Is TRAPPC2 p.Thr63= (c.189T>C) pathogenic?

TRAPPC2 p.Thr63= (c.189T>C) is classified Likely benign in TRAPPC2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-06-08). Very rare (popmax 0.00176%, sas).

How common is TRAPPC2 p.Thr63= (c.189T>C) in the general population?

TRAPPC2 p.Thr63= (c.189T>C) is very rare (popmax 0.00176%, sas) (gnomAD).

TRAPPC2 p.Thr63=

c.189T>C · VCV4708959

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00176%, sas)

⚠ 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 -4.7	GERP -4.8
Overall
CADD	1.822	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00176% South Asian · 1/56,957 alleles

Filtering AF 0.000105% ClinGen BA1/BS1 input FAF95, joint · FAF99 7.1e-05%

Overall 0.000413% 5/1,211,748 alleles · very rare exomes 5/1,097,840 · genomes 0/113,908 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00176%	56,957
European (non-Finnish)	0.000447%	223,841

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.Thr63=
Coding: c.189T>C
MANE Select: NM_001011658
Type: single nucleotide variant
Location: chrX:13716583 (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-thr63 (accessed [today's date]).

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