Is LDB3 p.Ala38Pro (c.112G>C) pathogenic?

LDB3 p.Ala38Pro (c.112G>C) is classified Uncertain significance in LDB3 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-07-05). AlphaMissense: likely pathogenic (0.995); Absent from gnomAD v4.1.

How common is LDB3 p.Ala38Pro (c.112G>C) in the general population?

LDB3 p.Ala38Pro (c.112G>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about LDB3 p.Ala38Pro (c.112G>C)?

AlphaMissense predicts likely pathogenic (score 0.995) — an in-silico prediction, not a clinical call.

LDB3 p.Ala38Pro

c.112G>C · VCV4908457

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.995 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.995	likely pathogenic · top 10% in LDB3
REVEL	0.785	moderately pathogenic-leaning
SaProt	LLR -15.48	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 12	GERP 2.5, phastCons 1
Regional constraint	o/e 0.95	unconstrained · MANE · 64 kb · p 0.14 · regional, not allelic
Overall
CADD	31.0	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — 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.Ala38Pro
Coding: c.112G>C
MANE Select: NM_007078
Type: single nucleotide variant
Location: chr10:86679385 (GRCh38)
Gene constraint: LOEUF 0.864 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 61.98 · 2 PDB
Residue 38: the pdz domain; an α-helix

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

Similar variants

LDB3 p.Ala38= Likely benign ★★ 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
LDB3 c.246-3C>T Uncertain significance ★★ same type
LDB3 c.322-1G>A Uncertain significance ★★ same type
LDB3 c.859+3G>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-ala38pro (accessed [today's date]).

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