Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 5.08%, afr) — 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 -13 | GERP -4.5 |
| Overall | ||
| CADD | 0.214 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
5.08%
African / African-American · 3,811/75,052 alleles
Filtering AF
4.94%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.89%
Overall
0.338%
5,458/1,612,716 alleles · common
exomes 3,170/1,460,374 · genomes 2,288/152,342 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 5.08% | 20 |
| Ashkenazi Jewishnot grpmax-eligible | 1.79% | 56 |
| Remaining individualsnot grpmax-eligible | 0.619% | 161 |
| Admixed American | 0.52% | 192 |
| Middle Eastern | 0.479% | 209 |
| European (non-Finnish) | 0.0309% | 3,241 |
| South Asian | 0.0209% | 4,794 |
| East Asian | 0.0156% | 6,412 |
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.Ser323=
- Coding
- c.969C>T
- MANE Select
- NM_001012759
- dbSNP
- rs2340974
- Type
- single nucleotide variant
- Location
- chr16:88713742 (GRCh38)
- Gene constraint
- LOEUF 1.535 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 80.27
Similar variants
- CTU2 p.Ser323Cys 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-ser323 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown