BPNT1 — 29 ClinVar variants
All ClinVar germline BPNT1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 27 flagged for review →
1 Pathogenic · 1 Likely benign · 27 Uncertain significance
Full BPNT1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 27
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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BPNT1 p.Ile265Leu
Pathogenic
No assertion criteria
hypercholesterolemia, familial, 1
Predictors lean, ClinVar uncertain 23
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
- BPNT1 p.Ala177Thr Uncertain significance Single submitter
- BPNT1 p.Ala239Ser Uncertain significance Single submitter
- BPNT1 p.Ala286Val Uncertain significance Single submitter
- BPNT1 p.Ala63Val Uncertain significance Single submitter
- BPNT1 p.Arg196Gln Uncertain significance Single submitter
- BPNT1 p.Arg217Gln Uncertain significance Single submitter
- BPNT1 p.Arg28His Uncertain significance Single submitter
- BPNT1 p.Arg52Gln Uncertain significance Single submitter
- BPNT1 p.Asn132Asp Uncertain significance Single submitter
- BPNT1 p.Asp117Gly Uncertain significance Single submitter
- BPNT1 p.Asp162Asn Uncertain significance Single submitter
- BPNT1 p.Cys249Phe Uncertain significance Single submitter
- BPNT1 p.Gln152Lys Uncertain significance Single submitter
- BPNT1 p.Ile137Thr Uncertain significance Single submitter
- BPNT1 p.Ile150Thr Uncertain significance Single submitter
- BPNT1 p.Ile18Thr Uncertain significance Single submitter
- BPNT1 p.Ile87Thr Uncertain significance Single submitter
- BPNT1 p.Leu136Arg Uncertain significance Single submitter
- BPNT1 p.Lys245Glu Uncertain significance Single submitter
- BPNT1 p.Met56Ile Uncertain significance Single submitter
- BPNT1 p.Thr195Ala Uncertain significance Single submitter
- BPNT1 p.Thr41Asn Uncertain significance Single submitter
- BPNT1 p.Val135Phe Uncertain significance Single submitter
Predictors split 3
The independent predictors disagree with each other — read with care.
All BPNT1 variants
Pathogenic 1
- p.Ile265Leu No assertion criteria hypercholesterolemia, familial, 1 ⚠
Likely benign 1
- p.Asp213Asn Single submitter ⚠
Uncertain significance 27
- p.Ala177Thr Single submitter ⚠
- p.Ala239Ser Single submitter ⚠
- p.Ala286Val Single submitter ⚠
- p.Ala63Val Single submitter ⚠
- p.Arg196Gln Single submitter ⚠
- p.Arg217Gln Single submitter ⚠
- p.Arg28Cys Single submitter ⚠
- p.Arg28His Single submitter ⚠
- p.Arg52Gln Single submitter ⚠
- p.Asn132Asp Single submitter ⚠
- p.Asp117Gly Single submitter ⚠
- p.Asp162Asn Single submitter ⚠
- p.Cys249Phe Single submitter ⚠
- p.Gln152Lys Single submitter ⚠
- p.Ile137Thr Single submitter ⚠
- p.Ile150Thr Single submitter ⚠
- p.Ile18Thr Single submitter ⚠
- p.Ile87Thr Single submitter ⚠
- p.Leu136Arg Single submitter ⚠
- p.Lys245Glu Single submitter ⚠
- p.Met56Ile Single submitter ⚠
- p.Ser14Phe Single submitter
- p.Thr195Ala Single submitter ⚠
- p.Thr41Asn Single submitter ⚠
- p.Val113Ala Single submitter
- p.Val113Leu Single submitter ⚠
- p.Val135Phe Single submitter ⚠