Is LDB3 p.Pro418Ser (c.1252C>T) pathogenic?

LDB3 p.Pro418Ser (c.1252C>T) is classified Uncertain significance in LDB3 (ClinVar, Single submitter, 1 submitter; last evaluated 2020-12-08). AlphaMissense: likely benign (0.0807); Absent from gnomAD v4.1; Associated with Cardiovascular phenotype.

What condition is associated with LDB3 p.Pro418Ser (c.1252C>T)?

LDB3 p.Pro418Ser (c.1252C>T) is associated with Cardiovascular phenotype (ClinVar).

How common is LDB3 p.Pro418Ser (c.1252C>T) in the general population?

LDB3 p.Pro418Ser (c.1252C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about LDB3 p.Pro418Ser (c.1252C>T)?

AlphaMissense predicts likely benign (score 0.0807) — an in-silico prediction, not a clinical call.

LDB3 p.Pro418Ser

c.1252C>T · rs1846868508 · VCV1761032

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0807 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Cardiovascular phenotype

Computational evidence

Protein change
AlphaMissense	0.0807	likely benign
REVEL	0.093	moderately benign-leaning
SaProt	LLR -8.63	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.4	GERP 1.6, phastCons 1
Regional constraint	o/e 0.95	unconstrained · MANE · 64 kb · p 0.14 · regional, not allelic
Overall
CADD	22.3	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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.Pro418Ser
Coding: c.1252C>T
MANE Select: NM_007078
dbSNP: rs1846868508
Type: single nucleotide variant
Location: chr10:86716347 (GRCh38)
Gene constraint: LOEUF 0.864 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 61.98 · 2 PDB
Residue 418: 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

Similar variants

LDB3 p.Pro418Arg Conflicting classifications of pathogenicity ★ ⚠ same residue
LDB3 p.Pro418Leu Uncertain significance ★★ ⚠ same residue
LDB3 p.Pro418= 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

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-pro418ser (accessed [today's date]).

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