CTR9 c.593-8T>A
Uncertain significance
Multiple submitters
Classification
Uncertain significance
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00669%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| Splice region | acceptor -8 | acceptor splice region (-8, within the last 20 intronic nt) · inside the BP7-excluded zone |
|---|---|---|
| SpliceAI | Δ0.25 | acceptor loss, 8 bp away · masked 0 · deltas |
| Pangolin | Δ0.25 | loss · gain 0.05 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 0.97 | GERP 0.66, phastCons 1 |
| Non-coding constraint | Z 2.90 | 1 kb window · o/e 0.79 · regional · uncalibrated |
| Overall | ||
| CADD | 13.55 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00669%
Admixed American · 4/59,828 alleles
Filtering AF
0.00299%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00267%
Overall
0.00316%
51/1,612,398 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00669% | 14,957 |
| European (non-Finnish) | 0.0039% | 25,630 |
| African / African-American | 0.00134% | 74,858 |
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.593-8T>A
- MANE Select
- NM_014633
- dbSNP
- rs779845463
- Type
- single nucleotide variant
- Location
- chr11:10760165 (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 type
- CTR9 p.Ile17Thr Pathogenic/Likely pathogenic ★★ same type
- CTR9 p.Pro25Arg Pathogenic/Likely pathogenic ★★ same type
- CTR9 c.1960+3G>A Uncertain significance ★★ same type
- CTR9 c.2109+4A>G Uncertain significance ★★ same type
- CTR9 c.2445-3T>C Uncertain significance ★★ same type
- CTR9 c.45+5G>T Uncertain significance ★★ same type
- CTR9 p.Ala198= Uncertain significance ★★ 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-593-minus-8t-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown