Is TRAPPC2 p.Met53fs (c.157_158del) pathogenic?

TRAPPC2 p.Met53fs (c.157158del) is classified Pathogenic in TRAPPC2 (ClinVar, No assertion criteria, 1 submitter; last evaluated 1999-08-01). No gnomAD frequency available for this variant; Associated with spondyloepiphyseal dysplasia tarda.

What condition is associated with TRAPPC2 p.Met53fs (c.157_158del)?

TRAPPC2 p.Met53fs (c.157_158del) is associated with spondyloepiphyseal dysplasia tarda (ClinVar).

How common is TRAPPC2 p.Met53fs (c.157_158del) in the general population?

TRAPPC2 p.Met53fs (c.157_158del) 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.Met53fs

c.157_158del · rs587776750 · VCV11509

Pathogenic No assertion criteria

Classification

Pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

spondyloepiphyseal dysplasia tarda

⚠ 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 5.9	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.Met53fs
Coding: c.157_158del
MANE Select: NM_001011658
dbSNP: rs587776750
Type: Deletion
Location: chrX:13716614 (GRCh38)

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

Disease context

spondyloepiphyseal dysplasia tarda — 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-met53fs (accessed [today's date]).

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