Is BPTF p.Arg749fs (c.2245dup) pathogenic?

BPTF p.Arg749fs (c.2245dup) is classified Pathogenic in BPTF (ClinVar, Single submitter, 1 submitter; last evaluated 2018-07-19). Absent from gnomAD.

How common is BPTF p.Arg749fs (c.2245dup) in the general population?

BPTF p.Arg749fs (c.2245dup) is absent from gnomAD (gnomAD).

BPTF p.Arg749fs

c.2245dup · rs1598468564 · VCV817147

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

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 6 of 28
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 12	GERP 6.5, phastCons 1
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.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: BPTF
Protein: p.Arg749fs
Coding: c.2245dup
MANE Select: NM_182641
dbSNP: rs1598468564
Type: Duplication
Location: chr17:67893557 (GRCh38)
Gene constraint: LOEUF 0.09 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Residue 749: the 'disordered' region; the 'interaction with keap1' region

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

Similar variants

BPTF p.Ser71fs Pathogenic ★★ same type
BPTF c.1864+712dup Likely pathogenic ★ same type
BPTF p.Ala1952fs Pathogenic ★ same type
BPTF p.Ala2289fs Pathogenic ★ same type
BPTF p.Arg2593fs Pathogenic ★ same type
BPTF p.Arg95fs Likely pathogenic ★ same type
BPTF p.Asn2876Ter Likely pathogenic ★ same type
BPTF p.Asp566fs Pathogenic ★ 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-arg749fs (accessed [today's date]).

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