CTU2 p.Ser158=
c.474G>A · rs759082825 · VCV2055160
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0365%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>T here scores Δ0.34 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -20 | GERP -4.3 |
| Overall | ||
| CADD | 0.005 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0365%
European (non-Finnish) · 431/1,179,472 alleles
Filtering AF
0.0337%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0325%
Overall
0.0282%
454/1,610,286 alleles · ultra-rare
exomes 438/1,457,992 · genomes 16/152,294 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0365% | 2,737 |
| Remaining individualsnot grpmax-eligible | 0.0112% | 8,898 |
| Finnishnot grpmax-eligible | 0.00956% | 10,465 |
| South Asian | 0.0066% | 15,154 |
| African / African-American | 0.00534% | 18,738 |
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.Ser158=
- Coding
- c.474G>A
- MANE Select
- NM_001012759
- dbSNP
- rs759082825
- Type
- single nucleotide variant
- Location
- chr16:88712642 (GRCh38)
- Gene constraint
- LOEUF 1.535 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 80.27
Similar variants
- CTU2 p.Ser158Leu 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-ser158 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown