Is TRAPPC2 p.Phe75fs (c.225del) pathogenic?

TRAPPC2 p.Phe75fs (c.225del) is classified Pathogenic in TRAPPC2 (ClinVar, Single submitter, 1 submitter). No gnomAD frequency available for this variant; Associated with spondyloepiphyseal dysplasia tarda, X-linked.

What condition is associated with TRAPPC2 p.Phe75fs (c.225del)?

TRAPPC2 p.Phe75fs (c.225del) is associated with spondyloepiphyseal dysplasia tarda, X-linked (ClinVar).

How common is TRAPPC2 p.Phe75fs (c.225del) in the general population?

TRAPPC2 p.Phe75fs (c.225del) is no gnomAD frequency available for this variant (gnomAD).

How is Spondyloepiphyseal dysplasia tarda inherited?

Typically Autosomal dominant, Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

TRAPPC2 p.Phe75fs

c.225del · rs2518618741 · VCV2577913

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

spondyloepiphyseal dysplasia tarda, X-linked

⚠ 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.
Consequence	frameshift	predicted loss-of-function; NMD-escape possible for C-terminal truncations
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 4	GERP 2.4, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: TRAPPC2
Protein: p.Phe75fs
Coding: c.225del
MANE Select: NM_001011658
dbSNP: rs2518618741
Type: Deletion
Location: chrX:13716547 (GRCh38)

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

Disease context

spondyloepiphyseal dysplasia tarda, X-linked — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Spondyloepiphyseal dysplasia tarda (Orphanet):

Inheritance: Autosomal dominant, Autosomal recessive, X-linked recessive
Onset: Adolescent, Adult, Childhood
Prevalence: 1-9 / 1 000 000 (Worldwide)

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-phe75fs (accessed [today's date]).

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