DLC1 p.His389=
c.1167C>T · rs562065329 · VCV2892949
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.03%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>C here scores Δ0.47 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -5.3 | GERP -5.8 |
| Overall | ||
| CADD | 0.053 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.03%
Admixed American · 18/59,986 alleles
Filtering AF
0.0194%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.016%
Overall
0.00465%
75/1,612,250 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.03% | 3,333 |
| South Asian | 0.00659% | 15,165 |
| Remaining individualsnot grpmax-eligible | 0.00481% | 20,781 |
| European (non-Finnish) | 0.00398% | 25,105 |
| African / African-American | 0.00133% | 74,988 |
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.His389=
- Coding
- c.1167C>T
- MANE Select
- NM_003746 · reported on NM_182643
- dbSNP
- rs562065329
- Type
- single nucleotide variant
- Location
- chr8:13401476 (GRCh38)
- Structure
- AlphaFold pLDDT 95.45 · 22 PDB
Similar variants
- DLC1 p.His389Gln Uncertain significance ★ ⚠ same residue
- 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
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-his389 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown