BPNT2 p.Thr294=
c.882A>G · rs368856658 · VCV1681088
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0657%, mid)
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 -4.3 | GERP -3.2 |
| Overall | ||
| CADD | 4.904 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0657%
Middle Eastern · 4/6,084 alleles
Filtering AF
0.0224%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0188%
Overall
0.00496%
80/1,612,724 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0657% | 1,521 |
| South Asian | 0.0308% | 3,247 |
| Remaining individualsnot grpmax-eligible | 0.016% | 6,244 |
| European (non-Finnish) | 0.00314% | 31,871 |
| Admixed American | 0.00167% | 59,848 |
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.Thr294=
- Coding
- c.882A>G
- MANE Select
- NM_017813
- dbSNP
- rs368856658
- Type
- single nucleotide variant
- Location
- chr8:56963991 (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-thr294 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown