Is TRAPPC12 p.Pro23= (c.69T>A) pathogenic?

TRAPPC12 p.Pro23= (c.69T>A) is classified Likely benign in TRAPPC12 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-08-16). Absent from gnomAD v4.1; Associated with TRAPPC12-related disorder.

What condition is associated with TRAPPC12 p.Pro23= (c.69T>A)?

TRAPPC12 p.Pro23= (c.69T>A) is associated with TRAPPC12-related disorder (ClinVar).

How common is TRAPPC12 p.Pro23= (c.69T>A) in the general population?

TRAPPC12 p.Pro23= (c.69T>A) is absent from gnomAD v4.1 (gnomAD).

TRAPPC12 p.Pro23=

c.69T>A · rs2528224077 · VCV3053837

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

TRAPPC12-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -2.4	GERP -4.1
Overall
CADD	0.504	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: TRAPPC12
Protein: p.Pro23=
Coding: c.69T>A
MANE Select: NM_016030
dbSNP: rs2528224077
Type: single nucleotide variant
Location: chr2:3387692 (GRCh38)
Gene constraint: LOEUF 1.192 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 68.52
Residue 23: the 'disordered' region

Full TRAPPC12 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

TRAPPC12-related disorder

Similar variants

TRAPPC12 p.Pro23Arg Uncertain significance ★ ⚠ same residue
TRAPPC12 p.Pro23Leu Uncertain significance ★ ⚠ same residue
TRAPPC12 p.Gln284Ter Likely pathogenic ★ same condition
TRAPPC12 c.*3G>C Likely benign same condition
TRAPPC12 c.*5C>T Likely benign same condition
TRAPPC12 p.Ala330= Likely benign same condition
TRAPPC12 p.Ala599= Likely benign same condition
TRAPPC12 p.Leu399= Likely benign 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/trappc12-p-pro23 (accessed [today's date]).

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