DLL3 p.Pro117=
c.351T>C · rs769556737 · VCV1364330
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00852%, 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 · T>G here scores Δ0.33 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 4.9 | GERP 0.047, phastCons 1 |
| Overall | ||
| CADD | 16.07 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00852%
Admixed American · 5/58,716 alleles
Filtering AF
0.00329%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0021%
Overall
0.000348%
5/1,435,780 alleles · very rare
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.Pro117=
- Coding
- c.351T>C
- MANE Select
- NM_203486
- dbSNP
- rs769556737
- Type
- single nucleotide variant
- Location
- chr19:39499473 (GRCh38)
- Gene constraint
- LOEUF 1.512 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 65.42
Similar variants
- DLL3 p.Pro117Ser Uncertain significance ★ ⚠ same residue
- 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
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-pro117 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown