DLL3 p.Arg205=
c.615C>G · rs780088167 · VCV1576807
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0465%, mid)
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 -2.7 | GERP -2.2 |
| Overall | ||
| CADD | 3.014 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0465%
Middle Eastern · 2/4,298 alleles
Filtering AF
0.0162%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0136%
Overall
0.00721%
109/1,511,612 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0465% | 2,149 |
| South Asian | 0.0246% | 4,071 |
| African / African-American | 0.0113% | 8,818 |
| Admixed American | 0.0103% | 9,745 |
| European (non-Finnish) | 0.00616% | 16,245 |
| Remaining individualsnot grpmax-eligible | 0.0051% | 19,594 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00359% | 27,820 |
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
- DLL3
- Protein
- p.Arg205=
- Coding
- c.615C>G
- MANE Select
- NM_203486
- dbSNP
- rs780088167
- Type
- single nucleotide variant
- Location
- chr19:39503020 (GRCh38)
- Gene constraint
- LOEUF 1.512 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 65.42
- Residue 205
- the dsl domain
Similar variants
- DLL3 c.652+1G>T Likely pathogenic ★★ same type
- DLL3 p.Arg221Ter Pathogenic ★★ same type
- DLL3 p.Arg238Ter Pathogenic ★★ same type
- DLL3 p.Cys178Ter Likely pathogenic ★★ same type
- DLL3 p.Cys207Ter Pathogenic/Likely pathogenic ★★ same type
- DLL3 p.Cys379Tyr Pathogenic/Likely pathogenic ★★ same type
- DLL3 p.Gln346Ter Pathogenic/Likely pathogenic ★★ same type
- DLL3 p.Gly504Asp Pathogenic/Likely pathogenic ★★ 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/dll3-p-arg205 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown