CTR9 c.3095+4G>A
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00842%, amr)
Conditions
2
Predisposition to Wilms tumor
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +4 | donor splice region (+4, within the first 6 intronic nt) · inside the BP7-excluded zone |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.14 | GERP -3.8, phastCons 0.042 |
| Non-coding constraint | Z -0.74 | 1 kb window · o/e 1.06 · regional · uncalibrated |
| Overall | ||
| CADD | 9.626 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00842%
Admixed American · 5/59,384 alleles
Filtering AF
0.00326%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00208%
Overall
0.000824%
13/1,577,520 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00842% | 11,877 |
| African / African-American | 0.00542% | 18,453 |
| Remaining individualsnot grpmax-eligible | 0.00491% | 20,386 |
| European (non-Finnish) | 8.7e-05% | 1,149,502 |
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
- Coding
- c.3095+4G>A
- MANE Select
- NM_014633
- dbSNP
- rs1021694407
- Type
- single nucleotide variant
- Location
- chr11:10775637 (GRCh38)
- Gene constraint
- LOEUF 0.368 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 76.62 · 21 PDB
Similar variants
- CTR9 p.Asn455Ser Likely pathogenic ★★ same condition
- CTR9 p.Ile17Thr Pathogenic/Likely pathogenic ★★ same condition
- CTR9 p.Pro25Arg Pathogenic/Likely pathogenic ★★ same condition
- 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
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-c-3095-plus-4g-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown