Is APP p.Ile716Phe (c.2146A>T) pathogenic?

APP p.Ile716Phe (c.2146A>T) is classified Pathogenic in APP (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-05-16). AlphaMissense: likely pathogenic (0.7371); Absent from gnomAD v4.1; Associated with Alzheimer disease.

What condition is associated with APP p.Ile716Phe (c.2146A>T)?

APP p.Ile716Phe (c.2146A>T) is associated with Alzheimer disease (ClinVar).

How common is APP p.Ile716Phe (c.2146A>T) in the general population?

APP p.Ile716Phe (c.2146A>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about APP p.Ile716Phe (c.2146A>T)?

AlphaMissense predicts likely pathogenic (score 0.7371) — an in-silico prediction, not a clinical call.

APP p.Ile716Phe

c.2146A>T · rs63750399 · VCV2498894

Pathogenic Multiple submitters

Classification

Pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely pathogenic

0.7371 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Alzheimer disease

Computational evidence

Protein change
AlphaMissense	0.7371	likely pathogenic ✓ concordant with ClinVar
REVEL	0.944	strongly pathogenic-leaning
SaProt	LLR -7.66	tolerated
⇒ AlphaMissense and REVEL call this damaging; SaProt does not.
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	26.7	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.Ile716Phe
Coding: c.2146A>T
MANE Select: NM_000484
dbSNP: rs63750399
Type: single nucleotide variant
Location: chr21:25891787 (GRCh38)
Gene constraint: LOEUF 0.41 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 68.11 · 263 PDB
Residue 716: a UniProt-annotated variant site (in ad1); a turn; the 'interaction with psen1' region

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.Ile716= Benign ★★ same residue
APP p.Ile716Thr Pathogenic ★ ⚠ same residue
APP p.Ile716Val Pathogenic ★★ same residue
APP p.Ile716Met Likely pathogenic ★ ⚠ same residue
APP p.Ala713Thr Likely pathogenic ★★ ⚠ same condition
APP p.Asp694Asn Pathogenic ★★ ⚠ same condition
APP p.Glu693Gln Pathogenic ★★ ⚠ same condition
APP p.Thr714Ala 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-ile716phe (accessed [today's date]).

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