DGKQ p.Asp545=
c.1635C>T · VCV3770427
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 3.24%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.017 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -3.9 | GERP -2.6 |
| Overall | ||
| CADD | 0.395 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.24%
Middle Eastern · 196/6,058 alleles
Filtering AF
2.86%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.72%
Overall
0.7%
11,282/1,612,554 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 3.24% | 31 |
| Finnishnot grpmax-eligible | 1.8% | 55 |
| Ashkenazi Jewishnot grpmax-eligible | 1.62% | 62 |
| Remaining individualsnot grpmax-eligible | 0.872% | 115 |
| European (non-Finnish) | 0.698% | 143 |
| Admixed American | 0.617% | 162 |
| South Asian | 0.251% | 398 |
| African / African-American | 0.131% | 766 |
| East Asian | 0.00892% | 11,214 |
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.Asp545=
- Coding
- c.1635C>T
- MANE Select
- NM_001347
- Type
- single nucleotide variant
- Location
- chr4:965275 (GRCh38)
- Gene constraint
- LOEUF 1.294 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.56
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.Pro55= 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
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-asp545 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown