BPNT2 p.Val252=
c.756C>A · rs372306148 · VCV2413694
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00178%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.83 | donor gain · deltas |
|---|---|---|
| Pangolin | Δ0.63 | gain · loss 0.00 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 1.6 | GERP 0.58, phastCons 1 |
| Overall | ||
| CADD | 6.299 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00178%
European (non-Finnish) · 21/1,179,992 alleles
Filtering AF
0.00114%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000971%
Overall
0.0013%
21/1,613,990 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
- BPNT2
- Protein
- p.Val252=
- Coding
- c.756C>A
- MANE Select
- NM_017813
- dbSNP
- rs372306148
- Type
- single nucleotide variant
- Location
- chr8:56966243 (GRCh38)
- Gene constraint
- LOEUF 0.619 · pLI 0.79 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 88.55
Similar variants
- BPNT2 p.Arg187Ter Pathogenic ★★ same type
- BPNT2 c.-155C>G Uncertain significance ★★ same type
- BPNT2 c.*4264G>A Uncertain significance ★★ same type
- BPNT2 c.*5193A>G Uncertain significance ★★ same type
- BPNT2 p.Ala218Ser Uncertain significance ★★ ⚠ same type
- BPNT2 p.Arg187Gln Uncertain significance ★★ ⚠ same type
- BPNT2 p.Arg243Cys Uncertain significance ★★ ⚠ same type
- BPNT2 p.Arg243His 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/bpnt2-p-val252 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown