Is TRAPPC2 p.Ser110Ter (c.329C>A) pathogenic?

TRAPPC2 p.Ser110Ter (c.329C>A) is classified Pathogenic in TRAPPC2 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2002-01-01). No allele count reported in gnomAD v4.1 (AN 1,079,159); Associated with spondyloepiphyseal dysplasia tarda.

What condition is associated with TRAPPC2 p.Ser110Ter (c.329C>A)?

TRAPPC2 p.Ser110Ter (c.329C>A) is associated with spondyloepiphyseal dysplasia tarda (ClinVar).

How common is TRAPPC2 p.Ser110Ter (c.329C>A) in the general population?

TRAPPC2 p.Ser110Ter (c.329C>A) is no allele count reported in gnomAD v4.1 (AN 1,079,159) (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.Ser110Ter

c.329C>A · rs104894949 · VCV11515

Pathogenic No assertion criteria

Classification

Pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,079,159)

Conditions

spondyloepiphyseal dysplasia tarda

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	nonsense (stop-gain)	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	escapes	premature termination codon in the last exon (6 of 6) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.5	GERP 1.5, phastCons 1
Overall
CADD	36.0	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,079,159). 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.Ser110Ter
Coding: c.329C>A
MANE Select: NM_001011658
dbSNP: rs104894949
Type: single nucleotide variant
Location: chrX:13714501 (GRCh38)
Structure: AlphaFold pLDDT 92.44

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)

Similar variants

TRAPPC2 c.*1436C>T Uncertain significance ★★ same condition
TRAPPC2 c.*942G>T Uncertain significance ★★ same condition
TRAPPC2 c.*1052T>C Benign ★★ same condition
TRAPPC2 c.*1229C>T Likely benign ★★ same condition
TRAPPC2 c.*1739C>G Benign ★★ same condition
TRAPPC2 c.*830G>C Benign ★★ same condition
TRAPPC2 c.-19-3T>C Uncertain significance ★ same condition
TRAPPC2 c.*1032T>C Uncertain significance ★ same condition

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-ser110ter (accessed [today's date]).

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