TYMP p.Ser188=
c.564T>C · rs772137910 · VCV741626
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00669%, eas)
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 0.68 | GERP -2.6, phastCons 0.029 |
| Overall | ||
| CADD | 8.779 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00669%
East Asian · 3/44,822 alleles
Filtering AF
0.00178%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000892%
Overall
0.000248%
4/1,612,424 alleles · very rare
exomes 4/1,461,674 · genomes 0/150,750 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00669% | 14,941 |
| European (non-Finnish) | 8.48e-05% | 1,179,856 |
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
- TYMP
- Protein
- p.Ser188=
- Coding
- c.564T>C
- MANE Select
- NM_001953
- dbSNP
- rs772137910
- Type
- single nucleotide variant
- Location
- chr22:50527670 (GRCh38)
- Gene constraint
- LOEUF 1.518 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 92.82 · 4 PDB
Similar variants
- TYMP p.Ser188Thr Uncertain significance ★ ⚠ same residue
- TYMP c.1301-1G>A Likely pathogenic ★★ same type
- TYMP c.214+1G>T Likely pathogenic ★★ same type
- TYMP c.417+1G>A Pathogenic ★★ same type
- TYMP c.418-1G>A Likely pathogenic ★★ same type
- TYMP c.646+1G>A Pathogenic/Likely pathogenic ★★ same type
- TYMP c.647-1G>A Pathogenic/Likely pathogenic ★★ same type
- TYMP p.Ala216Val Likely pathogenic ★★ 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/tymp-p-ser188 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown