JAG2 p.Asp779=
c.2337C>T · rs141925862 · VCV714589
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.26%, afr)
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 -11 | GERP -4.2 |
| Overall | ||
| CADD | 5.007 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.26%
African / African-American · 190/73,120 alleles
Filtering AF
0.23%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.218%
Overall
0.0165%
255/1,548,810 alleles · rare
exomes 138/1,396,514 · genomes 117/152,296 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.26% | 385 |
| East Asian | 0.0366% | 2,729 |
| Remaining individualsnot grpmax-eligible | 0.025% | 3,998 |
| Admixed American | 0.0196% | 5,105 |
| South Asian | 0.00714% | 13,999 |
| European (non-Finnish) | 0.00166% | 60,355 |
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.Asp779=
- Coding
- c.2337C>T
- MANE Select
- NM_002226
- dbSNP
- rs141925862
- Type
- single nucleotide variant
- Location
- chr14:105147800 (GRCh38)
- Gene constraint
- LOEUF 0.495 · pLI 0.91 (gnomAD)
- Structure
- AlphaFold pLDDT 72.90 · 3 PDB
- Residue 779
- the egf-like 14 domain; a UniProt-annotated variant site (in lgmdr27)
Similar variants
- JAG2 p.Asp779Gly Uncertain significance ★ ⚠ same residue
- JAG2 p.Asp779His Uncertain significance ★ same residue
- 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
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-asp779 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown