Is TRAPPC2 p.Asn68= (c.204C>T) pathogenic?

TRAPPC2 p.Asn68= (c.204C>T) is classified Benign/Likely benign in TRAPPC2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-10-14). Rare (popmax 0.322%, mid).

How common is TRAPPC2 p.Asn68= (c.204C>T) in the general population?

TRAPPC2 p.Asn68= (c.204C>T) is rare (popmax 0.322%, mid) (gnomAD).

TRAPPC2 p.Asn68=

c.204C>T · rs200844691 · VCV2183506

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

rare (popmax 0.322%, mid)

⚠ 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 -3.8	GERP -4.8
Overall
CADD	2.56	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.322% Middle Eastern · 14/4,353 alleles

Filtering AF 0.238% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.224%

Overall 0.0276% 334/1,210,042 alleles · rare exomes 316/1,097,935 · genomes 18/112,107 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.322%	311
South Asian	0.273%	366
Remaining individualsnot grpmax-eligible	0.0357%	2,799
African / African-American	0.0157%	6,368
European (non-Finnish)	0.0153%	6,534
Admixed American	0.00218%	45,791
Finnishnot grpmax-eligible	0.00215%	46,562

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.Asn68=
Coding: c.204C>T
MANE Select: NM_001011658
dbSNP: rs200844691
Type: single nucleotide variant
Location: chrX:13716568 (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-asn68 (accessed [today's date]).

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