DMWD p.Ser559=
c.1677T>C · rs61744161 · VCV3056601
Benign
No assertion criteria
Classification
Benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 9.54%, afr) — too common for a highly-penetrant pathogenic allele
Conditions
1
DMWD-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Overall | ||
| CADD | 0.512 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
9.54%
African / African-American · 7,157/74,998 alleles
Filtering AF
9.36%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 9.28%
Overall
0.517%
8,330/1,611,122 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 9.54% | 10 |
| Remaining individualsnot grpmax-eligible | 0.717% | 139 |
| Admixed American | 0.635% | 157 |
| Middle Eastern | 0.165% | 605 |
| European (non-Finnish) | 0.0271% | 3,686 |
| South Asian | 0.0154% | 6,503 |
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
- DMWD
- Protein
- p.Ser559=
- Coding
- c.1677T>C
- MANE Select
- NM_004943
- dbSNP
- rs61744161
- Type
- single nucleotide variant
- Location
- chr19:45785819 (GRCh38)
- Gene constraint
- LOEUF 0.65 · pLI 0.07 (gnomAD)
- Structure
- AlphaFold pLDDT 69.73
- Residue 559
- the 'disordered' region
Disease context
DMWD-related disorder
Similar variants
- DMWD p.Ala109= Benign same condition
- DMWD p.Ala472= Benign same condition
- DMWD p.Ala582Val Benign ⚠ same condition
- DMWD p.Gly120= Benign same condition
- DMWD p.Gly415= Benign same condition
- DMWD p.Pro294= Benign same condition
- DMWD p.Pro417= Benign same condition
- DMWD p.Pro454= 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/dmwd-p-ser559 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown