Is BPTF p.Arg68fs (c.202del) pathogenic?

BPTF p.Arg68fs (c.202del) is classified Pathogenic in BPTF (ClinVar, Single submitter, 1 submitter; last evaluated 2025-09-11). Associated with Inborn genetic diseases.

What condition is associated with BPTF p.Arg68fs (c.202del)?

BPTF p.Arg68fs (c.202del) is associated with Inborn genetic diseases (ClinVar).

BPTF p.Arg68fs

c.202del · VCV4214990

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 1 of 28
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 2.1	GERP -0.55, phastCons 0.99
Region caveats
Repeat context	seg dup	· reads may not map uniquely · confidence, not pathogenicity

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Variant & gene context

Gene: BPTF
Protein: p.Arg68fs
Coding: c.202del
MANE Select: NM_182641
Type: Deletion
Location: chr17:67825926 (GRCh38)
Gene constraint: LOEUF 0.09 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Residue 68: the 'disordered' region

Full BPTF gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

BPTF p.Arg68Ser Uncertain significance ★★ ⚠ same residue
BPTF p.Arg68Met Uncertain significance ★ same residue
BPTF p.Arg68Thr Uncertain significance ★ ⚠ same residue
BPTF p.Asn789fs Pathogenic ★ same condition
BPTF p.Arg101_Gly105del Uncertain significance ★ same condition
BPTF p.Thr1631del Conflicting classifications of pathogenicity ★ same condition
BPTF p.Thr783fs Pathogenic ★★ same condition
BPTF p.Ala1197Val Uncertain significance ★★ ⚠ same condition

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-arg68fs (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown