Is BPTF p.Pro2685Ser (c.8053C>T) pathogenic?

BPTF p.Pro2685Ser (c.8053C>T) is classified Conflicting classifications of pathogenicity in BPTF (ClinVar, Conflicting submitters, 2 submitters; last evaluated 2025-01-01). AlphaMissense: likely benign (0.0947); Ultra-rare (popmax 0.0946%, afr); Associated with Inborn genetic diseases.

What condition is associated with BPTF p.Pro2685Ser (c.8053C>T)?

BPTF p.Pro2685Ser (c.8053C>T) is associated with Inborn genetic diseases (ClinVar).

How common is BPTF p.Pro2685Ser (c.8053C>T) in the general population?

BPTF p.Pro2685Ser (c.8053C>T) is ultra-rare (popmax 0.0946%, afr) (gnomAD).

What do computational predictors say about BPTF p.Pro2685Ser (c.8053C>T)?

AlphaMissense predicts likely benign (score 0.0947) — an in-silico prediction, not a clinical call.

BPTF p.Pro2685Ser

c.8053C>T · rs782449768 · VCV2173126

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.0947 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0946%, afr)

Missense predictors

0/2 damaging

AlphaMissense, REVEL

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0947	likely benign
REVEL	0.079	moderately benign-leaning
⇒ AlphaMissense and REVEL both call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2	GERP 1.2, phastCons 0.95
Regional constraint	o/e 1.02	unconstrained · MANE · 12 kb · p 0.83 · regional, not allelic
Overall
CADD	22.3	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM P2811S vs ClinVar P2685S) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0946% African / African-American · 61/64,464 alleles

Filtering AF 0.0756% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0687%

Overall 0.00523% 71/1,358,174 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0946%	1,057
Admixed American	0.00826%	12,102
Remaining individualsnot grpmax-eligible	0.00187%	53,386
South Asian	0.00125%	79,822
European (non-Finnish)	0.000405%	247,045

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.Pro2685Ser
Coding: c.8053C>T
MANE Select: NM_182641
dbSNP: rs782449768
Type: single nucleotide variant
Location: chr17:67959667 (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.Pro2685= Likely benign same residue
BPTF p.Ala1197Val Uncertain significance ★★ ⚠ same condition
BPTF p.Ala1252Val 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
BPTF p.Arg2352His Uncertain significance ★★ ⚠ same condition
BPTF p.Arg2858Gln 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-pro2685ser (accessed [today's date]).

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