BPTF p.Arg841Ter
c.2521C>T · VCV3381404
Pathogenic
Multiple submitters
Classification
Pathogenic
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
Consequence
nonsense (stop-gain)
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
intellectual disability
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function in a haploinsufficient gene (ClinGen) |
|---|---|---|
| NMD | predicted | premature termination codon in exon 7 of 28 |
| Splicing | ||
| SpliceAI | Δ0.43 | donor loss · deltas |
| Pangolin | Δ0.46 | loss · gain 0.35 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 1.8 | GERP 4.5, phastCons 1 |
| Overall | ||
| CADD | 40.0 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- BPTF
- Protein
- p.Arg841Ter
- Coding
- c.2521C>T
- MANE Select
- NM_182641
- Type
- single nucleotide variant
- Location
- chr17:67894143 (GRCh38)
- Gene constraint
- LOEUF 0.09 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Residue 841
- the 'interaction with maz' region
Similar variants
- BPTF p.Arg1078Ter Uncertain significance ★ same condition
- BPTF p.Ile2035Val Conflicting classifications of pathogenicity ★ ⚠ same condition
- BPTF p.Leu330fs Pathogenic ★ same condition
- BPTF p.Arg1322Ter Pathogenic/Likely pathogenic ★★ same type
- BPTF p.Arg1738Ter Pathogenic/Likely pathogenic ★★ same type
- BPTF p.Arg2858Ter 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-arg841ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown