BLTP1 p.Ser3067=
c.9201G>A · rs373249253 · VCV3039112
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0786%, afr)
Conditions
1
BLTP1-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.01 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP -1.2 | GERP -3 |
| Overall | ||
| CADD | 5.978 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0786%
African / African-American · 59/75,028 alleles
Filtering AF
0.0625%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0567%
Overall
0.00397%
64/1,613,872 alleles · ultra-rare
exomes 27/1,461,622 · genomes 37/152,250 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0786% | 1,272 |
| Admixed American | 0.00333% | 30,004 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,502 |
| Finnishnot grpmax-eligible | 0.00156% | 64,026 |
| European (non-Finnish) | 8.48e-05% | 1,179,812 |
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.Ser3067=
- Coding
- c.9201G>A
- MANE Select
- NM_001384125
- dbSNP
- rs373249253
- Type
- single nucleotide variant
- Location
- chr4:122286704 (GRCh38)
- Residue 3067
- a UniProt-annotated variant site (in alkkucs)
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-ser3067 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown