BLTP1 p.Asp1407=
c.4221T>C · rs1304604617 · VCV3053931
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00102%, nfe)
Conditions
1
BLTP1-related disorder
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 -1.5 | GERP -5.8 |
| Overall | ||
| CADD | 6.327 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00102%
European (non-Finnish) · 12/1,180,026 alleles
Filtering AF
0.000542%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000428%
Overall
0.000744%
12/1,613,796 alleles · very rare
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
- BLTP1
- Protein
- p.Asp1407=
- Coding
- c.4221T>C
- MANE Select
- NM_001384125
- dbSNP
- rs1304604617
- Type
- single nucleotide variant
- Location
- chr4:122239903 (GRCh38)
- Residue 1407
- a UniProt-annotated variant site (in alkkucs); the 'disordered' region
Disease context
BLTP1-related disorder
Similar variants
- BLTP1 p.Arg968Cys Likely pathogenic ★★ ⚠ same condition
- BLTP1 p.His3063Arg Uncertain significance ★★ same condition
- BLTP1 c.10312+2T>C Likely pathogenic ★ same condition
- BLTP1 c.11513+1G>C Likely pathogenic ★ same condition
- BLTP1 c.5184+1G>T Likely pathogenic ★ same condition
- BLTP1 p.Arg3190Ter Likely pathogenic ★ same condition
- BLTP1 p.Phe3799Ser Uncertain significance ★ same condition
- BLTP1 p.Val1878Ala 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/bltp1-p-asp1407 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown