Is APP p.Thr719Pro (c.2155A>C) pathogenic?

APP p.Thr719Pro (c.2155A>C) is classified Likely pathogenic in APP (ClinVar, Single submitter, 1 submitter; last evaluated 2021-10-27). AlphaMissense: likely pathogenic (0.9453); Absent from gnomAD v4.1; Associated with Alzheimer disease type 1.

What condition is associated with APP p.Thr719Pro (c.2155A>C)?

APP p.Thr719Pro (c.2155A>C) is associated with Alzheimer disease type 1 (ClinVar).

How common is APP p.Thr719Pro (c.2155A>C) in the general population?

APP p.Thr719Pro (c.2155A>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about APP p.Thr719Pro (c.2155A>C)?

AlphaMissense predicts likely pathogenic (score 0.9453) — an in-silico prediction, not a clinical call.

APP p.Thr719Pro

Q: How is Early-onset autosomal dominant Alzheimer disease inherited?

Typically Autosomal dominant (Orphanet). A genetic counselor can assess individual risk for a family.

c.2155A>C · rs2146237857 · VCV1342870

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9453 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Alzheimer disease type 1

Computational evidence

Protein change
AlphaMissense	0.9453	likely pathogenic ✓ concordant with ClinVar
REVEL	0.841	moderately pathogenic-leaning
SaProt	LLR -11.55	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.8	GERP 1.9, phastCons 1
Regional constraint	o/e 0.84	unconstrained · MANE · 289 kb · p 2e-07 · regional, not allelic
Overall
CADD	27.7	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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: APP
Protein: p.Thr719Pro
Coding: c.2155A>C
MANE Select: NM_000484
dbSNP: rs2146237857
Type: single nucleotide variant
Location: chr21:25891778 (GRCh38)
Gene constraint: LOEUF 0.41 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 68.11 · 263 PDB
Residue 719: the 'interaction with psen1' region

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

Disease context

Alzheimer disease type 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Early-onset autosomal dominant Alzheimer disease (Orphanet):

Inheritance: Autosomal dominant
Onset: Adult
Prevalence: 1-9 / 100 000 (Europe)

Similar variants

APP p.Ala713Thr Likely pathogenic ★★ ⚠ same condition
APP p.Thr714Ala Pathogenic ★★ ⚠ same condition
APP p.Val715Met Pathogenic/Likely pathogenic ★★ ⚠ same condition
APP p.Val717Ile Pathogenic ★★ ⚠ same condition
APP p.Val717Phe Pathogenic ★★ ⚠ same condition
APP p.Arg16Gln Uncertain significance ★★ ⚠ same condition
APP p.Glu665Asp Uncertain significance ★★ ⚠ same condition
APP p.Met338Val 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/app-p-thr719pro (accessed [today's date]).

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