Is CHAMP1 p.Pro110Arg (c.329C>G) pathogenic?

CHAMP1 p.Pro110Arg (c.329C>G) is classified Likely benign in CHAMP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-06-11). AlphaMissense: likely benign (0.1001); Ultra-rare (popmax 0.0657%, mid); Associated with Inborn genetic diseases.

What condition is associated with CHAMP1 p.Pro110Arg (c.329C>G)?

CHAMP1 p.Pro110Arg (c.329C>G) is associated with Inborn genetic diseases (ClinVar).

How common is CHAMP1 p.Pro110Arg (c.329C>G) in the general population?

CHAMP1 p.Pro110Arg (c.329C>G) is ultra-rare (popmax 0.0657%, mid) (gnomAD).

What do computational predictors say about CHAMP1 p.Pro110Arg (c.329C>G)?

AlphaMissense predicts likely benign (score 0.1001) — an in-silico prediction, not a clinical call.

CHAMP1 p.Pro110Arg

c.329C>G · VCV3266792

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1001 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0657%, mid)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1001	likely benign
REVEL	0.076	moderately benign-leaning
SaProt	LLR -7.22	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.23	GERP 0.77
Regional constraint	o/e 1.21	unconstrained · MANE · 1,781 bp · p 1.6e-08 · regional, not allelic
Overall
CADD	15.46	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

Grpmax group 0.0657% Middle Eastern · 4/6,084 alleles

Filtering AF 0.0224% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0135%

Overall 0.00223% 36/1,614,036 alleles · ultra-rare exomes 25/1,461,858 · genomes 11/152,178 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0657%	1,521
Admixed American	0.02%	5,000
Remaining individualsnot grpmax-eligible	0.0032%	31,240
South Asian	0.0022%	45,538
European (non-Finnish)	0.00136%	73,752

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.Pro110Arg
Coding: c.329C>G
MANE Select: NM_032436
Type: single nucleotide variant
Location: chr13:114324171 (GRCh38)
Gene constraint: LOEUF 0.16 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
Structure: AlphaFold pLDDT 48.04 · 4 PDB
Residue 110: the 'disordered' region

Full CHAMP1 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

CHAMP1 p.Ala304Val Uncertain significance ★★ ⚠ same condition
CHAMP1 p.Glu195Gly Uncertain significance ★★ ⚠ same condition
CHAMP1 p.Glu668Gln Uncertain significance ★★ ⚠ same condition
CHAMP1 p.Gly238Arg Uncertain significance ★★ ⚠ same condition
CHAMP1 p.Met671Thr Uncertain significance ★★ ⚠ same condition
CHAMP1 p.Pro150Leu Uncertain significance ★★ ⚠ same condition
CHAMP1 p.Pro265Ser Uncertain significance ★★ ⚠ same condition
CHAMP1 p.Pro477Ser 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/champ1-p-pro110arg (accessed [today's date]).

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