DLL3 p.Glu130=
c.390G>A · rs113780398 · VCV285283
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 8 submitters
gnomAD v4.1
Rare
rare (popmax 0.561%, mid)
Conditions
2
spondylocostal dysostosis 1, autosomal recessive
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 0.7 | GERP -0.89, phastCons 0.97 |
| Overall | ||
| CADD | 7.615 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.561%
Middle Eastern · 34/6,060 alleles
Filtering AF
0.413%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.362%
Overall
0.231%
3,731/1,613,680 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.561% | 178 |
| Admixed American | 0.313% | 319 |
| European (non-Finnish) | 0.265% | 377 |
| Remaining individualsnot grpmax-eligible | 0.222% | 449 |
| South Asian | 0.198% | 506 |
| African / African-American | 0.0467% | 2,144 |
| Finnishnot grpmax-eligible | 0.0375% | 2,667 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00676% | 14,790 |
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.Glu130=
- Coding
- c.390G>A
- MANE Select
- NM_203486
- dbSNP
- rs113780398
- Type
- single nucleotide variant
- Location
- chr19:39500653 (GRCh38)
- Gene constraint
- LOEUF 1.512 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 65.42
Similar variants
- DLL3 p.Glu130Lys Uncertain significance ★ ⚠ same residue
- DLL3 p.Glu130Ter Uncertain significance same residue
- DLL3 c.652+1G>T Likely pathogenic ★★ same condition
- DLL3 p.Arg238Ter Pathogenic ★★ same condition
- DLL3 p.Cys178Ter Likely pathogenic ★★ same condition
- DLL3 p.Cys207Ter Pathogenic/Likely pathogenic ★★ same condition
- DLL3 p.Cys379Tyr Pathogenic/Likely pathogenic ★★ same condition
- DLL3 p.Gln346Ter Pathogenic/Likely pathogenic ★★ same condition
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-glu130 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown