LTBP2 p.Asp414=
c.1242C>T · rs150213096 · VCV1595323
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.104%, 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 -3.3 | GERP -3.7 |
| Overall | ||
| CADD | 3.508 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.104%
African / African-American · 78/75,048 alleles
Filtering AF
0.0854%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0785%
Overall
0.0179%
289/1,611,520 alleles · rare
exomes 216/1,459,194 · genomes 73/152,326 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.104% | 962 |
| South Asian | 0.0988% | 1,012 |
| Remaining individualsnot grpmax-eligible | 0.04% | 2,498 |
| Middle Eastern | 0.0165% | 6,058 |
| Admixed American | 0.0117% | 8,575 |
| European (non-Finnish) | 0.0072% | 13,882 |
| Finnishnot grpmax-eligible | 0.00325% | 30,744 |
| East Asian | 0.00223% | 44,874 |
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
- LTBP2
- Protein
- p.Asp414=
- Coding
- c.1242C>T
- MANE Select
- NM_000428
- dbSNP
- rs150213096
- Type
- single nucleotide variant
- Location
- chr14:74552344 (GRCh38)
- Gene constraint
- LOEUF 0.595 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 58.33
- Residue 414
- the egf-like 2 domain
Similar variants
- LTBP2 c.2389-2A>G Likely pathogenic ★★ same type
- LTBP2 c.2659+2T>C Likely pathogenic ★★ same type
- LTBP2 c.2789-1G>A Likely pathogenic ★★ same type
- LTBP2 c.2789-2A>T Likely pathogenic ★★ same type
- LTBP2 c.3652+1G>A Likely pathogenic ★★ same type
- LTBP2 p.Arg299Ter Pathogenic ★★ same type
- LTBP2 p.Cys1438Tyr Likely pathogenic ★★ same type
- LTBP2 p.Gln1533Ter Pathogenic/Likely pathogenic ★★ 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/ltbp2-p-asp414 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown