LDB3 p.Ala170=
c.510C>A · VCV4908460
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.48e-05%, nfe)
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 1.8 | GERP 0.081, phastCons 1 |
| Overall | ||
| CADD | 11.15 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.48e-05%
European (non-Finnish) · 1/1,179,806 alleles
Overall
6.2e-05%
1/1,613,142 alleles · very rare
exomes 1/1,460,794 · genomes 0/152,348 · joint denominator
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.Ala170=
- Coding
- c.510C>A
- MANE Select
- NM_007078
- Type
- single nucleotide variant
- Location
- chr10:86681624 (GRCh38)
- Gene constraint
- LOEUF 0.864 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 61.98 · 2 PDB
- Residue 170
- the 'disordered' region
Similar variants
- LDB3 p.Ala170Ser Uncertain significance ★★ ⚠ same residue
- LDB3 p.Ala170Thr Conflicting classifications of pathogenicity ★ ⚠ same residue
- LDB3 p.Ala170Val Uncertain significance ★ ⚠ same residue
- LDB3 p.Ile170= 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
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-ala170 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown