Is AP4E1 p.Pro642Leu (c.1925C>T) pathogenic?

AP4E1 p.Pro642Leu (c.1925C>T) is classified Uncertain significance in AP4E1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-04-19). AlphaMissense: likely benign (0.1593); Ultra-rare (popmax 0.0868%, sas); Associated with Spastic paraplegia.

What condition is associated with AP4E1 p.Pro642Leu (c.1925C>T)?

AP4E1 p.Pro642Leu (c.1925C>T) is associated with Spastic paraplegia (ClinVar).

How common is AP4E1 p.Pro642Leu (c.1925C>T) in the general population?

AP4E1 p.Pro642Leu (c.1925C>T) is ultra-rare (popmax 0.0868%, sas) (gnomAD).

What do computational predictors say about AP4E1 p.Pro642Leu (c.1925C>T)?

AlphaMissense predicts likely benign (score 0.1593) — an in-silico prediction, not a clinical call.

AP4E1 p.Pro642Leu

c.1925C>T · VCV4526991

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.1593 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0868%, sas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Spastic paraplegia

Computational evidence

Protein change
AlphaMissense	0.1593	likely benign
REVEL	0.206	benign-leaning
SaProt	LLR -8.56	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.7	GERP 1.6, phastCons 1
Regional constraint	o/e 1.01	unconstrained · MANE · 94 kb · p 0.65 · regional, not allelic
Overall
CADD	26.7	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0868% South Asian · 79/91,014 alleles

Filtering AF 0.0713% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0657%

Overall 0.00508% 82/1,613,484 alleles · ultra-rare exomes 77/1,461,398 · genomes 5/152,086 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0868%	1,152
Remaining individualsnot grpmax-eligible	0.0032%	31,239
European (non-Finnish)	8.48e-05%	1,179,768

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: AP4E1
Protein: p.Pro642Leu
Coding: c.1925C>T
MANE Select: NM_007347
Type: single nucleotide variant
Location: chr15:50968336 (GRCh38)
Gene constraint: LOEUF 0.576 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 72.42 · 4 PDB

Full AP4E1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

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

Similar variants

AP4E1 p.Arg304Ter Pathogenic/Likely pathogenic ★★ same condition
AP4E1 p.Ala119Ser Uncertain significance ★★ ⚠ same condition
AP4E1 p.Ala45Thr Uncertain significance ★★ ⚠ same condition
AP4E1 p.Ala475Val Uncertain significance ★★ ⚠ same condition
AP4E1 p.Arg646Cys Uncertain significance ★★ same condition
AP4E1 p.Asn1086Ser Uncertain significance ★★ ⚠ same condition
AP4E1 p.Asp484Val Uncertain significance ★★ ⚠ same condition
AP4E1 p.Asp938Gly 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/ap4e1-p-pro642leu (accessed [today's date]).

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