BLTP1 p.Ala1060=
c.3180A>C · rs371248477 · VCV3047067
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0613%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.032 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.43 | GERP -4.2 |
| Overall | ||
| CADD | 7.744 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0613%
African / African-American · 46/75,066 alleles
Filtering AF
0.0471%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0422%
Overall
0.00873%
141/1,614,202 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0613% | 1,632 |
| Middle Eastern | 0.0495% | 2,020 |
| Admixed American | 0.045% | 2,223 |
| Remaining individualsnot grpmax-eligible | 0.0176% | 5,683 |
| European (non-Finnish) | 0.00458% | 21,852 |
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.Ala1060=
- Coding
- c.3180A>C
- MANE Select
- NM_001384125
- dbSNP
- rs371248477
- Type
- single nucleotide variant
- Location
- chr4:122230068 (GRCh38)
- Residue 1060
- 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-ala1060 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown