Is LDB3 p.Ala93= (c.279A>T) pathogenic?

LDB3 p.Ala93= (c.279A>T) is classified Likely benign in LDB3 (ClinVar, Single submitter, 1 submitter; last evaluated 2026-03-10). Absent from gnomAD v4.1.

How common is LDB3 p.Ala93= (c.279A>T) in the general population?

LDB3 p.Ala93= (c.279A>T) is absent from gnomAD v4.1 (gnomAD).

LDB3 p.Ala93=

c.279A>T · VCV4847338

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

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 -6.9	GERP -4.1
Overall
CADD	0.292	PHRED · no single calibrated threshold — expert panels disagree

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.Ala93=
Coding: c.279A>T
MANE Select: NM_007078
Type: single nucleotide variant
Location: chr10:86680115 (GRCh38)
Gene constraint: LOEUF 0.864 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 61.98 · 2 PDB
Residue 93: the 'disordered' region

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

Similar variants

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
LDB3 c.859+5G>C 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-ala93 (accessed [today's date]).

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