LDB1 — 51 ClinVar variants

All ClinVar germline LDB1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 27 flagged for review →

8 Pathogenic · 4 Likely pathogenic · 1 Conflicting · 2 Likely benign · 36 Uncertain significance

Full LDB1 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.

Predicted LoF vs a conflicting call 1

ClinVar submitters conflict, and it's a predicted loss-of-function change in a gene where LoF causes disease — flagged for review, not resolved (verify NMD-escape for C-terminal truncations). Non-missense.

LDB1 c.352+1G>A Conflicting Single submitter
autosomal dominant non-syndromic intellectual disability

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.

Predictors split 3

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

All LDB1 variants

Pathogenic 8

c.733-1G>T Single submitter LDB1-related disorder
p.Ala136fs Single submitter autosomal dominant non-syndromic intellectual disability
p.Arg356fs Single submitter autosomal dominant non-syndromic intellectual disability
p.Gln333Ter Single submitter autosomal dominant non-syndromic intellectual disability
p.Gln66Ter Single submitter autosomal dominant non-syndromic intellectual disability
p.Glu349fs Single submitter autosomal dominant non-syndromic intellectual disability
p.Ser317fs Single submitter autosomal dominant non-syndromic intellectual disability
p.Trp197Ter Single submitter autosomal dominant non-syndromic intellectual disability

Likely pathogenic 4

p.Arg121Trp Single submitter autosomal dominant non-syndromic intellectual disability
p.Arg193Trp Single submitter autosomal dominant non-syndromic intellectual disability
p.Gln203Ter Single submitter autosomal dominant non-syndromic intellectual disability
p.Thr359Pro Single submitter autosomal dominant non-syndromic intellectual disability

Conflicting classifications of pathogenicity 1

c.352+1G>A Single submitter autosomal dominant non-syndromic intellectual disability ⚠

Likely benign 2

p.Glu133Asp Single submitter
p.Thr166= Single submitter

Uncertain significance 36

c.648+5G>C Single submitter
p.Ala286Val Single submitter ⚠
p.Arg181Gln Single submitter autosomal dominant non-syndromic intellectual disability ⚠
p.Arg205Ter Single submitter
p.Arg244Ter Single submitter
p.Arg258His Single submitter ⚠
p.Arg290Cys Single submitter ⚠
p.Arg70Lys Single submitter ⚠
p.Asn229Ser Single submitter
p.Asn237Ser Single submitter ⚠
p.Asn315Ser Single submitter ⚠
p.Cys159Ser Single submitter ⚠
p.Gln161His Single submitter ⚠
p.Gln66fs Single submitter
p.Gln66Pro Single submitter ⚠
p.Glu353Lys Single submitter ⚠
p.Glu375Asp Single submitter ⚠
p.Gly120Ser Single submitter ⚠
p.Gly169Val Single submitter ⚠
p.Gly26Ser Single submitter ⚠
p.Gly304Cys Single submitter ⚠
p.Ile208Met Single submitter
p.Met222Ile Single submitter ⚠
p.Met307Val Single submitter ⚠
p.Pro31Arg Single submitter
p.Pro31Leu Single submitter ⚠
p.Ser19Leu Single submitter ⚠
p.Ser331fs Single submitter
p.Ser400Asn Single submitter ⚠
p.Thr174Ile Single submitter ⚠
p.Thr231Ser Single submitter ⚠
p.Thr45Pro Single submitter ⚠
p.Thr67fs Single submitter
p.Val334fs Single submitter
p.Val339Met Single submitter ⚠
p.Val42Met Single submitter ⚠