BPNT2 — 299 ClinVar variants

All ClinVar germline BPNT2 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 81 flagged for review →

8 Pathogenic · 3 Likely pathogenic · 4 Conflicting · 29 Benign · 2 Benign/Likely benign · 66 Likely benign · 187 Uncertain significance

Full BPNT2 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 81

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 40

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

Predictors split 41

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

All BPNT2 variants

Pathogenic 8

p.Arg187Ter Multiple submitters chondrodysplasia with joint dislocations, gPAPP type
p.Ala178fs Single submitter
p.Gln141Ter Single submitter
p.Glu44fs Single submitter
p.Thr159Ter Single submitter chondrodysplasia with joint dislocations, gPAPP type
p.Asp177Asn No assertion criteria chondrodysplasia with joint dislocations, gPAPP type
p.Ser108fs No assertion criteria chondrodysplasia with joint dislocations, gPAPP type
p.Thr183Pro No assertion criteria chondrodysplasia with joint dislocations, gPAPP type

Likely pathogenic 3

p.Arg238fs Single submitter chondrodysplasia with joint dislocations, gPAPP type
p.Leu336Pro Single submitter chondrodysplasia with joint dislocations, gPAPP type
p.Ser324fs Single submitter

Conflicting classifications of pathogenicity 4

p.Asp329= Single submitter chondrodysplasia with joint dislocations, gPAPP type
p.His314fs Single submitter chondrodysplasia with joint dislocations, gPAPP type
p.Leu112= Single submitter chondrodysplasia with joint dislocations, gPAPP type
p.Val347= Single submitter chondrodysplasia with joint dislocations, gPAPP type

Benign 29

c.387+61C>G Multiple submitters
c.550+76T>C Multiple submitters
c.647-79A>G Multiple submitters
c.809-276A>G Multiple submitters
c.*2288G>A Multiple submitters chondrodysplasia with joint dislocations, gPAPP type
c.*2508T>A Multiple submitters chondrodysplasia with joint dislocations, gPAPP type
c.*2608A>C Multiple submitters chondrodysplasia with joint dislocations, gPAPP type
c.*3204A>G Multiple submitters chondrodysplasia with joint dislocations, gPAPP type
c.*3673A>G Multiple submitters chondrodysplasia with joint dislocations, gPAPP type
c.*4209G>A Multiple submitters chondrodysplasia with joint dislocations, gPAPP type
c.*4430A>G Multiple submitters chondrodysplasia with joint dislocations, gPAPP type
c.*4890C>T Multiple submitters chondrodysplasia with joint dislocations, gPAPP type
c.*5505A>G Multiple submitters chondrodysplasia with joint dislocations, gPAPP type
c.*701C>T Multiple submitters chondrodysplasia with joint dislocations, gPAPP type
c.*764C>T Multiple submitters chondrodysplasia with joint dislocations, gPAPP type
c.*782G>A Multiple submitters chondrodysplasia with joint dislocations, gPAPP type
p.Lys286Glu Multiple submitters chondrodysplasia with joint dislocations, gPAPP type
p.Tyr189= Multiple submitters
c.551-8dup Single submitter
c.646+273del Single submitter
c.808+313G>A Single submitter
c.*147C>T Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*2382A>G Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*2631A>G Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*358G>A Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*3637C>G Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*5014A>G Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*5512T>C Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*5730A>G Single submitter chondrodysplasia with joint dislocations, gPAPP type

Benign/Likely benign 2

p.Glu322Lys Multiple submitters chondrodysplasia with joint dislocations, gPAPP type ⚠
p.Gly313= Multiple submitters chondrodysplasia with joint dislocations, gPAPP type

Likely benign 66

c.808+14C>T Multiple submitters
c.-146A>C Multiple submitters chondrodysplasia with joint dislocations, gPAPP type
p.Thr294= Multiple submitters
c.388-10T>C Single submitter
c.388-6A>C Single submitter
c.551-16del Single submitter
c.551-18T>C Single submitter
c.551-21_551-19del Single submitter
c.646+16G>A Single submitter
c.646+20T>C Single submitter
c.647-8del Single submitter
c.808+17G>A Single submitter
c.*1276A>G Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*1651G>A Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*1693A>C Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*1966A>G Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*2149G>T Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*2190G>A Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*3704A>G Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*4315C>T Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*4501T>G Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*4973G>T Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*5302C>T Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*5492G>A Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*5634A>G Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*5797C>T Single submitter chondrodysplasia with joint dislocations, gPAPP type
p.Ala2= Single submitter
p.Ala345= Single submitter
p.Ala49= Single submitter
p.Arg76= Single submitter
p.Asp62= Single submitter
p.Gly247= Single submitter
p.Gly267= Single submitter
p.Gly270= Single submitter
p.Gly34= Single submitter
p.Gly40= Single submitter
p.Gly51= Single submitter
p.His26= Single submitter
p.Ile239= Single submitter
p.Ile264= Single submitter
p.Ile331= Single submitter
p.Leu120= Single submitter
p.Leu21= Single submitter
p.Leu335= Single submitter
p.Leu346= Single submitter
p.Leu67= Single submitter
p.Lys298= Single submitter
p.Met203Val Single submitter
p.Pro175= Single submitter
p.Pro280= Single submitter
p.Ser212= Single submitter
p.Ser244= Single submitter
p.Thr132= Single submitter
p.Thr159= Single submitter
p.Thr60= Single submitter
p.Thr98= Single submitter
p.Tyr28= Single submitter
p.Tyr295= Single submitter
p.Tyr325= Single submitter
p.Val111= Single submitter
p.Val194= Single submitter
p.Val241= Single submitter
p.Val249= Single submitter
p.Val252= Single submitter
c.-4C>T No assertion criteria BPNT2-related disorder
p.Gly47= No assertion criteria BPNT2-related disorder

Uncertain significance 187

c.551-3_551-2del Multiple submitters
c.-155C>G Multiple submitters chondrodysplasia with joint dislocations, gPAPP type
c.*4264G>A Multiple submitters chondrodysplasia with joint dislocations, gPAPP type
c.*5193A>G Multiple submitters chondrodysplasia with joint dislocations, gPAPP type
p.Ala218Ser Multiple submitters chondrodysplasia with joint dislocations, gPAPP type ⚠
p.Arg187Gln Multiple submitters chondrodysplasia with joint dislocations, gPAPP type ⚠
p.Arg243Cys Multiple submitters ⚠
p.Arg243His Multiple submitters ⚠
p.Asp278Gly Multiple submitters ⚠
p.Cys17Gly Multiple submitters ⚠
p.Gly330Ser Multiple submitters chondrodysplasia with joint dislocations, gPAPP type ⚠
p.Gly51Glu Multiple submitters ⚠
p.Ile263Val Multiple submitters ⚠
p.Lys149Glu Multiple submitters ⚠
p.Lys235Arg Multiple submitters chondrodysplasia with joint dislocations, gPAPP type ⚠
p.Lys97Arg Multiple submitters ⚠
p.Val136Met Multiple submitters ⚠
p.Val15Leu Multiple submitters ⚠
p.Val190Ile Multiple submitters ⚠
c.-279T>C Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*1018T>C Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*106G>A Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*1084C>T Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*1123C>A Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*1314G>A Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*1328C>T Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*1338C>G Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*133C>G Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*1343A>G Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*14C>T Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*1620A>G Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*1652T>G Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*1800G>A Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*1834A>G Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*1952C>T Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*1960A>G Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*1996C>T Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*2005G>A Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*2009C>T Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*2047T>C Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*2058C>T Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*2088A>G Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*2138A>G Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*2141T>C Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*2165C>T Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*2166G>A Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*2181G>A Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*2444A>G Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*2458G>T Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*2475T>C Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*2512T>C Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*2544G>A Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*2607C>T Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*2630A>T Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*2649C>A Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*2674G>A Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*2726T>G Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*2825C>T Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*2993C>G Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*3054C>A Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*3060T>C Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*3173C>T Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*3193T>C Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*3235A>C Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*3258T>G Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*3408A>G Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*3505T>C Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*3619A>G Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*3653C>A Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*3679A>G Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*3739C>T Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*3805C>T Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*3876T>A Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*3922C>G Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*3927T>C Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*3957C>A Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*396A>T Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*4037T>C Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*4098G>A Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*4102A>G Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*4250A>G Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*4251T>C Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*4331G>A Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*4366G>A Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*4403T>C Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*4434C>T Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*447C>T Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*4496C>T Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*4589A>G Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*461G>A Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*4638T>C Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*4845A>G Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*4873G>A Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*4913G>A Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*4971C>T Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*5160C>A Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*5203A>T Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*5289C>T Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*5300G>T Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*5327C>G Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*5339T>C Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*5354A>G Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*5395A>G Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*5463G>C Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*553A>G Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*5607C>A Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*5692A>G Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*5752G>A Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*5786T>C Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*5803C>T Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*5804G>A Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*5821C>T Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*70G>T Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*928G>C Single submitter chondrodysplasia with joint dislocations, gPAPP type
c.*929A>T Single submitter chondrodysplasia with joint dislocations, gPAPP type
p.Ala102Gly Single submitter ⚠
p.Ala102Val Single submitter ⚠
p.Ala138Thr Single submitter ⚠
p.Ala2Asp Single submitter ⚠
p.Ala306Val Single submitter ⚠
p.Ala33Asp Single submitter ⚠
p.Arg229= Single submitter chondrodysplasia with joint dislocations, gPAPP type
p.Arg229Cys Single submitter ⚠
p.Arg229His Single submitter ⚠
p.Arg238Gly Single submitter ⚠
p.Arg64Ser Single submitter ⚠
p.Arg7= Single submitter chondrodysplasia with joint dislocations, gPAPP type
p.Arg83_Val84insGlyGlyAspGluValArgArg Single submitter chondrodysplasia with joint dislocations, gPAPP type
p.Asn225Asp Single submitter ⚠
p.Asn305Ser Single submitter ⚠
p.Asp104Asn Single submitter ⚠
p.Asp104Glu Single submitter ⚠
p.Asp153Ala Single submitter ⚠
p.Asp352His Single submitter ⚠
p.Asp57Tyr Single submitter ⚠
p.Asp62Glu Single submitter ⚠
p.Asp79Ala Single submitter ⚠
p.Glu103Lys Single submitter ⚠
p.Glu142del Single submitter
p.Glu142Lys Single submitter ⚠
p.Glu157Gln Single submitter ⚠
p.Glu157Gly Single submitter ⚠
p.Glu157Val Single submitter ⚠
p.Gly223Val Single submitter ⚠
p.Gly312Ala Single submitter ⚠
p.Gly334Glu Single submitter chondrodysplasia with joint dislocations, gPAPP type ⚠
p.Gly34Ser Single submitter ⚠
p.Gly46= Single submitter chondrodysplasia with joint dislocations, gPAPP type
p.Gly59Asp Single submitter ⚠
p.Gly77Ser Single submitter ⚠
p.His135Gln Single submitter ⚠
p.Ile173Val Single submitter ⚠
p.Ile296Val Single submitter ⚠
p.Leu11Val Single submitter ⚠
p.Leu24Ile Single submitter ⚠
p.Leu318= Single submitter chondrodysplasia with joint dislocations, gPAPP type
p.Leu38Val Single submitter ⚠
p.Leu90Phe Single submitter chondrodysplasia with joint dislocations, gPAPP type ⚠
p.Lys162Glu Single submitter ⚠
p.Lys188Arg Single submitter ⚠
p.Met219Ile Single submitter ⚠
p.Met66Ile Single submitter ⚠
p.Pro126Arg Single submitter ⚠
p.Pro151Ala Single submitter ⚠
p.Pro165Ala Single submitter ⚠
p.Pro165Leu Single submitter ⚠
p.Pro3Leu Single submitter ⚠
p.Pro45Ser Single submitter ⚠
p.Pro52Ser Single submitter ⚠
p.Ser246= Single submitter chondrodysplasia with joint dislocations, gPAPP type
p.Ser283Arg Single submitter ⚠
p.Ser283Asn Single submitter ⚠
p.Ser319Asn Single submitter ⚠
p.Ser37Gly Single submitter ⚠
p.Thr256Ala Single submitter ⚠
p.Thr256Ile Single submitter ⚠
p.Thr60Ile Single submitter ⚠
p.Trp146Leu Single submitter ⚠
p.Tyr119Cys Single submitter ⚠
p.Tyr119His Single submitter chondrodysplasia with joint dislocations, gPAPP type ⚠
p.Tyr119Phe Single submitter ⚠
p.Val23Leu Single submitter ⚠
p.Val241Leu Single submitter ⚠
p.Val249Ile Single submitter ⚠
p.Val71Leu Single submitter ⚠
p.Val71Met Single submitter ⚠
p.Val81Met Single submitter ⚠