DMPK p.Lys89=
c.267G>A · rs113426968 · VCV3047270
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.207%, afr)
Conditions
1
DMPK-related disorder
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 1.7 | GERP -1.4, phastCons 1 |
| Overall | ||
| CADD | 13.11 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.207%
African / African-American · 155/74,910 alleles
Filtering AF
0.18%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.17%
Overall
0.0115%
185/1,613,842 alleles · rare
exomes 86/1,461,662 · genomes 99/152,180 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.207% | 483 |
| Admixed American | 0.0267% | 3,750 |
| Remaining individualsnot grpmax-eligible | 0.0192% | 5,206 |
| Middle Eastern | 0.0164% | 6,080 |
| European (non-Finnish) | 8.47e-05% | 1,180,036 |
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
- DMPK
- Protein
- p.Lys89=
- Coding
- c.267G>A
- MANE Select
- NM_004409
- dbSNP
- rs113426968
- Type
- single nucleotide variant
- Location
- chr19:45779508 (GRCh38)
- Gene constraint
- LOEUF 0.67 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.91 · 2 PDB
- Residue 89
- a β-strand; the protein kinase domain
Disease context
DMPK-related disorder
Similar variants
- DMPK c.161-5C>G Likely benign same condition
- DMPK p.Ala425= Likely benign same condition
- DMPK p.Ala435= Likely benign same condition
- DMPK p.Asp69Asn Benign same condition
- DMPK p.Gly326= Likely benign same condition
- DMPK p.His296= Likely benign same condition
- DMPK p.Pro337Arg Likely benign ⚠ same condition
- DMPK p.Thr225= Likely benign same condition
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/dmpk-p-lys89 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown