TYMP p.Thr9=
c.27C>T · rs1412958358 · VCV1553503
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0168%, mid)
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 0.48 | GERP -2.8, phastCons 0.11 |
| Overall | ||
| CADD | 3.436 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0168%
Middle Eastern · 1/5,952 alleles
Overall
0.000186%
3/1,611,292 alleles · ultra-rare
exomes 3/1,459,016 · genomes 0/152,276 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0168% | 5,952 |
| South Asian | 0.0011% | 90,806 |
| European (non-Finnish) | 8.48e-05% | 1,179,391 |
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.Thr9=
- Coding
- c.27C>T
- MANE Select
- NM_001953
- dbSNP
- rs1412958358
- Type
- single nucleotide variant
- Location
- chr22:50529683 (GRCh38)
- Gene constraint
- LOEUF 1.518 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 92.82 · 4 PDB
- Residue 9
- the 'disordered' region
Similar variants
- TYMP p.Thr9Ser Uncertain significance ★ ⚠ same residue
- TYMP p.Thr9fs Likely pathogenic ★ 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
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-thr9 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown