Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.47%, 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 -7.1 | GERP -4.1 |
| Overall | ||
| CADD | 0.422 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.47%
African / African-American · 2,599/74,906 alleles
Filtering AF
3.36%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.31%
Overall
0.185%
2,973/1,607,116 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.47% | 29 |
| Remaining individualsnot grpmax-eligible | 0.289% | 346 |
| Admixed American | 0.268% | 373 |
| Middle Eastern | 0.132% | 755 |
| South Asian | 0.0121% | 8,236 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00342% | 29,254 |
| European (non-Finnish) | 0.00127% | 78,452 |
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
- CTU2
- Protein
- p.Cys449=
- Coding
- c.1347C>T
- MANE Select
- NM_001012759
- dbSNP
- rs2340976
- Type
- single nucleotide variant
- Location
- chr16:88714732 (GRCh38)
- Gene constraint
- LOEUF 1.535 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 80.27
Similar variants
- CTU2 p.Cys449Gly Uncertain significance ★ ⚠ same residue
- CTU2 c.1420-1G>A Likely pathogenic ★★ same type
- CTU2 c.282+5G>A Pathogenic ★★ same type
- CTU2 p.Gln243Ter Pathogenic/Likely pathogenic ★★ same type
- CTU2 p.Thr291= Pathogenic ★★ same type
- CTU2 p.Ala176Val Uncertain significance ★★ ⚠ same type
- CTU2 p.Ala400Thr Uncertain significance ★★ ⚠ same type
- CTU2 p.Arg270Cys 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/ctu2-p-cys449 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown