Is CTR9 p.Ser794Gly (c.2380A>G) pathogenic?

CTR9 p.Ser794Gly (c.2380A>G) is classified Conflicting classifications of pathogenicity in CTR9 (ClinVar, Conflicting submitters, 2 submitters; last evaluated 2026-06-01). AlphaMissense: likely benign (0.1008); Ultra-rare (popmax 0.03%, amr); Associated with Predisposition to Wilms tumor.

What condition is associated with CTR9 p.Ser794Gly (c.2380A>G)?

CTR9 p.Ser794Gly (c.2380A>G) is associated with Predisposition to Wilms tumor (ClinVar).

How common is CTR9 p.Ser794Gly (c.2380A>G) in the general population?

CTR9 p.Ser794Gly (c.2380A>G) is ultra-rare (popmax 0.03%, amr) (gnomAD).

What do computational predictors say about CTR9 p.Ser794Gly (c.2380A>G)?

AlphaMissense predicts likely benign (score 0.1008) — an in-silico prediction, not a clinical call.

CTR9 p.Ser794Gly

c.2380A>G · rs547428593 · VCV2444870

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.1008 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.03%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Predisposition to Wilms tumor

Computational evidence

Protein change
AlphaMissense	0.1008	likely benign
REVEL	0.18	moderately benign-leaning
SaProt	LLR -8.18	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 11	GERP 2, phastCons 1
Regional constraint	o/e 0.67	unconstrained · MANE · 2,375 bp · p 3.7e-05 · regional, not allelic
Overall
CADD	22.5	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

Grpmax group 0.03% Admixed American · 18/59,936 alleles

Filtering AF 0.0194% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.016%

Overall 0.00156% 25/1,603,768 alleles · ultra-rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.03%	3,330
European (non-Finnish)	0.000598%	167,267

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: CTR9
Protein: p.Ser794Gly
Coding: c.2380A>G
MANE Select: NM_014633
dbSNP: rs547428593
Type: single nucleotide variant
Location: chr11:10771552 (GRCh38)
Gene constraint: LOEUF 0.368 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 76.62 · 21 PDB
Residue 794: an α-helix

Full CTR9 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Predisposition to Wilms tumor

Similar variants

CTR9 c.1960+3G>A Uncertain significance ★★ same condition
CTR9 c.45+5G>T Uncertain significance ★★ same condition
CTR9 p.Ala370Thr Uncertain significance ★★ ⚠ same condition
CTR9 p.Ala567Ser Uncertain significance ★★ same condition
CTR9 p.Arg1095Lys Uncertain significance ★★ ⚠ same condition
CTR9 p.Arg1122His Uncertain significance ★★ ⚠ same condition
CTR9 p.Lys282Arg Uncertain significance ★★ ⚠ same condition
CTR9 p.Tyr385Cys 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/ctr9-p-ser794gly (accessed [today's date]).

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