TP53RK p.Pro173=
c.519C>G · rs141087837 · VCV783076
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 6 submitters
gnomAD v4.1
Rare
rare (popmax 0.115%, mid)
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 -4 | GERP -5.2 |
| Overall | ||
| CADD | 0.315 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.115%
Middle Eastern · 7/6,062 alleles
Filtering AF
0.0542%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0384%
Overall
0.0298%
481/1,614,166 alleles · rare
exomes 442/1,461,890 · genomes 39/152,276 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.115% | 866 |
| Remaining individualsnot grpmax-eligible | 0.056% | 1,786 |
| European (non-Finnish) | 0.0342% | 2,921 |
| African / African-American | 0.0213% | 4,690 |
| Admixed American | 0.0183% | 5,457 |
| South Asian | 0.00659% | 15,179 |
| Finnishnot grpmax-eligible | 0.00312% | 32,021 |
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.Pro173=
- Coding
- c.519C>G
- MANE Select
- NM_033550
- dbSNP
- rs141087837
- Type
- single nucleotide variant
- Location
- chr20:46686996 (GRCh38)
- Gene constraint
- LOEUF 1.776 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 91.58 · 6 PDB
- Residue 173
- the protein kinase domain; a β-strand
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.Arg86= 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-pro173 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown