Is BPTF p.Ala152= (c.456C>T) pathogenic?

BPTF p.Ala152= (c.456C>T) is classified Likely benign in BPTF (ClinVar, No assertion criteria, 1 submitter; last evaluated 2021-04-21). Very rare (popmax 0.00446%, eas); Associated with BPTF-related disorder.

What condition is associated with BPTF p.Ala152= (c.456C>T)?

BPTF p.Ala152= (c.456C>T) is associated with BPTF-related disorder (ClinVar).

How common is BPTF p.Ala152= (c.456C>T) in the general population?

BPTF p.Ala152= (c.456C>T) is very rare (popmax 0.00446%, eas) (gnomAD).

BPTF p.Ala152=

c.456C>T · rs148162720 · VCV3032982

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00446%, eas)

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 -0.23	GERP -1.2, phastCons 0.46
Overall
CADD	11.03	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00446% East Asian · 2/44,796 alleles

Filtering AF 0.00166% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00143%

Overall 0.002% 32/1,602,430 alleles · very rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00446%	22,398
European (non-Finnish)	0.00239%	41,771
Admixed American	0.00167%	59,960
African / African-American	0.00134%	74,680

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.Ala152=
Coding: c.456C>T
MANE Select: NM_182641
dbSNP: rs148162720
Type: single nucleotide variant
Location: chr17:67826180 (GRCh38)
Gene constraint: LOEUF 0.09 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Residue 152: 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.Ala152Gly Uncertain significance ★ ⚠ same residue
BPTF p.Ala152Val 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

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-ala152 (accessed [today's date]).

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