BLTP1 p.Arg1771=
c.5313A>G · VCV3261089
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00496%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| REVEL | 0.182 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | Δ0.42 | acceptor loss, 2 bp away · masked 0 · deltas |
| Constraint at this position | ||
| Conservation | phyloP 1.6 | GERP 0.45, phastCons 1 |
| Overall | ||
| CADD | 11.23 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00496%
European (non-Finnish) · 58/1,170,096 alleles
Filtering AF
0.00389%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00356%
Overall
0.00381%
61/1,602,126 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00496% | 20,174 |
| Remaining individualsnot grpmax-eligible | 0.00483% | 20,687 |
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.Arg1771=
- Coding
- c.5313A>G
- MANE Select
- NM_001384125
- Type
- single nucleotide variant
- Location
- chr4:122247158 (GRCh38)
- Residue 1771
- a UniProt-annotated variant site (in alkkucs)
Similar variants
- BLTP1 p.Arg968Cys Likely pathogenic ★★ ⚠ same type
- BLTP1 c.1498+4A>G Uncertain significance ★★ same type
- BLTP1 p.Ala2332Thr Uncertain significance ★★ ⚠ same type
- BLTP1 p.Arg1317His Uncertain significance ★★ same type
- BLTP1 p.Arg1791Lys Uncertain significance ★★ ⚠ same type
- BLTP1 p.Arg2095His Uncertain significance ★★ same type
- BLTP1 p.Arg2279Cys Uncertain significance ★★ same type
- BLTP1 p.Arg3665Gln 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/bltp1-p-arg1771 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown