CTR9 c.1194+15del
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.186%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +15 | near-intronic (+15 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP -0.25 | GERP -2.3, phastCons 0.011 |
| Overall | ||
| CADD | 3.264 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.186%
Middle Eastern · 11/5,910 alleles
Filtering AF
0.104%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0807%
Overall
0.00474%
75/1,582,608 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.186% | 537 |
| African / African-American | 0.0232% | 4,316 |
| Remaining individualsnot grpmax-eligible | 0.0163% | 6,119 |
| South Asian | 0.00461% | 21,696 |
| European (non-Finnish) | 0.00275% | 36,381 |
| Admixed American | 0.00184% | 54,388 |
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.1194+15del
- MANE Select
- NM_014633
- dbSNP
- rs759756278
- Type
- Deletion
- Location
- chr11:10763887 (GRCh38)
- Gene constraint
- LOEUF 0.368 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 76.62 · 21 PDB
Similar variants
- CTR9 p.Ala198fs Uncertain significance ★ same type
- CTR9 p.Asp771fs Uncertain significance ★ same type
- CTR9 p.Ile6fs Uncertain significance ★ same type
- CTR9 p.Leu733del Uncertain significance ★ same type
- CTR9 p.Lys958_Lys959del Uncertain significance ★ same type
- CTR9 c.1687-137del Likely benign ★ same type
- CTR9 c.2373-23_2373-19del Likely benign ★ same type
- CTR9 c.2581-11_2581-3del Likely benign ★ 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/ctr9-c-1194-plus-15del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown