INTS6 — 101 ClinVar variants
All ClinVar germline INTS6 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 70 flagged for review →
7 Pathogenic · 3 Likely pathogenic · 5 Benign · 3 Likely benign · 83 Uncertain significance
Full INTS6 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 70
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.
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INTS6 p.Thr137Ile
Pathogenic
No assertion criteria
INTELLECTUAL DEVELOPMENTAL DISORDER, AUTOSOMAL DOMINANT 78
Predictors lean, ClinVar uncertain 61
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
- INTS6 p.Ala44Gly Uncertain significance Single submitter
- INTS6 p.Ala530Ser Uncertain significance Single submitter
- INTS6 p.Ala742Thr Uncertain significance Single submitter
- INTS6 p.Ala784Val Uncertain significance Single submitter
- INTS6 p.Arg206His Uncertain significance Single submitter
- INTS6 p.Arg301Cys Uncertain significance Single submitter
- INTS6 p.Arg301His Uncertain significance Single submitter
- INTS6 p.Arg487Gln Uncertain significance Single submitter
- INTS6 p.Arg747Trp Uncertain significance Single submitter
- INTS6 p.Arg876Gln Uncertain significance Single submitter
- INTS6 p.Asn149Thr Uncertain significance Single submitter
- INTS6 p.Asn730Thr Uncertain significance Single submitter
- INTS6 p.Asn750Ser Uncertain significance Single submitter
- INTS6 p.Asn787Asp Uncertain significance Single submitter
- INTS6 p.Asn879Ser Uncertain significance Single submitter
- INTS6 p.Asp241Tyr Uncertain significance Single submitter
- INTS6 p.Asp468Gly Uncertain significance Single submitter
- INTS6 p.Asp535Asn Uncertain significance Single submitter
- INTS6 p.Asp692Val Uncertain significance Single submitter
- INTS6 p.Gln185His Uncertain significance Single submitter
- INTS6 p.Gln688Glu Uncertain significance Single submitter
- INTS6 p.Gln838Glu Uncertain significance Single submitter
- INTS6 p.Glu184Gly Uncertain significance Single submitter
- INTS6 p.Glu481Gly Uncertain significance Single submitter
- INTS6 p.Glu776Ala Uncertain significance Single submitter
- INTS6 p.His70Asp Uncertain significance Single submitter
- INTS6 p.His774Arg Uncertain significance Single submitter
- INTS6 p.His836Arg Uncertain significance Single submitter
- INTS6 p.His836Tyr Uncertain significance Single submitter
- INTS6 p.Ile62Val Uncertain significance Single submitter
- INTS6 p.Ile653Val Uncertain significance Single submitter
- INTS6 p.Ile864Met Uncertain significance Single submitter
- INTS6 p.Leu191Phe Uncertain significance Single submitter
- INTS6 p.Leu322Arg Uncertain significance Single submitter
- INTS6 p.Leu52Gln Uncertain significance Single submitter
- INTS6 p.Lys797Arg Uncertain significance Single submitter
- INTS6 p.Lys798Arg Uncertain significance Single submitter
- INTS6 p.Met179Thr Uncertain significance Single submitter
- INTS6 p.Met317Leu Uncertain significance Single submitter
- INTS6 p.Met495Val Uncertain significance Single submitter
- INTS6 p.Met51Ile Uncertain significance Single submitter
- INTS6 p.Pro606Thr Uncertain significance Single submitter
- INTS6 p.Pro741Ser Uncertain significance Single submitter
- INTS6 p.Ser295Leu Uncertain significance Single submitter
- INTS6 p.Ser411Leu Uncertain significance Single submitter
- INTS6 p.Ser703Leu Uncertain significance Single submitter
- INTS6 p.Ser804Arg Uncertain significance Single submitter
- INTS6 p.Ser886Asn Uncertain significance Single submitter
- INTS6 p.Ser886Ile Uncertain significance Single submitter
- INTS6 p.Thr106Ser Uncertain significance Single submitter
- INTS6 p.Thr705Ile Uncertain significance Single submitter
- INTS6 p.Thr706Ser Uncertain significance Single submitter
- INTS6 p.Thr728Ile Uncertain significance Single submitter
- INTS6 p.Thr734Met Uncertain significance Single submitter
- INTS6 p.Tyr446Cys Uncertain significance Single submitter
- INTS6 p.Tyr60Cys Uncertain significance Single submitter
- INTS6 p.Tyr60His Uncertain significance Single submitter
-
INTS6 p.Val381Gly
Uncertain significance
Single submitter
INTS6-related disorder
- INTS6 p.Val470Ile Uncertain significance Single submitter
- INTS6 p.Val479Leu Uncertain significance Single submitter
- INTS6 p.Val808Leu Uncertain significance Single submitter
Predictors split 8
The independent predictors disagree with each other — read with care.
