CTR9 p.His487=
c.1461C>T · rs3736326 · VCV1166401
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Common
common (popmax 84%, eas) — too common for a highly-penetrant pathogenic allele
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 -0.55 | GERP -4.1, phastCons 0.077 |
| Overall | ||
| CADD | 2.046 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
84%
East Asian · 37,654/44,824 alleles
Filtering AF
83.3%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 83%
Overall
59.9%
965,208/1,611,330 alleles · common
exomes 881,188/1,459,278 · genomes 84,020/152,052 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 84% | 1 |
| South Asian | 75.6% | 1 |
| Admixed American | 72.9% | 1 |
| Middle Eastern | 65% | 2 |
| Ashkenazi Jewishnot grpmax-eligible | 64.2% | 2 |
| Finnishnot grpmax-eligible | 62.8% | 2 |
| Remaining individualsnot grpmax-eligible | 60.6% | 2 |
| European (non-Finnish) | 58.3% | 2 |
| Amishnot grpmax-eligible | 45.5% | 2 |
| African / African-American | 36.4% | 3 |
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.His487=
- Coding
- c.1461C>T
- MANE Select
- NM_014633
- dbSNP
- rs3736326
- Type
- single nucleotide variant
- Location
- chr11:10764595 (GRCh38)
- Gene constraint
- LOEUF 0.368 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 76.62 · 21 PDB
- Residue 487
- a turn
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 c.593-8T>A 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-his487 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown