Is BPTF p.Asp160Glu (c.480C>G) pathogenic?

BPTF p.Asp160Glu (c.480C>G) is classified Benign in BPTF (ClinVar, Single submitter, 2 submitters; last evaluated 2026-01-27). AlphaMissense: likely benign (0.0886); Common (popmax 12.9%, afr) — too common for a highly-penetrant pathogenic allele.

What do computational predictors say about BPTF p.Asp160Glu (c.480C>G)?

AlphaMissense predicts likely benign (score 0.0886) — an in-silico prediction, not a clinical call.

BPTF p.Asp160Glu

Q: How common is BPTF p.Asp160Glu (c.480C>G) in the general population?

BPTF p.Asp160Glu (c.480C>G) is common (popmax 12.9%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.480C>G · rs73351760 · VCV1970967

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.0886 · ACMG-weighted

gnomAD v4.1

Common

common (popmax 12.9%, afr) — too common for a highly-penetrant pathogenic allele

Missense predictors

0/2 damaging

AlphaMissense, REVEL

Computational evidence

Protein change
AlphaMissense	0.0886	likely benign
REVEL	0.135	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 0.16	GERP -1.2, phastCons 0.98
Regional constraint	o/e 0.86	unconstrained · MANE · 28 kb · p 0.058 · regional, not allelic
Overall
CADD	17.05	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 12.9% African / African-American · 9,673/74,926 alleles

Filtering AF 12.7% ClinGen BA1/BS1 input FAF95, joint · FAF99 12.6%

Overall 0.678% 10,931/1,612,342 alleles · common

Ancestry group	Frequency	1 in
African / African-Americangrpmax	12.9%	8
Remaining individualsnot grpmax-eligible	0.844%	118
Admixed American	0.825%	121
Middle Eastern	0.334%	299
South Asian	0.0428%	2,334
European (non-Finnish)	0.015%	6,659

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.Asp160Glu
Coding: c.480C>G
MANE Select: NM_182641
dbSNP: rs73351760
Type: single nucleotide variant
Location: chr17:67826204 (GRCh38)
Gene constraint: LOEUF 0.09 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Residue 160: the 'disordered' region

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

Similar variants

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BPTF p.Arg841Ter Pathogenic ★★ same type
BPTF c.1864+562A>T Uncertain significance ★★ same type
BPTF c.1865-5651C>G Uncertain significance ★★ ⚠ same type
BPTF p.Ala1197Val Uncertain significance ★★ ⚠ same type
BPTF p.Ala1252Val Uncertain significance ★★ ⚠ same type

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-asp160glu (accessed [today's date]).

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