Is LDB3 p.Ser569= (c.1707T>C) pathogenic?

LDB3 p.Ser569= (c.1707T>C) is classified Likely benign in LDB3 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-11-14). Very rare (popmax 0.00223%, eas); Associated with Cardiovascular phenotype.

What condition is associated with LDB3 p.Ser569= (c.1707T>C)?

LDB3 p.Ser569= (c.1707T>C) is associated with Cardiovascular phenotype (ClinVar).

How common is LDB3 p.Ser569= (c.1707T>C) in the general population?

LDB3 p.Ser569= (c.1707T>C) is very rare (popmax 0.00223%, eas) (gnomAD).

LDB3 p.Ser569=

c.1707T>C · rs2492815846 · VCV1778487

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00223%, eas)

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 0.42	GERP -1.8, phastCons 0.99
Overall
CADD	9.857	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00223% East Asian · 1/44,890 alleles

Overall 0.000124% 2/1,614,228 alleles · very rare exomes 2/1,461,864 · genomes 0/152,364 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00223%	44,890
European (non-Finnish)	8.47e-05%	1,180,022

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.Ser569=
Coding: c.1707T>C
MANE Select: NM_007078
dbSNP: rs2492815846
Type: single nucleotide variant
Location: chr10:86717994 (GRCh38)
Gene constraint: LOEUF 0.864 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 61.98 · 2 PDB
Residue 569: the lim zinc-binding 1 domain; a UniProt-annotated variant site (in cmd2l; likely pathogenic)

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

Similar variants

LDB3 c.246-3C>T Uncertain significance ★★ same condition
LDB3 c.860-3C>T Uncertain significance ★★ same condition
LDB3 p.Ala119Val Uncertain significance ★★ ⚠ same condition
LDB3 p.Ala126Val Uncertain significance ★★ ⚠ same condition
LDB3 p.Ala248Thr Uncertain significance ★★ same condition
LDB3 p.Ala264Thr Uncertain significance ★★ ⚠ same condition
LDB3 p.Ala365Asp Uncertain significance ★★ ⚠ same condition
LDB3 p.Ala365Val 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-ser569 (accessed [today's date]).

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