Is LDB3 p.Val55Ala (c.164T>C) pathogenic?

LDB3 p.Val55Ala (c.164T>C) is classified Uncertain significance in LDB3 (ClinVar, Single submitter, 1 submitter; last evaluated 2026-04-09). AlphaMissense: ambiguous (0.4206); Absent from gnomAD v4.1; Associated with Cardiovascular phenotype.

What condition is associated with LDB3 p.Val55Ala (c.164T>C)?

LDB3 p.Val55Ala (c.164T>C) is associated with Cardiovascular phenotype (ClinVar).

How common is LDB3 p.Val55Ala (c.164T>C) in the general population?

LDB3 p.Val55Ala (c.164T>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about LDB3 p.Val55Ala (c.164T>C)?

AlphaMissense predicts ambiguous (score 0.4206) — an in-silico prediction, not a clinical call.

LDB3 p.Val55Ala

c.164T>C · VCV4859152

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.4206 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/2 damaging

REVEL, SaProt · AlphaMissense indeterminate

Conditions

Cardiovascular phenotype

Computational evidence

Protein change
AlphaMissense	0.4206	ambiguous
REVEL	0.099	moderately benign-leaning
SaProt	LLR -10.37	damaging
⇒ SaProt calls this damaging; REVEL does not; AlphaMissense is indeterminate.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 7.9	GERP 1.6, phastCons 1
Regional constraint	o/e 0.95	unconstrained · MANE · 64 kb · p 0.14 · regional, not allelic
Overall
CADD	25.2	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: LDB3
Protein: p.Val55Ala
Coding: c.164T>C
MANE Select: NM_007078
Type: single nucleotide variant
Location: chr10:86679437 (GRCh38)
Gene constraint: LOEUF 0.864 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 61.98 · 2 PDB
Residue 55: the pdz domain; a UniProt-annotated variant site (in)

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 p.Val55Ile Benign/Likely benign ★★ same residue
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

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-val55ala (accessed [today's date]).

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