BPTF p.Pro82del
c.229CCG[5] · rs955533308 · VCV1970930
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.804%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2.8 | GERP 0.33, phastCons 1 |
| Overall | ||
| CADD | 12.6 | PHRED · no single calibrated threshold — expert panels disagree |
| Region caveats | ||
| Repeat context | tandem | (GCC)n simple repeat, segmental duplication · ambiguous alignment · reads may not map uniquely · confidence, not pathogenicity |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.804%
African / African-American · 455/56,606 alleles
Filtering AF
0.743%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.719%
Overall
0.0623%
625/1,003,180 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.804% | 124 |
| East Asian | 0.0931% | 1,074 |
| Admixed American | 0.0837% | 1,194 |
| Finnishnot grpmax-eligible | 0.0774% | 1,292 |
| Remaining individualsnot grpmax-eligible | 0.0583% | 1,714 |
| Middle Eastern | 0.0493% | 2,028 |
| South Asian | 0.0272% | 3,680 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0219% | 4,570 |
| European (non-Finnish) | 0.0132% | 7,600 |
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.Pro82del
- Coding
- c.229CCG[5]
- MANE Select
- NM_182641
- dbSNP
- rs955533308
- Type
- Microsatellite
- Location
- chr17:67825952 (GRCh38)
- Gene constraint
- LOEUF 0.09 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Residue 82
- the 'disordered' region
Similar variants
- BPTF p.Pro82_Ala83insPro Likely benign ★★ same residue
- BPTF p.Pro82_Ala83insProPro Uncertain significance ★ same residue
- BPTF p.Thr783fs Pathogenic ★★ same type
- BPTF p.Asp184_Asp185dup Uncertain significance ★★ same type
- BPTF p.Glu874del Uncertain significance ★★ same type
- BPTF p.2676APP[4] Benign ★★ same type
- BPTF p.2676APP[5] Benign/Likely benign ★★ same type
- BPTF p.2676APP[6] Benign/Likely benign ★★ 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-pro82del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown