Is TRAPPC9 p.Phe627= (c.1881C>T) pathogenic?

TRAPPC9 p.Phe627= (c.1881C>T) is classified Likely benign in TRAPPC9 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2026-01-11). Ultra-rare (popmax 0.0217%, amr); Associated with Inborn genetic diseases.

What condition is associated with TRAPPC9 p.Phe627= (c.1881C>T)?

TRAPPC9 p.Phe627= (c.1881C>T) is associated with Inborn genetic diseases (ClinVar).

How common is TRAPPC9 p.Phe627= (c.1881C>T) in the general population?

TRAPPC9 p.Phe627= (c.1881C>T) is ultra-rare (popmax 0.0217%, amr) (gnomAD).

TRAPPC9 p.Phe627=

c.1881C>T · rs774534679 · VCV588579

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0217%, amr)

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 -1.5	GERP -3.3
Overall
CADD	3.408	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0217% Admixed American · 13/59,992 alleles

Filtering AF 0.0127% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0101%

Overall 0.00248% 40/1,614,008 alleles · ultra-rare exomes 35/1,461,878 · genomes 5/152,130 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0217%	4,615
East Asian	0.0134%	7,482
African / African-American	0.012%	8,324
Remaining individualsnot grpmax-eligible	0.0048%	20,827
South Asian	0.0022%	45,540
European (non-Finnish)	0.000593%	168,577

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.Phe627=
Coding: c.1881C>T
MANE Select: NM_001160372
dbSNP: rs774534679
Type: single nucleotide variant
Location: chr8:140287708 (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-phe627 (accessed [today's date]).

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