DGKQ p.Pro55=
c.165C>T · rs10003371 · VCV784034
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.95%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.206 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.059 | GERP -0.69, phastCons 0.001 |
| Overall | ||
| CADD | 7.915 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.95%
African / African-American · 3,354/67,740 alleles
Filtering AF
4.81%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.75%
Overall
0.257%
3,736/1,454,916 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4.95% | 20 |
| Admixed American | 0.367% | 272 |
| Remaining individualsnot grpmax-eligible | 0.282% | 354 |
| Middle Eastern | 0.141% | 710 |
| South Asian | 0.00808% | 12,374 |
| European (non-Finnish) | 0.0061% | 16,401 |
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
- DGKQ
- Protein
- p.Pro55=
- Coding
- c.165C>T
- MANE Select
- NM_001347
- dbSNP
- rs10003371
- Type
- single nucleotide variant
- Location
- chr4:973318 (GRCh38)
- Gene constraint
- LOEUF 1.294 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.56
- Residue 55
- the 'disordered' region
Similar variants
- DGKQ c.1367-16G>C Benign ★★ same type
- DGKQ c.2316-10C>T Benign ★★ same type
- DGKQ p.Asp730= Benign ★★ same type
- DGKQ p.Ala164Thr Uncertain significance ★ ⚠ same type
- DGKQ p.Ala228Val Uncertain significance ★ ⚠ same type
- DGKQ p.Ala229Gly Uncertain significance ★ ⚠ same type
- DGKQ p.Ala247Gly Uncertain significance ★ ⚠ same type
- DGKQ p.Ala247Val 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/dgkq-p-pro55 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown