Is AP4E1 p.Ser31= (c.93C>T) pathogenic?

AP4E1 p.Ser31= (c.93C>T) is classified Likely benign in AP4E1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-02-02). Ultra-rare (popmax 0.0333%, mid); Associated with Spastic paraplegia.

What condition is associated with AP4E1 p.Ser31= (c.93C>T)?

AP4E1 p.Ser31= (c.93C>T) is associated with Spastic paraplegia (ClinVar).

How common is AP4E1 p.Ser31= (c.93C>T) in the general population?

AP4E1 p.Ser31= (c.93C>T) is ultra-rare (popmax 0.0333%, mid) (gnomAD).

AP4E1 p.Ser31=

c.93C>T · rs779466797 · VCV2199003

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0333%, mid)

Conditions

Spastic paraplegia

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.16	GERP -0.32, phastCons 0.43
Overall
CADD	12.46	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0333% Middle Eastern · 2/5,998 alleles

Filtering AF 0.00588% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00244%

Overall 0.00261% 42/1,610,192 alleles · ultra-rare exomes 37/1,457,944 · genomes 5/152,248 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0333%	2,999
Ashkenazi Jewishnot grpmax-eligible	0.00679%	14,737
Admixed American	0.00335%	29,891
Remaining individualsnot grpmax-eligible	0.00321%	31,131
European (non-Finnish)	0.00288%	34,681

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.Ser31=
Coding: c.93C>T
MANE Select: NM_007347
dbSNP: rs779466797
Type: single nucleotide variant
Location: chr15:50908871 (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.Ser31Phe Uncertain significance ★ ⚠ same residue
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

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-ser31 (accessed [today's date]).

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