Is BPTF p.Ala23= (c.69C>T) pathogenic?

BPTF p.Ala23= (c.69C>T) is classified Likely benign in BPTF (ClinVar, No assertion criteria, 1 submitter; last evaluated 2022-11-03). Absent from gnomAD v4.1; Associated with BPTF-related disorder.

What condition is associated with BPTF p.Ala23= (c.69C>T)?

BPTF p.Ala23= (c.69C>T) is associated with BPTF-related disorder (ClinVar).

How common is BPTF p.Ala23= (c.69C>T) in the general population?

BPTF p.Ala23= (c.69C>T) is absent from gnomAD v4.1 (gnomAD).

BPTF p.Ala23=

c.69C>T · rs2509368596 · VCV3043804

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,035,106)

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 0.78	GERP 0.32, phastCons 1
Overall
CADD	11.27	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,035,106). 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.Ala23=
Coding: c.69C>T
MANE Select: NM_182641
dbSNP: rs2509368596
Type: single nucleotide variant
Location: chr17:67825793 (GRCh38)
Gene constraint: LOEUF 0.09 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Residue 23: the 'disordered' region

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

Disease context

BPTF-related disorder

Similar variants

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
BPTF p.Ser2307Cys 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-ala23 (accessed [today's date]).

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