Is TRAPPC2 p.Asp88fs (c.262_266del) pathogenic?

TRAPPC2 p.Asp88fs (c.262266del) is classified Pathogenic in TRAPPC2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-09-04). Very rare (popmax 0.000113%, nfe); Associated with TRAPPC2-related disorder.

What condition is associated with TRAPPC2 p.Asp88fs (c.262_266del)?

TRAPPC2 p.Asp88fs (c.262_266del) is associated with TRAPPC2-related disorder (ClinVar).

How common is TRAPPC2 p.Asp88fs (c.262_266del) in the general population?

TRAPPC2 p.Asp88fs (c.262_266del) is very rare (popmax 0.000113%, nfe) (gnomAD).

TRAPPC2 p.Asp88fs

c.262_266del · VCV3724048

Pathogenic Multiple submitters

Classification

Pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.000113%, nfe)

Conditions

TRAPPC2-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 in a haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 5 of 6
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.76	GERP 0.036, phastCons 1

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000113% European (non-Finnish) · 1/883,591 alleles

Overall 8.37e-05% 1/1,194,235 alleles · very rare exomes 1/1,080,084 · genomes 0/114,151 · joint denominator

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: TRAPPC2
Protein: p.Asp88fs
Coding: c.262_266del
MANE Select: NM_001011658
Type: Deletion
Location: chrX:13716062 (GRCh38)
Structure: AlphaFold pLDDT 92.44

Full TRAPPC2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

TRAPPC2-related disorder

Similar variants

TRAPPC2 p.Gln131fs Likely pathogenic ★ same type
TRAPPC2 p.Asn118fs Uncertain significance ★ same type
TRAPPC2 c.*263del Benign ★ same type
TRAPPC2 p.Val130fs Pathogenic same type

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/trappc2-p-asp88fs (accessed [today's date]).

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