CTU2 p.Val303=
c.909G>A · rs2290904 · VCV1599333
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Common
common (popmax 22.6%, 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 | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 3.3 | GERP -0.27, phastCons 1 |
| Overall | ||
| CADD | 7.733 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
22.6%
African / African-American · 16,927/74,980 alleles
Filtering AF
22.3%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 22.2%
Overall
13.1%
211,766/1,612,444 alleles · common
exomes 188,950/1,460,300 · genomes 22,816/152,144 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 22.6% | 4 |
| Middle Eastern | 21.6% | 5 |
| Ashkenazi Jewishnot grpmax-eligible | 21.1% | 5 |
| South Asian | 16.5% | 6 |
| Amishnot grpmax-eligible | 14.5% | 7 |
| Remaining individualsnot grpmax-eligible | 14.4% | 7 |
| European (non-Finnish) | 12.8% | 8 |
| Admixed American | 9.64% | 10 |
| East Asian | 5.7% | 18 |
| Finnishnot grpmax-eligible | 5.61% | 18 |
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.Val303=
- Coding
- c.909G>A
- MANE Select
- NM_001012759
- dbSNP
- rs2290904
- Type
- single nucleotide variant
- Location
- chr16:88713682 (GRCh38)
- Gene constraint
- LOEUF 1.535 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 80.27
Similar variants
- 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
- CTU2 p.Arg443Cys 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-val303 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown