BPNT2 p.Lys298=
c.894G>A · VCV4702740
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00246%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.013 | GERP -0.26, phastCons 0.82 |
| Overall | ||
| CADD | 6.058 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00246%
European (non-Finnish) · 29/1,179,574 alleles
Filtering AF
0.00172%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00149%
Overall
0.00198%
29/1,461,122 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.Lys298=
- Coding
- c.894G>A
- MANE Select
- NM_017813
- Type
- single nucleotide variant
- Location
- chr8:56963979 (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-lys298 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown