DLL3 p.Ala503=
c.1509G>A · rs2079650462 · VCV2747896
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no allele count reported in gnomAD v4.1 (AN 1,593,494)
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 -0.17 | GERP -2.2, phastCons 0.005 |
| Overall | ||
| CADD | 6.485 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 1,593,494). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- DLL3
- Protein
- p.Ala503=
- Coding
- c.1509G>A
- MANE Select
- NM_203486
- dbSNP
- rs2079650462
- Type
- single nucleotide variant
- Location
- chr19:39507454 (GRCh38)
- Gene constraint
- LOEUF 1.512 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 65.42
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-ala503 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown