Is TRAPPC2 p.Ala78= (c.234G>A) pathogenic?

TRAPPC2 p.Ala78= (c.234G>A) is classified Benign in TRAPPC2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-12-11). Ultra-rare (popmax 0.0459%, amr).

How common is TRAPPC2 p.Ala78= (c.234G>A) in the general population?

TRAPPC2 p.Ala78= (c.234G>A) is ultra-rare (popmax 0.0459%, amr) (gnomAD).

TRAPPC2 p.Ala78=

c.234G>A · VCV3705975

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0459%, 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 -7.9	GERP -4.5
Overall
CADD	0.9	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0459% Admixed American · 21/45,777 alleles

Filtering AF 0.0307% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0258%

Overall 0.00256% 31/1,209,936 alleles · ultra-rare exomes 29/1,097,876 · genomes 2/112,060 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0459%	2,180
Middle Eastern	0.0229%	4,374
South Asian	0.00176%	56,813
European (non-Finnish)	0.000894%	111,886

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.Ala78=
Coding: c.234G>A
MANE Select: NM_001011658
Type: single nucleotide variant
Location: chrX:13716538 (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-ala78 (accessed [today's date]).

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