DTYMK p.Thr171=
c.513G>A · rs150300178 · VCV2652117
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.39%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.031 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -4.8 | GERP -3.2 |
| Overall | ||
| CADD | 0.545 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.39%
Middle Eastern · 84/6,058 alleles
Filtering AF
1.15%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.06%
Overall
0.131%
2,112/1,614,162 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 1.39% | 72 |
| African / African-American | 0.812% | 123 |
| Admixed American | 0.57% | 176 |
| Remaining individualsnot grpmax-eligible | 0.349% | 287 |
| Ashkenazi Jewishnot grpmax-eligible | 0.098% | 1,021 |
| European (non-Finnish) | 0.0697% | 1,436 |
| South Asian | 0.00549% | 18,216 |
| Finnishnot grpmax-eligible | 0.00312% | 32,015 |
| East Asian | 0.00223% | 44,882 |
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
- DTYMK
- Protein
- p.Thr171=
- Coding
- c.513G>A
- MANE Select
- NM_012145
- dbSNP
- rs150300178
- Type
- single nucleotide variant
- Location
- chr2:241678467 (GRCh38)
- Gene constraint
- LOEUF 1.404 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 95.83 · 21 PDB
- Residue 171
- a β-strand
Similar variants
- DTYMK p.Thr171Ser Uncertain significance ★ ⚠ same residue
- DTYMK p.Pro81Leu Pathogenic/Likely pathogenic ★★ ⚠ same type
- DTYMK p.His35Tyr Benign ★★ ⚠ same type
- DTYMK p.Ala104Val Uncertain significance ★ ⚠ same type
- DTYMK p.Ala145Thr Uncertain significance ★ ⚠ same type
- DTYMK p.Ala198Val Uncertain significance ★ ⚠ same type
- DTYMK p.Ala29Gly Uncertain significance ★ ⚠ same type
- DTYMK p.Ala29Ser 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/dtymk-p-thr171 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown