DGKD p.Pro17=
c.51G>A · rs774345130 · VCV743421
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0484%, afr)
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 5.5 | GERP -0.1, phastCons 1 |
| Overall | ||
| CADD | 15.38 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0484%
African / African-American · 28/57,830 alleles
Filtering AF
0.0343%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0296%
Overall
0.00348%
37/1,061,968 alleles · ultra-rare
exomes 21/916,268 · genomes 16/145,700 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0484% | 2,065 |
| Middle Eastern | 0.0438% | 2,284 |
| Remaining individualsnot grpmax-eligible | 0.00614% | 16,274 |
| Admixed American | 0.00446% | 22,442 |
| European (non-Finnish) | 0.000574% | 174,155 |
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.Pro17=
- Coding
- c.51G>A
- MANE Select
- NM_152879
- dbSNP
- rs774345130
- Type
- single nucleotide variant
- Location
- chr2:233354569 (GRCh38)
- Gene constraint
- LOEUF 0.547 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 72.02 · 2 PDB
- Residue 17
- the 'regulates association with membranes' region; the 'disordered' region
Similar variants
- DGKD p.Pro17Ala Uncertain significance ★ ⚠ same residue
- DGKD p.Pro17Thr Uncertain significance ★ ⚠ same residue
- 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
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-pro17 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown