TP53RK p.Arg62=
c.186C>T · VCV3587306
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0173%, eas)
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 5.4 | GERP 0.56, phastCons 1 |
| Overall | ||
| CADD | 14.62 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0173%
East Asian · 7/40,546 alleles
Filtering AF
0.00805%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00569%
Overall
0.000523%
8/1,529,728 alleles · ultra-rare
exomes 7/1,377,484 · genomes 1/152,244 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0173% | 5,792 |
| European (non-Finnish) | 8.73e-05% | 1,145,094 |
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.Arg62=
- Coding
- c.186C>T
- MANE Select
- NM_033550
- Type
- single nucleotide variant
- Location
- chr20:46689229 (GRCh38)
- Gene constraint
- LOEUF 1.776 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 91.58 · 6 PDB
- Residue 62
- the protein kinase domain; a β-strand
Similar variants
- TP53RK p.Arg62His Uncertain significance ★ ⚠ same residue
- 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.Arg86= Likely benign ★★ same condition
- TP53RK p.Pro173= Likely benign ★★ same condition
- TP53RK p.Thr145Ala Benign/Likely benign ★★ 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-arg62 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown