DLC1 p.Glu590=
c.1770G>A · VCV3674011
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0374%, 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 -0.22 | GERP -0.17, phastCons 0.23 |
| Overall | ||
| CADD | 4.699 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0374%
African / African-American · 28/74,934 alleles
Filtering AF
0.0265%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0229%
Overall
0.0018%
29/1,613,430 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0374% | 2,676 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,462 |
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
- DLC1
- Protein
- p.Glu590=
- Coding
- c.1770G>A
- MANE Select
- NM_003746 · reported on NM_182643
- Type
- single nucleotide variant
- Location
- chr8:13100567 (GRCh38)
- Structure
- AlphaFold pLDDT 95.45 · 22 PDB
Similar variants
- DLC1 c.2991-5C>A Uncertain significance ★★ same type
- DLC1 p.Ala1268Val Uncertain significance ★★ ⚠ same type
- DLC1 p.Ala1278Thr Uncertain significance ★★ ⚠ same type
- DLC1 p.Ala167Pro Uncertain significance ★★ ⚠ same type
- DLC1 p.Ala350Val Uncertain significance ★★ ⚠ same type
- DLC1 p.Ala752Gly Uncertain significance ★★ ⚠ same type
- DLC1 p.Ala821Thr Uncertain significance ★★ ⚠ same type
- DLC1 p.Ala821Val 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/dlc1-p-glu590 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown