DGKD p.Ser666=
c.1998C>T · rs369697514 · VCV759276
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0517%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -4.3 | GERP -2.1 |
| Overall | ||
| CADD | 9.613 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0517%
Admixed American · 31/59,962 alleles
Filtering AF
0.0374%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0325%
Overall
0.00948%
153/1,613,750 alleles · ultra-rare
exomes 135/1,461,426 · genomes 18/152,324 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0517% | 1,934 |
| Middle Eastern | 0.0165% | 6,062 |
| Remaining individualsnot grpmax-eligible | 0.0096% | 10,414 |
| European (non-Finnish) | 0.00949% | 10,534 |
| African / African-American | 0.00266% | 37,529 |
| East Asian | 0.00223% | 44,852 |
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.Ser666=
- Coding
- c.1998C>T
- MANE Select
- NM_152879
- dbSNP
- rs369697514
- Type
- single nucleotide variant
- Location
- chr2:233450091 (GRCh38)
- Gene constraint
- LOEUF 0.547 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 72.02 · 2 PDB
- Residue 666
- 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-ser666 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown