Is TRAPPC9 p.Phe1083= (c.3249C>T) pathogenic?

TRAPPC9 p.Phe1083= (c.3249C>T) is classified Benign/Likely benign in TRAPPC9 (ClinVar, Multiple submitters, 6 submitters; last evaluated 2026-06-01). Rare (popmax 0.887%, nfe); Associated with Inborn genetic diseases.

What condition is associated with TRAPPC9 p.Phe1083= (c.3249C>T)?

TRAPPC9 p.Phe1083= (c.3249C>T) is associated with Inborn genetic diseases (ClinVar).

How common is TRAPPC9 p.Phe1083= (c.3249C>T) in the general population?

TRAPPC9 p.Phe1083= (c.3249C>T) is rare (popmax 0.887%, nfe) (gnomAD).

TRAPPC9 p.Phe1083=

c.3249C>T · rs112551069 · VCV130632

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 6 submitters

gnomAD v4.1

Rare

rare (popmax 0.887%, nfe)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.42	indeterminate
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · G>C here scores Δ0.36 · evaluated, not missing
Constraint at this position
Conservation	phyloP 0.17	GERP -1.1, phastCons 0.81
Overall
CADD	9.163	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.887% European (non-Finnish) · 10,382/1,171,098 alleles

Filtering AF 0.872% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.866%

Overall 0.781% 12,463/1,596,098 alleles · rare exomes 11,701/1,443,746 · genomes 762/152,352 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.887%	113
Finnishnot grpmax-eligible	0.865%	116
Remaining individualsnot grpmax-eligible	0.79%	127
South Asian	0.608%	165
Ashkenazi Jewishnot grpmax-eligible	0.469%	213
Admixed American	0.44%	227
Middle Eastern	0.248%	403
African / African-American	0.148%	673

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.Phe1083=
Coding: c.3249C>T
MANE Select: NM_001160372
dbSNP: rs112551069
Type: single nucleotide variant
Location: chr8:139732009 (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.Phe1083Leu 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-phe1083 (accessed [today's date]).

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