- INTS6 p.Arg469Gly Uncertain significance Single submitter
- INTS6 p.Glu57Lys Uncertain significance Single submitter
- INTS6 p.Gly30Val Uncertain significance Single submitter
- INTS6 p.His875Leu Uncertain significance Single submitter
- INTS6 p.Ile465Arg Uncertain significance Single submitter
- INTS6 p.Leu604Pro Uncertain significance Single submitter
- INTS6 p.Lys641Ile Uncertain significance Single submitter
- INTS6 p.Lys643Thr Uncertain significance Single submitter
All INTS6 variants
Pathogenic 7
- p.Ala544_Tyr545insTer Single submitter
- p.Arg610Ter Single submitter
- p.Gln185Ter Single submitter
- p.Ile233fs Single submitter
- c.613+3_613+6del No assertion criteria INTELLECTUAL DEVELOPMENTAL DISORDER, AUTOSOMAL DOMINANT 78
- p.His400Arg No assertion criteria INTELLECTUAL DEVELOPMENTAL DISORDER, AUTOSOMAL DOMINANT 78
- p.Thr137Ile No assertion criteria INTELLECTUAL DEVELOPMENTAL DISORDER, AUTOSOMAL DOMINANT 78 ⚠
Likely pathogenic 3
- p.Arg206Cys Single submitter
- p.Gln228Glu Single submitter INTS6-associated neurodevelopmental disorder
- p.Val278fs Single submitter INTS6-related disorder
Benign 5
- p.Thr749Ala Multiple submitters
- c.740-3T>C Single submitter
- c.340-3T>C No assertion criteria INTS6-related disorder
- p.Ser856= No assertion criteria INTS6-related disorder
- p.Thr405= No assertion criteria INTS6-related disorder
Likely benign 3
- p.Ala738Gly No assertion criteria INTS6-related disorder
- p.Asp518= No assertion criteria INTS6-related disorder
- p.Leu845= No assertion criteria INTS6-related disorder
Uncertain significance 83
- c.613+2T>C Single submitter
- p.Ala44Gly Single submitter ⚠
- p.Ala530Ser Single submitter ⚠
- p.Ala742Thr Single submitter ⚠
- p.Ala784Val Single submitter ⚠
- p.Arg206His Single submitter ⚠
- p.Arg301Cys Single submitter ⚠
- p.Arg301His Single submitter ⚠
- p.Arg469Gly Single submitter ⚠
- p.Arg487Gln Single submitter ⚠
- p.Arg747Trp Single submitter ⚠
- p.Arg876Gln Single submitter ⚠
- p.Asn149Thr Single submitter ⚠
- p.Asn385Ser Single submitter
- p.Asn730Thr Single submitter ⚠
- p.Asn750Ser Single submitter ⚠
- p.Asn787Asp Single submitter ⚠
- p.Asn879Ser Single submitter ⚠
- p.Asp241Tyr Single submitter ⚠
- p.Asp468Gly Single submitter ⚠
- p.Asp535Asn Single submitter ⚠
- p.Asp692Val Single submitter ⚠
- p.Gln16Ter Single submitter
- p.Gln185His Single submitter ⚠
- p.Gln688Glu Single submitter ⚠
- p.Gln838Glu Single submitter ⚠
- p.Glu184Gly Single submitter ⚠
- p.Glu481Gly Single submitter ⚠
- p.Glu57Lys Single submitter ⚠
- p.Glu776Ala Single submitter ⚠
- p.Glu873Ter Single submitter
- p.Gly30Val Single submitter ⚠
- p.His70Asp Single submitter ⚠
- p.His774Arg Single submitter ⚠
- p.His836Arg Single submitter ⚠
- p.His836Tyr Single submitter ⚠
- p.His875Leu Single submitter ⚠
- p.Ile465Arg Single submitter ⚠
- p.Ile62Val Single submitter ⚠
- p.Ile653Val Single submitter ⚠
- p.Ile864Met Single submitter ⚠
- p.Leu191Phe Single submitter ⚠
- p.Leu322Arg Single submitter ⚠
- p.Leu52Gln Single submitter ⚠
- p.Leu536Ter Single submitter
- p.Leu552Val Single submitter
- p.Leu604Pro Single submitter ⚠
- p.Lys326Ter Single submitter autism spectrum disorder
- p.Lys641Ile Single submitter ⚠
- p.Lys643Thr Single submitter ⚠
- p.Lys797Arg Single submitter ⚠
- p.Lys798Arg Single submitter ⚠
- p.Met179Thr Single submitter ⚠
- p.Met317Leu Single submitter ⚠
- p.Met495Val Single submitter ⚠
- p.Met51Ile Single submitter ⚠
- p.Pro323fs Single submitter
- p.Pro43fs Single submitter
- p.Pro606Thr Single submitter ⚠
- p.Pro741Ser Single submitter ⚠
- p.Ser295Leu Single submitter ⚠
- p.Ser411Leu Single submitter ⚠
- p.Ser703Leu Single submitter ⚠
- p.Ser737Ter Single submitter
- p.Ser804Arg Single submitter ⚠
- p.Ser886Asn Single submitter ⚠
- p.Ser886Ile Single submitter ⚠
- p.Thr106Ser Single submitter ⚠
- p.Thr705Ile Single submitter ⚠
- p.Thr706Ser Single submitter ⚠
- p.Thr728Ile Single submitter ⚠
- p.Thr734Met Single submitter ⚠
- p.Tyr446Cys Single submitter ⚠
- p.Tyr497fs Single submitter
- p.Tyr60Cys Single submitter ⚠
- p.Tyr60His Single submitter ⚠
- p.Val381Gly Single submitter INTS6-related disorder ⚠
- p.Val470Ile Single submitter ⚠
- p.Val479Leu Single submitter ⚠
- p.Val808Leu Single submitter ⚠
- c.1275+1G>A No assertion criteria INTS6-related disorder
- p.Arg550Ter No assertion criteria INTS6-related disorder
- p.Gly30= No assertion criteria INTS6-related disorder