CTR9 p.Ala198=
c.594G>A · rs754545267 · VCV1430954
Uncertain significance
Multiple submitters
Classification
Uncertain significance
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0368%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.85 | acceptor gain · deltas |
|---|---|---|
| Pangolin | Δ0.59 | gain · loss 0.14 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 0.49 | GERP -1.9, phastCons 1 |
| Overall | ||
| CADD | 22.6 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0368%
Admixed American · 22/59,842 alleles
Filtering AF
0.0249%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0209%
Overall
0.0049%
79/1,612,574 alleles · ultra-rare
exomes 64/1,460,432 · genomes 15/152,142 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0368% | 2,720 |
| Middle Eastern | 0.0165% | 6,078 |
| South Asian | 0.011% | 9,089 |
| European (non-Finnish) | 0.00373% | 26,798 |
| African / African-American | 0.00267% | 37,427 |
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.Ala198=
- Coding
- c.594G>A
- MANE Select
- NM_014633
- dbSNP
- rs754545267
- Type
- single nucleotide variant
- Location
- chr11:10760174 (GRCh38)
- Gene constraint
- LOEUF 0.368 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 76.62 · 21 PDB
- Residue 198
- an α-helix
Similar variants
- CTR9 p.Ala198fs Uncertain significance ★ same residue
- 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
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-ala198 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown