Is TRAPPC9 p.Pro1096= (c.3288G>A) pathogenic?

TRAPPC9 p.Pro1096= (c.3288G>A) is classified Likely benign in TRAPPC9 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-11-25). Ultra-rare (popmax 0.0213%, afr); Associated with Inborn genetic diseases.

What condition is associated with TRAPPC9 p.Pro1096= (c.3288G>A)?

TRAPPC9 p.Pro1096= (c.3288G>A) is associated with Inborn genetic diseases (ClinVar).

How common is TRAPPC9 p.Pro1096= (c.3288G>A) in the general population?

TRAPPC9 p.Pro1096= (c.3288G>A) is ultra-rare (popmax 0.0213%, afr) (gnomAD).

TRAPPC9 p.Pro1096=

c.3288G>A · rs570688248 · VCV362063

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0213%, afr)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.04	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -20	GERP -2.5
Overall
CADD	0.04	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0213% African / African-American · 16/75,038 alleles

Filtering AF 0.0133% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0109%

Overall 0.00465% 75/1,613,408 alleles · ultra-rare exomes 65/1,461,098 · genomes 10/152,310 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0213%	4,690
Middle Eastern	0.0165%	6,048
Remaining individualsnot grpmax-eligible	0.0096%	10,413
East Asian	0.00669%	14,955
European (non-Finnish)	0.00373%	26,815
Admixed American	0.00333%	30,007
South Asian	0.00329%	30,355

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: TRAPPC9
Protein: p.Pro1096=
Coding: c.3288G>A
MANE Select: NM_001160372
dbSNP: rs570688248
Type: single nucleotide variant
Location: chr8:139731220 (GRCh38)
Gene constraint: LOEUF 0.786 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 82.98

Full TRAPPC9 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

TRAPPC9 p.Pro1096Leu Uncertain significance ★ ⚠ same residue
TRAPPC9 p.Arg472Ter Pathogenic/Likely pathogenic ★★ same condition
TRAPPC9 p.Glu123Ter Pathogenic ★★ same condition
TRAPPC9 p.Glu97Ter Pathogenic ★★ same condition
TRAPPC9 c.-212G>C Uncertain significance ★★ same condition
TRAPPC9 c.-4C>A Uncertain significance ★★ same condition
TRAPPC9 c.-69C>T Uncertain significance ★★ same condition
TRAPPC9 c.-74C>A 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/trappc9-p-pro1096 (accessed [today's date]).

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