DLC1 p.Ser593=
c.1779C>A · rs143622533 · VCV2716628
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.179%, 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 -13 | GERP -3.8 |
| Overall | ||
| CADD | 0.004 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.179%
African / African-American · 134/75,056 alleles
Filtering AF
0.154%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.145%
Overall
0.00905%
146/1,613,374 alleles · rare
exomes 74/1,461,058 · genomes 72/152,316 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.179% | 560 |
| Remaining individualsnot grpmax-eligible | 0.016% | 6,249 |
| Admixed American | 0.00167% | 59,998 |
| European (non-Finnish) | 8.48e-05% | 1,179,862 |
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.Ser593=
- Coding
- c.1779C>A
- MANE Select
- NM_182643
- dbSNP
- rs143622533
- Type
- single nucleotide variant
- Location
- chr8:13100558 (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-ser593 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown