Is LDB3 p.Ala389= (c.1167C>T) pathogenic?

LDB3 p.Ala389= (c.1167C>T) is classified Benign/Likely benign in LDB3 (ClinVar, Multiple submitters, 7 submitters; last evaluated 2025-11-19). Rare (popmax 0.122%, sas); Associated with Cardiovascular phenotype.

What condition is associated with LDB3 p.Ala389= (c.1167C>T)?

LDB3 p.Ala389= (c.1167C>T) is associated with Cardiovascular phenotype, dilated cardiomyopathy 1C, myofibrillar myopathy 4 (ClinVar).

How common is LDB3 p.Ala389= (c.1167C>T) in the general population?

LDB3 p.Ala389= (c.1167C>T) is rare (popmax 0.122%, sas) (gnomAD).

LDB3 p.Ala389=

c.1167C>T · rs768844187 · VCV227496

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 7 submitters

gnomAD v4.1

Rare

rare (popmax 0.122%, sas)

Conditions

Cardiovascular phenotype

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 -1.6	GERP -3.6
Overall
CADD	0.901	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.122% South Asian · 111/91,080 alleles

Filtering AF 0.103% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0965%

Overall 0.00899% 145/1,613,214 alleles · rare exomes 138/1,460,856 · genomes 7/152,358 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.122%	821
East Asian	0.0267%	3,739
Remaining individualsnot grpmax-eligible	0.0256%	3,905
Middle Eastern	0.0165%	6,058
African / African-American	0.00266%	37,540
European (non-Finnish)	0.000254%	393,337

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.Ala389=
Coding: c.1167C>T
MANE Select: NM_007078
dbSNP: rs768844187
Type: single nucleotide variant
Location: chr10:86709986 (GRCh38)
Gene constraint: LOEUF 0.864 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 61.98 · 2 PDB
Residue 389: the 'disordered' region

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

Disease context

Cardiovascular phenotype — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: dilated cardiomyopathy 1C myofibrillar myopathy 4

Similar variants

LDB3 p.Ala389Thr Uncertain significance ★★ ⚠ same residue
LDB3 p.Ala389Pro Uncertain significance ★ ⚠ same residue
LDB3 p.Ala389Gly Uncertain significance ★★ same residue
LDB3 p.Ala147Thr Pathogenic/Likely pathogenic ★★ same condition
LDB3 p.Ala165Val Pathogenic/Likely pathogenic ★★ same condition
LDB3 c.1231+4A>C Uncertain significance ★★ same condition
LDB3 c.1858-11C>A Uncertain significance ★★ same condition
LDB3 c.246-3C>T Uncertain significance ★★ same condition

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-ala389 (accessed [today's date]).

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