Is TRAPPC9 p.Ser925= (c.2775C>T) pathogenic?

TRAPPC9 p.Ser925= (c.2775C>T) is classified Likely benign in TRAPPC9 (ClinVar, Multiple submitters, 5 submitters; last evaluated 2025-07-16). Ultra-rare (popmax 0.0831%, eas); Associated with Inborn genetic diseases.

What condition is associated with TRAPPC9 p.Ser925= (c.2775C>T)?

TRAPPC9 p.Ser925= (c.2775C>T) is associated with Inborn genetic diseases (ClinVar).

How common is TRAPPC9 p.Ser925= (c.2775C>T) in the general population?

TRAPPC9 p.Ser925= (c.2775C>T) is ultra-rare (popmax 0.0831%, eas) (gnomAD).

TRAPPC9 p.Ser925=

c.2775C>T · rs547773428 · VCV1668955

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0831%, eas)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP -9.7	GERP -3.2
Overall
CADD	0.374	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0831% East Asian · 34/40,894 alleles

Filtering AF 0.0612% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0536%

Overall 0.00451% 70/1,551,234 alleles · ultra-rare exomes 57/1,398,952 · genomes 13/152,282 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0831%	1,203
Middle Eastern	0.017%	5,872
African / African-American	0.0082%	12,193
Remaining individualsnot grpmax-eligible	0.00666%	15,026
Admixed American	0.00392%	25,504
Finnishnot grpmax-eligible	0.00335%	29,814
European (non-Finnish)	0.00174%	57,348
South Asian	0.00119%	84,042

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.Ser925=
Coding: c.2775C>T
MANE Select: NM_001160372
dbSNP: rs547773428
Type: single nucleotide variant
Location: chr8:139988761 (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-ser925 (accessed [today's date]).

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