BPTF p.Thr1385=
c.4155T>A · rs138069789 · VCV727867
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.333%, 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 -0.25 | GERP -4.3 |
| Overall | ||
| CADD | 1.032 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.333%
European (non-Finnish) · 3,930/1,179,254 alleles
Filtering AF
0.325%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.321%
Overall
0.273%
4,394/1,611,368 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.333% | 300 |
| South Asian | 0.228% | 439 |
| Remaining individualsnot grpmax-eligible | 0.178% | 562 |
| Middle Eastern | 0.132% | 756 |
| Admixed American | 0.123% | 815 |
| African / African-American | 0.0536% | 1,864 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0372% | 2,687 |
| Finnishnot grpmax-eligible | 0.0188% | 5,325 |
| East Asian | 0.00669% | 14,948 |
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.Thr1385=
- Coding
- c.4155T>A
- MANE Select
- NM_182641
- dbSNP
- rs138069789
- Type
- single nucleotide variant
- Location
- chr17:67912039 (GRCh38)
- Gene constraint
- LOEUF 0.09 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Residue 1385
- the 'disordered' region
Similar variants
- BPTF p.Thr1385Ala Conflicting classifications of pathogenicity ★ ⚠ same residue
- BPTF p.Thr1385Asn Uncertain significance ★ ⚠ same residue
- BPTF p.Thr1385fs Likely pathogenic ★ 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
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-thr1385 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown