Is BPTF p.2676APP[6] (c.8035GCCCCTCCA[5]) pathogenic?

BPTF p.2676APP[6] (c.8035GCCCCTCCA[5]) is classified Benign/Likely benign in BPTF (ClinVar, Multiple submitters, 4 submitters; last evaluated 2026-02-01). Rare (popmax 0.771%, mid); Associated with Inborn genetic diseases.

What condition is associated with BPTF p.2676APP[6] (c.8035GCCCCTCCA[5])?

BPTF p.2676APP[6] (c.8035GCCCCTCCA[5]) is associated with Inborn genetic diseases (ClinVar).

How common is BPTF p.2676APP[6] (c.8035GCCCCTCCA[5]) in the general population?

BPTF p.2676APP[6] (c.8035GCCCCTCCA[5]) is rare (popmax 0.771%, mid) (gnomAD).

BPTF p.2676APP[6]

c.8035GCCCCTCCA[5] · rs60308484 · VCV1275134

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

rare (popmax 0.771%, mid)

Conditions

Inborn genetic diseases

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 -3.7	GERP -1.8
Overall
CADD	2.365	PHRED · no single calibrated threshold — expert panels disagree
Region caveats
Repeat context	tandem	CCAGCCCCT simple repeat · ambiguous alignment · confidence, not pathogenicity

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.771% Middle Eastern · 44/5,706 alleles

Filtering AF 0.59% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.527%

Overall 0.219% 3,369/1,539,320 alleles · rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.771%	130
Ashkenazi Jewishnot grpmax-eligible	0.297%	337
Remaining individualsnot grpmax-eligible	0.261%	384
European (non-Finnish)	0.253%	395
South Asian	0.0782%	1,279
Finnishnot grpmax-eligible	0.0771%	1,297
Admixed American	0.0745%	1,341
African / African-American	0.0656%	1,524

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.2676APP[6]
Coding: c.8035GCCCCTCCA[5]
MANE Select: NM_182641
dbSNP: rs60308484
Type: Microsatellite
Location: chr17:67959642 (GRCh38)
Gene constraint: LOEUF 0.09 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)

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.Thr783fs Pathogenic ★★ same condition
BPTF p.Pro82_Ala83insPro Likely benign ★★ same condition
BPTF p.Ala1197Val Uncertain significance ★★ ⚠ same condition
BPTF p.Ala1252Val Uncertain significance ★★ ⚠ same condition
BPTF p.Ala2819Phe Uncertain significance ★★ same condition
BPTF p.Arg1078Gln Uncertain significance ★★ same condition
BPTF p.Arg2139His Uncertain significance ★★ ⚠ same condition
BPTF p.Arg215His 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-2676app-6 (accessed [today's date]).

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