DMKN p.Ser252=
c.756G>A · VCV4084017
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.494%, sas)
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 -4.8 | GERP -1.6 |
| Overall | ||
| CADD | 6.542 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.494%
South Asian · 441/89,312 alleles
Filtering AF
0.456%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.441%
Overall
0.0322%
515/1,601,368 alleles · rare
exomes 473/1,453,120 · genomes 42/148,248 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.494% | 203 |
| Remaining individualsnot grpmax-eligible | 0.0274% | 3,646 |
| Middle Eastern | 0.0209% | 4,794 |
| European (non-Finnish) | 0.00476% | 21,011 |
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
- DMKN
- Protein
- p.Ser252=
- Coding
- c.756G>A
- MANE Select
- NM_033317
- Type
- single nucleotide variant
- Location
- chr19:35511573 (GRCh38)
- Gene constraint
- LOEUF 1.044 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 42.31 · 1 PDB
- Residue 252
- the 'disordered' region
Similar variants
- DMKN p.Gly100Arg Uncertain significance ★ ⚠ same type
- DMKN p.Gly27Arg Uncertain significance ★ ⚠ same type
- DMKN p.Ser281Gly Uncertain significance ★ ⚠ same type
- DMKN p.Ala417Thr Likely benign ★ same type
- DMKN p.Gly284Ser Likely benign ★ same type
- DMKN p.His111Arg Likely benign ★ 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/dmkn-p-ser252 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown