LDB3 p.Pro435=
c.1305T>C · rs1009984915 · VCV1329289
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.567%, afr)
Conditions
2
cardiomyopathy
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 -2.8 | GERP -1.5 |
| Overall | ||
| CADD | 1.781 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.567%
African / African-American · 94/16,564 alleles
Filtering AF
0.475%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.44%
Overall
0.0749%
471/629,120 alleles · rare
exomes 223/616,172 · genomes 248/12,948 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.567% | 176 |
| Admixed American | 0.315% | 317 |
| Middle Eastern | 0.197% | 507 |
| Finnishnot grpmax-eligible | 0.16% | 627 |
| South Asian | 0.137% | 729 |
| Remaining individualsnot grpmax-eligible | 0.0885% | 1,130 |
| East Asian | 0.0564% | 1,772 |
| European (non-Finnish) | 0.0412% | 2,426 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0377% | 2,649 |
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.Pro435=
- Coding
- c.1305T>C
- MANE Select
- NM_007078
- dbSNP
- rs1009984915
- Type
- single nucleotide variant
- Location
- chr10:86716400 (GRCh38)
- Gene constraint
- LOEUF 0.864 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 61.98 · 2 PDB
- Residue 435
- the 'disordered' region
Similar variants
- LDB3 p.Ala147Thr Pathogenic/Likely pathogenic ★★ same condition
- LDB3 p.Ala165Val Pathogenic/Likely pathogenic ★★ same condition
- LDB3 p.Ala389Thr Uncertain significance ★★ ⚠ same condition
- LDB3 p.Ala501Val Uncertain significance ★★ ⚠ same condition
- LDB3 p.Arg404Gln Uncertain significance ★★ ⚠ same condition
- LDB3 p.Arg559Gln Uncertain significance ★★ ⚠ same condition
- LDB3 p.Asp47Asn Uncertain significance ★★ ⚠ same condition
- LDB3 p.Gln707Ter 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-pro435 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown