CTR9 p.Ser1041=
c.3123T>C · rs140160202 · VCV2886982
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0187%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -2.2 | GERP -2.2 |
| Overall | ||
| CADD | 6.321 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0187%
African / African-American · 14/74,910 alleles
Filtering AF
0.0112%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00905%
Overall
0.00112%
18/1,612,732 alleles · ultra-rare
exomes 8/1,460,582 · genomes 10/152,150 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0187% | 5,351 |
| Admixed American | 0.005% | 19,985 |
| European (non-Finnish) | 8.48e-05% | 1,179,002 |
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.Ser1041=
- Coding
- c.3123T>C
- MANE Select
- NM_014633
- dbSNP
- rs140160202
- Type
- single nucleotide variant
- Location
- chr11:10778706 (GRCh38)
- Gene constraint
- LOEUF 0.368 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 76.62 · 21 PDB
- Residue 1041
- the 'disordered' region; a modified residue (phosphoserine)
Similar variants
- CTR9 p.Ser1041Thr 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-ser1041 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown