TP53RK p.Arg86=
c.258G>T · rs956957888 · VCV1952929
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0552%, afr)
Conditions
1
Galloway-Mowat syndrome 4
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 -0.063 | GERP -3, phastCons 0.62 |
| Overall | ||
| CADD | 8.528 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0552%
African / African-American · 37/67,030 alleles
Filtering AF
0.0411%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0363%
Overall
0.00259%
37/1,428,618 alleles · ultra-rare
exomes 13/1,276,290 · genomes 24/152,328 · joint denominator
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.Arg86=
- Coding
- c.258G>T
- MANE Select
- NM_033550
- dbSNP
- rs956957888
- Type
- single nucleotide variant
- Location
- chr20:46689157 (GRCh38)
- Gene constraint
- LOEUF 1.776 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 91.58 · 6 PDB
- Residue 86
- the protein kinase domain; an α-helix
Similar variants
- TP53RK p.Leu200Val Uncertain significance ★★ ⚠ same condition
- TP53RK p.Lys230Thr Uncertain significance ★★ ⚠ same condition
- TP53RK p.Val120Met Uncertain significance ★★ ⚠ same condition
- TP53RK p.Ala56Pro Likely benign ★★ same condition
- TP53RK p.Pro173= Likely benign ★★ same condition
- TP53RK p.Thr145Ala Benign/Likely benign ★★ same condition
- TP53RK p.Lys65Gln Likely pathogenic ★ same condition
- TP53RK p.Tyr225Ter Likely pathogenic ★ same condition
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-arg86 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown