LTBP4 p.Arg1069Ter
c.3205C>T · VCV3696513
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
nonsense (stop-gain)
predicted LoF
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. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 22 of 30 |
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1 | GERP -0.99, phastCons 0.75 |
| Overall | ||
| CADD | 37.0 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
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
- LTBP4
- Protein
- p.Arg1069Ter
- Coding
- c.3205C>T
- MANE Select
- NM_001042545
- 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.Arg1069= Likely benign ★ 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-arg1069ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown