CTU1 p.Arg17=
c.51C>A · rs1193474464 · VCV2650366
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0509%, mid)
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 0.47 | GERP -0.26, phastCons 1 |
| Overall | ||
| CADD | 5.2 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0509%
Middle Eastern · 2/3,932 alleles
Filtering AF
0.00902%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0037%
Overall
0.0022%
28/1,272,758 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0509% | 1,966 |
| Remaining individualsnot grpmax-eligible | 0.00847% | 11,808 |
| Finnishnot grpmax-eligible | 0.00292% | 34,202 |
| European (non-Finnish) | 0.00208% | 48,167 |
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
- CTU1
- Protein
- p.Arg17=
- Coding
- c.51C>A
- MANE Select
- NM_145232
- dbSNP
- rs1193474464
- Type
- single nucleotide variant
- Location
- chr19:51104519 (GRCh38)
- Gene constraint
- LOEUF 1.978 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.51
Similar variants
- CTU1 p.Arg17Pro Uncertain significance ★ ⚠ same residue
- CTU1 p.Ala131Gly Uncertain significance ★ ⚠ same type
- CTU1 p.Ala131Ser Uncertain significance ★ ⚠ same type
- CTU1 p.Ala131Val Uncertain significance ★ ⚠ same type
- CTU1 p.Ala154Gly Uncertain significance ★ ⚠ same type
- CTU1 p.Ala154Pro Uncertain significance ★ ⚠ same type
- CTU1 p.Ala206Thr Uncertain significance ★ ⚠ same type
- CTU1 p.Ala240Thr 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/ctu1-p-arg17 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown