DGKD p.Ser560=
c.1680G>A · rs765268127 · VCV746305
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0783%, amr)
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 -8.6 | GERP -3.7 |
| Overall | ||
| CADD | 1.312 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0783%
Admixed American · 47/60,000 alleles
Filtering AF
0.0604%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0542%
Overall
0.0134%
216/1,613,230 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0783% | 1,277 |
| Remaining individualsnot grpmax-eligible | 0.024% | 4,165 |
| European (non-Finnish) | 0.0129% | 7,761 |
| African / African-American | 0.00267% | 37,447 |
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
- DGKD
- Protein
- p.Ser560=
- Coding
- c.1680G>A
- MANE Select
- NM_152879
- dbSNP
- rs765268127
- Type
- single nucleotide variant
- Location
- chr2:233449168 (GRCh38)
- Gene constraint
- LOEUF 0.547 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 72.02 · 2 PDB
- Residue 560
- the 'disordered' region
Similar variants
- DGKD c.2375+10A>G Benign ★★ same type
- DGKD p.Leu406= Benign ★★ same type
- DGKD p.Pro568= Benign/Likely benign ★★ same type
- DGKD p.Thr1052= Benign ★★ same type
- DGKD p.Ala1047Gly Uncertain significance ★ ⚠ same type
- DGKD p.Ala1109Val Uncertain significance ★ ⚠ same type
- DGKD p.Ala1134Val Uncertain significance ★ ⚠ same type
- DGKD p.Ala1140Gly 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/dgkd-p-ser560 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown