CTU2 p.Ser84=
c.252G>T · rs549719454 · VCV1949261
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0217%, amr)
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 -8.6 | GERP -3.9 |
| Overall | ||
| CADD | 0.352 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0217%
Admixed American · 13/60,026 alleles
Filtering AF
0.0127%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0101%
Overall
0.00103%
15/1,461,740 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0217% | 4,617 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,502 |
| European (non-Finnish) | 8.47e-05% | 1,179,999 |
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.Ser84=
- Coding
- c.252G>T
- MANE Select
- NM_001012759
- dbSNP
- rs549719454
- Type
- single nucleotide variant
- Location
- chr16:88710252 (GRCh38)
- Gene constraint
- LOEUF 1.535 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 80.27
Similar variants
- CTU2 p.Ser84Leu 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-ser84 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown