Is APP p.Thr297= (c.891G>A) pathogenic?

APP p.Thr297= (c.891G>A) is classified Likely benign in APP (ClinVar, Single submitter, 1 submitter; last evaluated 2022-06-27). Ultra-rare (popmax 0.0134%, eas); Associated with Alzheimer disease.

What condition is associated with APP p.Thr297= (c.891G>A)?

APP p.Thr297= (c.891G>A) is associated with Alzheimer disease (ClinVar).

How common is APP p.Thr297= (c.891G>A) in the general population?

APP p.Thr297= (c.891G>A) is ultra-rare (popmax 0.0134%, eas) (gnomAD).

APP p.Thr297=

c.891G>A · rs773857944 · VCV1646719

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0134%, eas)

Conditions

Alzheimer disease

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.167	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.1	GERP 1.1, phastCons 0.43
Overall
CADD	12.36	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0134% East Asian · 6/44,880 alleles

Filtering AF 0.00579% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00394%

Overall 0.00173% 28/1,614,220 alleles · ultra-rare exomes 26/1,461,870 · genomes 2/152,350 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0134%	7,480
South Asian	0.00549%	18,217
Remaining individualsnot grpmax-eligible	0.0032%	31,254
European (non-Finnish)	0.00127%	78,668

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: APP
Protein: p.Thr297=
Coding: c.891G>A
MANE Select: NM_000484
dbSNP: rs773857944
Type: single nucleotide variant
Location: chr21:26000157 (GRCh38)
Gene constraint: LOEUF 0.41 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 68.11 · 263 PDB
Residue 297: the bpti/kunitz inhibitor domain

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

Disease context

Alzheimer disease — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

APP p.Thr297Met Benign ★ same residue
APP p.Thr297Ser Uncertain significance ★ ⚠ same residue
APP p.Ala713Thr Likely pathogenic ★★ ⚠ same condition
APP p.Asp694Asn Pathogenic ★★ ⚠ same condition
APP p.Glu693Gln Pathogenic ★★ ⚠ same condition
APP p.Ile716Phe Pathogenic ★★ ⚠ same condition
APP p.Thr714Ala Pathogenic ★★ ⚠ same condition
APP p.Val715Met Pathogenic/Likely pathogenic ★★ ⚠ 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/app-p-thr297 (accessed [today's date]).

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