Is SCAPER p.Ala499fs (c.1496del) pathogenic?

SCAPER p.Ala499fs (c.1496del) is classified Likely pathogenic in SCAPER (ClinVar, Single submitter, 1 submitter; last evaluated 2023-11-02). Associated with SCAPER-related disorder.

What condition is associated with SCAPER p.Ala499fs (c.1496del)?

SCAPER p.Ala499fs (c.1496del) is associated with SCAPER-related disorder (ClinVar).

SCAPER p.Ala499fs

c.1496del · VCV4925982

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

SCAPER-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 13 of 32
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 4.1	GERP 0.73, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Variant & gene context

Gene: SCAPER
Protein: p.Ala499fs
Coding: c.1496del
MANE Select: NM_020843
Type: Deletion
Location: chr15:76765454 (GRCh38)
Gene constraint: LOEUF 0.666 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 68.35 · 2 PDB

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

Disease context

SCAPER-related disorder

Similar variants

SCAPER p.Glu290fs Likely pathogenic ★ same condition
SCAPER p.Lys871fs Likely pathogenic ★ same condition
SCAPER p.Ser1236fs Likely pathogenic ★ same condition
SCAPER p.Val1261fs Likely pathogenic ★ same condition
SCAPER p.Ala872fs Likely pathogenic ★★ same condition
SCAPER p.Arg112Ter Likely pathogenic ★★ same condition
SCAPER p.Ile746fs Pathogenic ★★ same condition
SCAPER c.1035+1G>C 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/scaper-p-ala499fs (accessed [today's date]).

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