DLC1 p.Asp86=
c.258C>T · rs146650078 · VCV2144478
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0217%, amr)
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 2.1 | GERP -3.8, phastCons 1 |
| Overall | ||
| CADD | 7.958 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0217%
Admixed American · 13/59,990 alleles
Filtering AF
0.0127%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0102%
Overall
0.0116%
188/1,613,768 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0217% | 4,615 |
| African / African-American | 0.0174% | 5,758 |
| Middle Eastern | 0.0164% | 6,084 |
| European (non-Finnish) | 0.0125% | 8,027 |
| Remaining individualsnot grpmax-eligible | 0.0112% | 8,927 |
| South Asian | 0.00659% | 15,181 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,606 |
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.Asp86=
- Coding
- c.258C>T
- MANE Select
- NM_003746 · reported on NM_182643
- dbSNP
- rs146650078
- Type
- single nucleotide variant
- Location
- chr8:13499814 (GRCh38)
- Structure
- AlphaFold pLDDT 95.45 · 22 PDB
- Residue 86
- the 'interaction with esr1' region; a β-strand
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-asp86 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown