BPTF p.Ser1293=
c.3879T>A · rs145233454 · VCV2763175
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0191%, 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 1.2 | GERP -1.8, phastCons 1 |
| Overall | ||
| CADD | 5.242 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0191%
European (non-Finnish) · 225/1,180,042 alleles
Filtering AF
0.017%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0162%
Overall
0.0148%
239/1,614,104 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0191% | 5,245 |
| Remaining individualsnot grpmax-eligible | 0.0096% | 10,414 |
| African / African-American | 0.00667% | 14,992 |
| Finnishnot grpmax-eligible | 0.00312% | 32,019 |
| Admixed American | 0.00167% | 60,002 |
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
- BPTF
- Protein
- p.Ser1293=
- Coding
- c.3879T>A
- MANE Select
- NM_182641
- dbSNP
- rs145233454
- Type
- single nucleotide variant
- Location
- chr17:67911763 (GRCh38)
- Gene constraint
- LOEUF 0.09 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Residue 1293
- the 'disordered' region
Similar variants
- BPTF p.Ser1293Phe Uncertain significance ★ ⚠ same residue
- BPTF p.Ser1293Pro Uncertain significance ★ ⚠ same residue
- BPTF p.Arg1322Ter Pathogenic/Likely pathogenic ★★ same type
- BPTF p.Arg1738Ter Pathogenic/Likely pathogenic ★★ same type
- BPTF p.Arg2858Ter Pathogenic ★★ same type
- BPTF p.Arg841Ter Pathogenic ★★ same type
- BPTF c.1864+562A>T Uncertain significance ★★ same type
- BPTF c.1865-5651C>G 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/bptf-p-ser1293 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown