CTR9 p.Arg962del
c.2877GAG[1] · VCV4754559
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00161%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 5.5 | GERP 0.73, phastCons 1 |
| Overall | ||
| CADD | 19.38 | PHRED · no single calibrated threshold — expert panels disagree |
| Region caveats | ||
| Repeat context | tandem | GA-rich low complexity · ambiguous alignment · confidence, not pathogenicity |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00161%
European (non-Finnish) · 19/1,177,750 alleles
Filtering AF
0.00103%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000831%
Overall
0.00131%
21/1,609,096 alleles · very rare
exomes 20/1,456,864 · genomes 1/152,232 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00161% | 61,987 |
| Remaining individualsnot grpmax-eligible | 0.00161% | 62,248 |
| South Asian | 0.00111% | 90,318 |
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.Arg962del
- Coding
- c.2877GAG[1]
- MANE Select
- NM_014633
- Type
- Microsatellite
- Location
- chr11:10774161 (GRCh38)
- Gene constraint
- LOEUF 0.368 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 76.62 · 21 PDB
- Residue 962
- the 'disordered' region
Similar variants
- CTR9 p.Glu100_Lys101insTer Uncertain significance ★ same type
- CTR9 p.Glu968del Uncertain significance ★ same type
- CTR9 p.Lys956fs Uncertain significance ★ same type
- CTR9 c.1687-139AAAG[2] Likely benign ★ same type
- CTR9 c.2227-15_2227-12del Likely benign ★ same type
- CTR9 c.3095+104_3095+109del Benign ★ same type
- CTR9 c.592+19_592+23del 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-p-arg962del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown