CTU2 p.Leu167=
c.501G>A · rs138003612 · VCV786948
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.66%, 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 -10 | GERP -4.3 |
| Overall | ||
| CADD | 0.009 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.66%
African / African-American · 1,997/74,956 alleles
Filtering AF
2.57%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.53%
Overall
0.14%
2,261/1,610,648 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.66% | 38 |
| Admixed American | 0.212% | 472 |
| Remaining individualsnot grpmax-eligible | 0.196% | 511 |
| Middle Eastern | 0.021% | 4,762 |
| South Asian | 0.0044% | 22,744 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,550 |
| European (non-Finnish) | 0.000763% | 131,062 |
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.Leu167=
- Coding
- c.501G>A
- MANE Select
- NM_001012759
- dbSNP
- rs138003612
- Type
- single nucleotide variant
- Location
- chr16:88712669 (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-leu167 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown