Is LDB3 p.Glu137= (c.411G>A) pathogenic?

LDB3 p.Glu137= (c.411G>A) is classified Likely benign in LDB3 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-01-02). Very rare (popmax 0.000186%).

How common is LDB3 p.Glu137= (c.411G>A) in the general population?

LDB3 p.Glu137= (c.411G>A) is very rare (popmax 0.000186%) (gnomAD).

LDB3 p.Glu137=

c.411G>A · rs1442836813 · VCV799184

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.000186%)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.5	GERP -0.23, phastCons 1
Overall
CADD	6.758	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000186%

Overall 0.000186% 3/1,612,364 alleles · very rare exomes 3/1,460,062 · genomes 0/152,302 · joint denominator

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: LDB3
Protein: p.Glu137=
Coding: c.411G>A
MANE Select: NM_007078
dbSNP: rs1442836813
Type: single nucleotide variant
Location: chr10:86681525 (GRCh38)
Gene constraint: LOEUF 0.864 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 61.98 · 2 PDB
Residue 137: the 'disordered' region

Full LDB3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

LDB3 p.Glu137Asp Uncertain significance ★ ⚠ same residue
LDB3 p.Glu137Val Uncertain significance ★ ⚠ same residue
LDB3 p.Pro137His Uncertain significance ★ same residue
LDB3 p.Pro137Leu Uncertain significance ★ same residue
LDB3 p.Ala147Thr Pathogenic/Likely pathogenic ★★ same type
LDB3 p.Ala165Val Pathogenic/Likely pathogenic ★★ same type
LDB3 c.1231+4A>C Uncertain significance ★★ same type
LDB3 c.1858-11C>A Uncertain significance ★★ same type

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/ldb3-p-glu137 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown