Is TRAPPC2 p.His87= (c.261T>C) pathogenic?

TRAPPC2 p.His87= (c.261T>C) is classified Likely benign in TRAPPC2 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-07-23). Very rare (popmax 0.00408%, nfe).

How common is TRAPPC2 p.His87= (c.261T>C) in the general population?

TRAPPC2 p.His87= (c.261T>C) is very rare (popmax 0.00408%, nfe) (gnomAD).

TRAPPC2 p.His87=

c.261T>C · VCV3626884

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00408%, nfe)

⚠ 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 2.5	GERP 0.12, phastCons 1
Overall
CADD	10.94	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00408% European (non-Finnish) · 36/882,562 alleles

Filtering AF 0.00299% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00265%

Overall 0.00302% 36/1,190,993 alleles · very rare exomes 32/1,078,024 · genomes 4/112,969 · joint denominator

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.His87=
Coding: c.261T>C
MANE Select: NM_001011658
Type: single nucleotide variant
Location: chrX:13716067 (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-his87 (accessed [today's date]).

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