BLTP2 p.Ser112=
c.336C>T · rs142215136 · VCV2647596
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0343%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>C here scores Δ0.44 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.001 | GERP -2.1, phastCons 0.03 |
| Overall | ||
| CADD | 8.912 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0343%
European (non-Finnish) · 405/1,180,020 alleles
Filtering AF
0.0315%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0305%
Overall
0.0272%
439/1,614,012 alleles · ultra-rare
exomes 405/1,461,872 · genomes 34/152,140 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0343% | 2,914 |
| Remaining individualsnot grpmax-eligible | 0.0208% | 4,806 |
| African / African-American | 0.0174% | 5,762 |
| Finnishnot grpmax-eligible | 0.00625% | 16,008 |
| Admixed American | 0.005% | 19,999 |
| East Asian | 0.00223% | 44,894 |
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
- BLTP2
- Protein
- p.Ser112=
- Coding
- c.336C>T
- MANE Select
- NM_014680
- dbSNP
- rs142215136
- Type
- single nucleotide variant
- Location
- chr17:28643224 (GRCh38)
- Structure
- AlphaFold pLDDT 71.37
Similar variants
- BLTP2 p.Ala1395Ser Uncertain significance ★ ⚠ same type
- BLTP2 p.Ala1564Thr Uncertain significance ★ ⚠ same type
- BLTP2 p.Ala1826Thr Uncertain significance ★ ⚠ same type
- BLTP2 p.Ala248Thr Uncertain significance ★ ⚠ same type
- BLTP2 p.Ala324Thr Uncertain significance ★ ⚠ same type
- BLTP2 p.Ala393Thr Uncertain significance ★ ⚠ same type
- BLTP2 p.Ala539Thr Uncertain significance ★ ⚠ same type
- BLTP2 p.Ala694Gly 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/bltp2-p-ser112 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown