Is BPTF p.Ser2598= (c.7794T>C) pathogenic?

BPTF p.Ser2598= (c.7794T>C) is classified Likely benign in BPTF (ClinVar, No assertion criteria, 1 submitter; last evaluated 2022-07-08). Very rare (popmax 0.00536%, afr); Associated with BPTF-related disorder.

What condition is associated with BPTF p.Ser2598= (c.7794T>C)?

BPTF p.Ser2598= (c.7794T>C) is associated with BPTF-related disorder (ClinVar).

How common is BPTF p.Ser2598= (c.7794T>C) in the general population?

BPTF p.Ser2598= (c.7794T>C) is very rare (popmax 0.00536%, afr) (gnomAD).

BPTF p.Ser2598=

c.7794T>C · rs138188947 · VCV3054137

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00536%, afr)

Conditions

BPTF-related disorder

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 -8.6	GERP -4.9
Overall
CADD	0.385	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00536% African / African-American · 4/74,596 alleles

Filtering AF 0.00175% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00104%

Overall 0.000372% 6/1,613,098 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00536%	18,649
European (non-Finnish)	0.00017%	589,870

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.Ser2598=
Coding: c.7794T>C
MANE Select: NM_182641
dbSNP: rs138188947
Type: single nucleotide variant
Location: chr17:67948174 (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

BPTF-related disorder

Similar variants

BPTF p.Ser2598Cys Uncertain significance ★★ ⚠ same residue
BPTF p.Leu935Phe Uncertain significance ★★ ⚠ same condition
BPTF p.Ala83Gly Uncertain significance ★ ⚠ same condition
BPTF p.Ile2057Asn Uncertain significance ★ same condition
BPTF p.Ile218Thr Uncertain significance ★ same condition
BPTF p.Lys1445Asn Uncertain significance ★ ⚠ same condition
BPTF p.Met324Leu Uncertain significance ★ same condition
BPTF p.Ser1154Arg 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-ser2598 (accessed [today's date]).

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