Is TRAPPC2 p.Arg122Ter (c.364C>T) pathogenic?

TRAPPC2 p.Arg122Ter (c.364C>T) is classified Pathogenic in TRAPPC2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-11-01). No allele count reported in gnomAD v4.1 (AN 1,165,705).

How common is TRAPPC2 p.Arg122Ter (c.364C>T) in the general population?

TRAPPC2 p.Arg122Ter (c.364C>T) is no allele count reported in gnomAD v4.1 (AN 1,165,705) (gnomAD).

TRAPPC2 p.Arg122Ter

c.364C>T · rs2046258303 · VCV1457801

Pathogenic Multiple submitters

Classification

Pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,165,705)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	nonsense (stop-gain)	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	escapes	premature termination codon in the last exon (6 of 6) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.6	GERP 2.4, phastCons 1
Overall
CADD	37.0	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,165,705). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: TRAPPC2
Protein: p.Arg122Ter
Coding: c.364C>T
MANE Select: NM_001011658
dbSNP: rs2046258303
Type: single nucleotide variant
Location: chrX:13714466 (GRCh38)
Structure: AlphaFold pLDDT 92.44

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

Similar variants

TRAPPC2 c.*1436C>T Uncertain significance ★★ same type
TRAPPC2 c.*942G>T Uncertain significance ★★ same type
TRAPPC2 c.*1052T>C Benign ★★ same type
TRAPPC2 c.*1229C>T Likely benign ★★ same type
TRAPPC2 c.*1739C>G Benign ★★ same type
TRAPPC2 c.*29C>T Likely benign ★★ same type
TRAPPC2 c.*830G>C Benign ★★ same type
TRAPPC2 p.Phe109= Likely benign ★★ 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-arg122ter (accessed [today's date]).

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