Is TRAPPC9 p.Ser924= (c.2772C>T) pathogenic?

TRAPPC9 p.Ser924= (c.2772C>T) is classified Likely benign in TRAPPC9 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2026-01-27). Rare (popmax 0.167%, afr); Associated with Inborn genetic diseases.

What condition is associated with TRAPPC9 p.Ser924= (c.2772C>T)?

TRAPPC9 p.Ser924= (c.2772C>T) is associated with Inborn genetic diseases (ClinVar).

How common is TRAPPC9 p.Ser924= (c.2772C>T) in the general population?

TRAPPC9 p.Ser924= (c.2772C>T) is rare (popmax 0.167%, afr) (gnomAD).

TRAPPC9 p.Ser924=

c.2772C>T · rs143221169 · VCV588560

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

rare (popmax 0.167%, afr)

Conditions

Inborn genetic diseases

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 3.3	GERP 0.64, phastCons 0.48
Overall
CADD	5.618	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.167% African / African-American · 122/73,174 alleles

Filtering AF 0.143% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.134%

Overall 0.0144% 223/1,551,340 alleles · rare exomes 127/1,399,014 · genomes 96/152,326 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.167%	600
Admixed American	0.0568%	1,759
Middle Eastern	0.0508%	1,968
Remaining individualsnot grpmax-eligible	0.0349%	2,862
European (non-Finnish)	0.00418%	23,895

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.Ser924=
Coding: c.2772C>T
MANE Select: NM_001160372
dbSNP: rs143221169
Type: single nucleotide variant
Location: chr8:139988764 (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.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
TRAPPC9 p.Ala1093Val 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-ser924 (accessed [today's date]).

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