Is TRAPPC2 p.Asp32= (c.96C>T) pathogenic?

TRAPPC2 p.Asp32= (c.96C>T) is classified Benign in TRAPPC2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-10-01). Ultra-rare (popmax 0.0109%, amr).

How common is TRAPPC2 p.Asp32= (c.96C>T) in the general population?

TRAPPC2 p.Asp32= (c.96C>T) is ultra-rare (popmax 0.0109%, amr) (gnomAD).

TRAPPC2 p.Asp32=

c.96C>T · VCV4747909

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0109%, amr)

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -5.6	GERP -4.9
Overall
CADD	0.14	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0109% Admixed American · 5/45,742 alleles

Filtering AF 0.00498% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00455%

Overall 0.00554% 67/1,209,585 alleles · ultra-rare exomes 64/1,097,247 · genomes 3/112,338 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0109%	9,148
European (non-Finnish)	0.00637%	15,698
Remaining individualsnot grpmax-eligible	0.00631%	15,851
East Asian	0.00592%	16,890

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.Asp32=
Coding: c.96C>T
MANE Select: NM_001011658
Type: single nucleotide variant
Location: chrX:13716676 (GRCh38)

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

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-asp32 (accessed [today's date]).

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