Is CHAMP1 p.Pro292= (c.876G>A) pathogenic?

CHAMP1 p.Pro292= (c.876G>A) is classified Benign in CHAMP1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-03-28). Common (popmax 18.4%, amr) — too common for a highly-penetrant pathogenic allele; Associated with CHAMP1-related disorder.

What condition is associated with CHAMP1 p.Pro292= (c.876G>A)?

CHAMP1 p.Pro292= (c.876G>A) is associated with CHAMP1-related disorder (ClinVar).

CHAMP1 p.Pro292=

Q: How common is CHAMP1 p.Pro292= (c.876G>A) in the general population?

CHAMP1 p.Pro292= (c.876G>A) is common (popmax 18.4%, amr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.876G>A · rs3813133 · VCV3059016

Benign No assertion criteria

Classification

Benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Common

common (popmax 18.4%, amr) — too common for a highly-penetrant pathogenic allele

Conditions

CHAMP1-related disorder

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 -0.7	GERP -2.9
Overall
CADD	8.107	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 18.4% Admixed American · 11,015/59,950 alleles

Filtering AF 18.1% ClinGen BA1/BS1 input FAF95, joint · FAF99 18%

Overall 8.3% 133,917/1,613,386 alleles · common exomes 119,535/1,461,418 · genomes 14,382/151,968 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	18.4%	5
East Asian	14.2%	7
Middle Eastern	13.4%	7
African / African-American	11.7%	9
Ashkenazi Jewishnot grpmax-eligible	11.6%	9
South Asian	9.67%	10
Remaining individualsnot grpmax-eligible	8.8%	11
Finnishnot grpmax-eligible	7.74%	13
European (non-Finnish)	7.14%	14
Amishnot grpmax-eligible	0.548%	182

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: CHAMP1
Protein: p.Pro292=
Coding: c.876G>A
MANE Select: NM_032436
dbSNP: rs3813133
Type: single nucleotide variant
Location: chr13:114324718 (GRCh38)
Gene constraint: LOEUF 0.16 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
Structure: AlphaFold pLDDT 48.04 · 4 PDB
Residue 292: the 'disordered' region; the 'mediates interaction with mad2l2' region

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

Disease context

CHAMP1-related disorder

Similar variants

CHAMP1 p.Arg398Ter Pathogenic ★★ same condition
CHAMP1 p.Arg497Ter Pathogenic ★★ same condition
CHAMP1 p.Glu687Lys Uncertain significance ★★ ⚠ same condition
CHAMP1 p.Asp593Asn Uncertain significance ★ ⚠ same condition
CHAMP1 p.Ile351Val Uncertain significance ★ ⚠ same condition
CHAMP1 p.Pro159Leu Uncertain significance ★ ⚠ same condition
CHAMP1 p.Gln657Ter Pathogenic same condition
CHAMP1 p.Glu553Ter Pathogenic 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/champ1-p-pro292 (accessed [today's date]).

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