LTBP4 p.Arg1069=
c.3205C>A · rs1028864026 · VCV2868332
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00267%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1 | GERP -0.99, phastCons 0.75 |
| Overall | ||
| CADD | 6.753 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00267%
African / African-American · 2/74,962 alleles
Filtering AF
0.000443%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000166%
Overall
0.000124%
2/1,610,578 alleles · very rare
exomes 2/1,458,288 · genomes 0/152,290 · 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
- LTBP4
- Protein
- p.Arg1069=
- Coding
- c.3205C>A
- MANE Select
- NM_001042545
- dbSNP
- rs1028864026
- Type
- single nucleotide variant
- Location
- chr19:40619481 (GRCh38)
- Gene constraint
- LOEUF 0.734 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 62.53
- Residue 1069
- the egf-like 12; calcium-binding domain
Similar variants
- LTBP4 p.Arg1069Ter Pathogenic ★ same residue
- LTBP4 c.1307-2A>G Pathogenic/Likely pathogenic ★★ same type
- LTBP4 p.Arg677Ter Pathogenic/Likely pathogenic ★★ same type
- LTBP4 p.Arg691Ter Pathogenic ★★ same type
- LTBP4 c.2944+5G>C Uncertain significance ★★ same type
- LTBP4 c.3070+4C>T Uncertain significance ★★ same type
- LTBP4 c.*121C>G Uncertain significance ★★ same type
- LTBP4 p.Ala1090Thr 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/ltbp4-p-arg1069 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown