Is CHAMP1 p.Glu299fs (c.893dup) pathogenic?

CHAMP1 p.Glu299fs (c.893dup) is classified Likely pathogenic in CHAMP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-08-01). No gnomAD frequency available for this variant.

How common is CHAMP1 p.Glu299fs (c.893dup) in the general population?

CHAMP1 p.Glu299fs (c.893dup) is no gnomAD frequency available for this variant (gnomAD).

CHAMP1 p.Glu299fs

c.893dup · rs2139419654 · VCV1298574

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a LoF-intolerant gene
NMD	escapes	premature termination codon in the last exon (3 of 3) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 3.6	GERP 1.7, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: CHAMP1
Protein: p.Glu299fs
Coding: c.893dup
MANE Select: NM_032436
dbSNP: rs2139419654
Type: Duplication
Location: chr13:114324731 (GRCh38)
Gene constraint: LOEUF 0.16 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
Structure: AlphaFold pLDDT 48.04 · 4 PDB
Residue 299: the 'disordered' region; the 'mediates interaction with mad2l2' region

Full CHAMP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CHAMP1 p.Glu562delinsProTer Likely pathogenic ★ same type
CHAMP1 p.Glu677fs Likely pathogenic ★ same type
CHAMP1 p.Glu688fs Likely pathogenic ★ same type
CHAMP1 p.Lys565fs Pathogenic ★ same type
CHAMP1 p.Lys618fs Pathogenic ★ same type
CHAMP1 p.Pro283fs Likely pathogenic ★ same type
CHAMP1 p.Pro320_Arg321insTer Pathogenic ★ same type
CHAMP1 p.Ser217Ter Pathogenic ★ 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/champ1-p-glu299fs (accessed [today's date]).

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