JAG2 p.Ser102=
c.306C>T · rs78862296 · VCV714526
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.66%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 4.7 | GERP -3.4, phastCons 1 |
| Overall | ||
| CADD | 15.78 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.66%
African / African-American · 1,172/70,510 alleles
Filtering AF
1.58%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.55%
Overall
0.0926%
1,447/1,562,172 alleles · low-frequency
exomes 712/1,410,960 · genomes 735/151,212 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.66% | 60 |
| Middle Eastern | 0.271% | 369 |
| Remaining individualsnot grpmax-eligible | 0.161% | 623 |
| Admixed American | 0.129% | 775 |
| European (non-Finnish) | 0.00757% | 13,203 |
| South Asian | 0.00462% | 21,644 |
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
- JAG2
- Protein
- p.Ser102=
- Coding
- c.306C>T
- MANE Select
- NM_002226
- dbSNP
- rs78862296
- Type
- single nucleotide variant
- Location
- chr14:105167868 (GRCh38)
- Gene constraint
- LOEUF 0.495 · pLI 0.91 (gnomAD)
- Structure
- AlphaFold pLDDT 72.90 · 3 PDB
- Residue 102
- a β-strand
Similar variants
- JAG2 p.Gly839Arg Likely pathogenic ★★ same type
- JAG2 p.Arg466His Uncertain significance ★★ ⚠ same type
- JAG2 p.Arg686His Uncertain significance ★★ ⚠ same type
- JAG2 p.Arg979Cys Uncertain significance ★★ ⚠ same type
- JAG2 p.Gly994Arg Uncertain significance ★★ ⚠ same type
- JAG2 p.Pro1130Leu Uncertain significance ★★ ⚠ same type
- JAG2 p.Pro157Leu Uncertain significance ★★ ⚠ same type
- JAG2 p.Val1147Met 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/jag2-p-ser102 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown