Is TP53RK p.Pro193= (c.579A>G) pathogenic?

TP53RK p.Pro193= (c.579A>G) is classified Likely benign in TP53RK (ClinVar, Single submitter, 1 submitter; last evaluated 2022-09-26). Absent from gnomAD v4.1.

How common is TP53RK p.Pro193= (c.579A>G) in the general population?

TP53RK p.Pro193= (c.579A>G) is absent from gnomAD v4.1 (gnomAD).

TP53RK p.Pro193=

c.579A>G · rs748844904 · VCV2019940

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

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 -15	GERP -5.2
Overall
CADD	0.188	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: TP53RK
Protein: p.Pro193=
Coding: c.579A>G
MANE Select: NM_033550
dbSNP: rs748844904
Type: single nucleotide variant
Location: chr20:46686936 (GRCh38)
Gene constraint: LOEUF 1.776 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 91.58 · 6 PDB
Residue 193: the protein kinase domain; an α-helix

Full TP53RK gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

TP53RK p.Pro193fs Conflicting classifications of pathogenicity ★ 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-pro193 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown