TP53RK p.Arg90=
c.270C>T · rs753676121 · VCV2074378
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.024%, 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 3.5 | GERP 0.5, phastCons 1 |
| Overall | ||
| CADD | 12.69 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.024%
Admixed American · 8/33,394 alleles
Filtering AF
0.0119%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00869%
Overall
0.000709%
10/1,409,526 alleles · ultra-rare
exomes 9/1,257,322 · genomes 1/152,204 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.024% | 4,174 |
| Remaining individualsnot grpmax-eligible | 0.00185% | 54,134 |
| European (non-Finnish) | 9.19e-05% | 1,087,550 |
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
- TP53RK
- Protein
- p.Arg90=
- Coding
- c.270C>T
- MANE Select
- NM_033550
- dbSNP
- rs753676121
- Type
- single nucleotide variant
- Location
- chr20:46689145 (GRCh38)
- Gene constraint
- LOEUF 1.776 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 91.58 · 6 PDB
- Residue 90
- the protein kinase domain; an α-helix
Similar variants
- TP53RK p.Arg90Cys Uncertain significance ★ ⚠ same residue
- TP53RK p.Arg243His Uncertain significance ★★ ⚠ same type
- TP53RK p.Leu200Val Uncertain significance ★★ ⚠ same type
- TP53RK p.Lys230Thr Uncertain significance ★★ ⚠ same type
- TP53RK p.Val120Met Uncertain significance ★★ ⚠ same type
- TPRKB p.Ala92Thr Uncertain significance ★★ same type
- TPRKB p.Arg14Thr Uncertain significance ★★ ⚠ same type
- TPRKB p.Asn88Ser 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/tp53rk-p-arg90 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown