TYMP p.Ile40=
c.120C>T · rs935752285 · VCV2020836
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00133%, afr)
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 0.7 | GERP -4.1, phastCons 0.12 |
| Overall | ||
| CADD | 9.374 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00133%
African / African-American · 1/74,956 alleles
Overall
6.2e-05%
1/1,613,062 alleles · very rare
exomes 0/1,460,768 · genomes 1/152,294 · joint denominator
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.Ile40=
- Coding
- c.120C>T
- MANE Select
- NM_001953
- dbSNP
- rs935752285
- Type
- single nucleotide variant
- Location
- chr22:50529590 (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 40
- an α-helix
Similar variants
- TYMP p.Ile40Met Uncertain significance ★ ⚠ same residue
- TYMP p.Ile40Val 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
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-ile40 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown