TP53RK p.Pro172=
c.516C>T · VCV3587288
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00167%, amr)
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 -0.26 | GERP -5.2, phastCons 0.04 |
| Overall | ||
| CADD | 5.691 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00167%
Admixed American · 1/60,002 alleles
Filtering AF
0.000878%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000717%
Overall
0.00112%
18/1,614,072 alleles · very rare
exomes 17/1,461,888 · genomes 1/152,184 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00167% | 60,002 |
| European (non-Finnish) | 0.00144% | 69,415 |
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.Pro172=
- Coding
- c.516C>T
- MANE Select
- NM_033550
- Type
- single nucleotide variant
- Location
- chr20:46686999 (GRCh38)
- Gene constraint
- LOEUF 1.776 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 91.58 · 6 PDB
- Residue 172
- the protein kinase domain; a β-strand
Similar variants
- TP53RK p.Pro172Thr 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-pro172 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown