Arg17Leu Single submitter neurodevelopmental disorder with motor and language delay, ocular defects, and brain abnormalities
p.Arg43Ter Single submitter neurodevelopmental disorder with motor and language delay, ocular defects, and brain abnormalities
p.His414Tyr No assertion criteria neurodevelopmental disorder with motor and language delay, ocular defects, and brain abnormalities
p.Leu138Phe No assertion criteria neurodevelopmental disorder with motor and language delay, ocular defects, and brain abnormalities

Likely pathogenic 5

c.1738-1G>A Single submitter neurodevelopmental disorder with motor and language delay, ocular defects, and brain abnormalities
p.Arg521fs Single submitter neurodevelopmental disorder with motor and language delay, ocular defects, and brain abnormalities
p.Glu171fs Single submitter neurodevelopmental disorder with motor and language delay, ocular defects, and brain abnormalities
p.Val551fs No assertion criteria neurodevelopmental disorder with motor and language delay, ocular defects, and brain abnormalities
p.Val551Glu No assertion criteria neurodevelopmental disorder with motor and language delay, ocular defects, and brain abnormalities

Conflicting classifications of pathogenicity 2

p.Ala313fs Single submitter neurodevelopmental disorder with motor and language delay, ocular defects, and brain abnormalities
p.Ala473Val Single submitter ⚠

Benign 5

c.1607+18C>A Multiple submitters
p.Arg196= Multiple submitters
p.Phe294= Multiple submitters
p.Ala341= Single submitter
p.Asp580= Single submitter

Likely benign 20

c.28+1334G>A Single submitter
c.429+232C>T Single submitter
c.767+9C>T Single submitter
c.957+18G>A Single submitter
c.-3A>G Single submitter
p.Ala527= Single submitter
p.Ala561= Single submitter
p.Arg514= Single submitter
p.Arg529= Single submitter
p.Asp212= Single submitter
p.Gln524= Single submitter
p.Gly156= Single submitter
p.Leu378= Single submitter
p.Leu483= Single submitter
p.Leu587= Single submitter
p.Leu590= Single submitter
p.Pro453= Single submitter
p.Thr526Met Single submitter
p.Tyr50= Single submitter
p.Val556Ile Single submitter

Uncertain significance 123

c.28+1406C>T Multiple submitters neurodevelopmental disorder with motor and language delay, ocular defects, and brain abnormalities
p.Ala241Thr Multiple submitters ⚠
p.Arg231Cys Multiple submitters neurodevelopmental disorder with motor and language delay, ocular defects, and brain abnormalities ⚠
p.Gln467His Multiple submitters ⚠
p.Glu227Lys Multiple submitters neurodevelopmental disorder with motor and language delay, ocular defects, and brain abnormalities
p.His157Arg Multiple submitters ⚠
p.Ala111Thr Single submitter ⚠
p.Ala25Val Single submitter ⚠
p.Ala393Val Single submitter ⚠
p.Ala405Val Single submitter ⚠
p.Ala466Thr Single submitter ⚠
p.Ala466Val Single submitter ⚠
p.Ala473Thr Single submitter ⚠
p.Ala498Thr Single submitter ⚠
p.Ala76Thr Single submitter ⚠
p.Arg17Gln Single submitter ⚠
p.Arg196Cys Single submitter ⚠
p.Arg196His Single submitter ⚠
p.Arg258Cys Single submitter ⚠
p.Arg291Cys Single submitter
p.Arg463Trp Single submitter ⚠
p.Arg477Gln Single submitter ⚠
p.Arg477Trp Single submitter ⚠
p.Arg491Gln Single submitter ⚠
p.Arg514Cys Single submitter ⚠
p.Arg529Cys Single submitter ⚠
p.Arg529His Single submitter ⚠
p.Asn40Ser Single submitter ⚠
p.Asn440Ser Single submitter
p.Asp146Gly Single submitter ⚠
p.Asp212Glu Single submitter ⚠
p.Asp394Asn Single submitter ⚠
p.Asp42His Single submitter
p.Asp580Ala Single submitter ⚠
p.Asp87Tyr Single submitter
p.Gln544Arg Single submitter ⚠
p.Gln597Glu Single submitter ⚠
p.Glu117Val Single submitter ⚠
p.Glu247Lys Single submitter ⚠
p.Glu257Gln Single submitter ⚠
p.Glu257Val Single submitter ⚠
p.Glu371Lys Single submitter ⚠
p.Glu442Gln Single submitter ⚠
p.Glu442Lys Single submitter
p.Glu525Gln Single submitter ⚠
p.Glu554Gly Single submitter neurodevelopmental disorder with motor and language delay, ocular defects, and brain abnormalities ⚠
p.Gly26Ser Single submitter ⚠
p.Gly455Ser Single submitter neurodevelopmental disorder with motor and language delay, ocular defects, and brain abnormalities ⚠
p.Gly468Ala Single submitter ⚠
p.Gly468Glu Single submitter ⚠
p.Gly503Arg Single submitter ⚠
p.Gly549Asp Single submitter ⚠
p.Gly55Ser Single submitter neurodevelopmental disorder with motor and language delay, ocular defects, and brain abnormalities ⚠
p.His277Tyr Single submitter ⚠
p.His516Tyr Single submitter ⚠
p.His541Tyr Single submitter ⚠
p.His68Pro Single submitter ⚠
p.His94Gln Single submitter ⚠
p.Ile110Val Single submitter ⚠
p.Ile24Thr Single submitter ⚠
p.Ile283Val Single submitter ⚠
p.Ile398Ser Single submitter ⚠
p.Leu328Gln Single submitter ⚠
p.Leu509Val Single submitter ⚠
p.Leu528Ser Single submitter ⚠
p.Leu557Val Single submitter ⚠
p.Lys234= Single submitter
p.Lys303Arg Single submitter ⚠
p.Lys303Glu Single submitter ⚠
p.Lys500Glu Single submitter ⚠
p.Lys539Arg Single submitter ⚠
p.Met30Leu Single submitter
p.Met387Thr Single submitter ⚠
p.Met399Thr Single submitter neurodevelopmental disorder with motor and language delay, ocular defects, and brain abnormalities ⚠
p.Met437Ile Single submitter ⚠
p.Met465Ile Single submitter ⚠
p.Met465Thr Single submitter ⚠
p.Met485Val Single submitter ⚠
p.Met83Ile Single submitter ⚠
p.Phe294Cys Single submitter ⚠
p.Phe490Leu Single submitter ⚠
p.Pro318Leu Single submitter ⚠
p.Pro407Leu Single submitter ⚠
p.Pro547Arg Single submitter ⚠
p.Pro547Ser Single submitter ⚠
p.Pro547Thr Single submitter ⚠
p.Pro567Ser Single submitter ⚠
p.Pro8Leu Single submitter ⚠
p.Pro95Arg Single submitter ⚠
p.Pro95Leu Single submitter ⚠
p.Ser172Ala Single submitter ⚠
p.Ser172Cys Single submitter ⚠
p.Ser23Cys Single submitter ⚠
p.Ser390Gly Single submitter ⚠
p.Ser449Arg Single submitter ⚠
p.Ser457Leu Single submitter ⚠
p.Ser488Asn Single submitter ⚠
p.Ser49Phe Single submitter ⚠
p.Ser532Asn Single submitter ⚠
p.Thr141Met Single submitter ⚠
p.Thr182Ile Single submitter ⚠
p.Thr205Met Single submitter ⚠
p.Thr293Ile Single submitter ⚠
p.Thr443Arg Single submitter
p.Thr443Met Single submitter ⚠
p.Thr482Asn Single submitter ⚠
p.Thr482Ser Single submitter ⚠
p.Thr520Ala Single submitter ⚠
p.Trp576Ser Single submitter neurodevelopmental disorder with motor and language delay, ocular defects, and brain abnormalities ⚠
p.Tyr91His Single submitter ⚠
p.Val144Ile Single submitter ⚠
p.Val158Met Single submitter ⚠
p.Val168Gly Single submitter ⚠
p.Val321Ala Single submitter ⚠
p.Val321Leu Single submitter ⚠
p.Val355Met Single submitter ⚠
p.Val380Ile Single submitter ⚠
p.Val433Leu Single submitter ⚠
p.Val515Met Single submitter neurodevelopmental disorder with motor and language delay, ocular defects, and brain abnormalities ⚠
p.Val553Met Single submitter ⚠
p.Val64Ala Single submitter ⚠
p.Val6Asp Single submitter ⚠
p.Val6Ile Single submitter ⚠