TPRKB p.Ser41=
c.123A>C · rs772184234 · VCV2889385
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0185%, amr)
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 -0.11 | GERP -3, phastCons 0.38 |
| Overall | ||
| CADD | 4.977 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0185%
Admixed American · 11/59,606 alleles
Filtering AF
0.0103%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.008%
Overall
0.000806%
13/1,612,804 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0185% | 5,419 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,424 |
| European (non-Finnish) | 8.48e-05% | 1,179,686 |
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
- TPRKB
- Protein
- p.Ser41=
- Coding
- c.123A>C
- MANE Select
- NM_033550 · reported on NM_016058
- dbSNP
- rs772184234
- Type
- single nucleotide variant
- Location
- chr2:73734447 (GRCh38)
- Structure
- AlphaFold pLDDT 91.58 · 6 PDB
- Residue 41
- the protein kinase domain; a β-strand; a binding site
Similar variants
- 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
- TPRKB p.Glu12Lys 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/tprkb-p-ser41 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown