Is TRAPPC4 p.Phe4Val (c.10T>G) pathogenic?

TRAPPC4 p.Phe4Val (c.10T>G) is classified Uncertain significance in TRAPPC4 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-12-16). AlphaMissense: likely pathogenic (0.8263); Absent from gnomAD v4.1.

How common is TRAPPC4 p.Phe4Val (c.10T>G) in the general population?

TRAPPC4 p.Phe4Val (c.10T>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about TRAPPC4 p.Phe4Val (c.10T>G)?

AlphaMissense predicts likely pathogenic (score 0.8263) — an in-silico prediction, not a clinical call.

TRAPPC4 p.Phe4Val

c.10T>G · rs2496970295 · VCV2267619

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.8263 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

Computational evidence

Protein change
AlphaMissense	0.8263	likely pathogenic
REVEL	0.568	indeterminate
SaProt	LLR -9.76	tolerated
⇒ AlphaMissense calls this damaging; SaProt does not; REVEL is indeterminate.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.9	GERP 1.6, phastCons 1
Regional constraint	o/e 1.02	unconstrained · MANE · 3,028 bp · p 0.78 · regional, not allelic
Overall
CADD	27.5	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: TRAPPC4
Protein: p.Phe4Val
Coding: c.10T>G
MANE Select: NM_016146
dbSNP: rs2496970295
Type: single nucleotide variant
Location: chr11:119018805 (GRCh38)
Gene constraint: LOEUF 1.689 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 91.02 · 3 PDB
Residue 4: a β-strand

Full TRAPPC4 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

TRAPPC4 c.454+3A>G Pathogenic/Likely pathogenic ★★ same type
TRAPPC4 c.176-31C>G Benign ★★ same type
TRAPPC4 c.176-40C>G Benign ★★ same type
TRAPPC4 c.176-43C>T Benign ★★ same type
TRAPPC4 c.350+129T>C Benign ★★ same type
TRAPPC4 c.350+58C>T Benign ★★ same type
TRAPPC4 c.351-58C>A Benign ★★ same type
TRAPPC4 c.454+225G>T Benign ★★ same type

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/trappc4-p-phe4val (accessed [today's date]).

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