JAG2 p.Phe369=
c.1107C>T · rs35006456 · VCV713522
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.06%, 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 -3.5 | GERP -4.4 |
| Overall | ||
| CADD | 7.609 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.06%
African / African-American · 3,047/75,042 alleles
Filtering AF
3.94%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.89%
Overall
0.215%
3,469/1,611,234 alleles · low-frequency
exomes 1,815/1,458,886 · genomes 1,654/152,348 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4.06% | 25 |
| East Asian | 0.308% | 325 |
| Remaining individualsnot grpmax-eligible | 0.197% | 507 |
| Admixed American | 0.142% | 703 |
| Middle Eastern | 0.099% | 1,010 |
| European (non-Finnish) | 0.00568% | 17,603 |
| Finnishnot grpmax-eligible | 0.00319% | 31,331 |
| South Asian | 0.0011% | 90,602 |
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.Phe369=
- Coding
- c.1107C>T
- MANE Select
- NM_002226
- dbSNP
- rs35006456
- Type
- single nucleotide variant
- Location
- chr14:105151672 (GRCh38)
- Gene constraint
- LOEUF 0.495 · pLI 0.91 (gnomAD)
- Structure
- AlphaFold pLDDT 72.90 · 3 PDB
- Residue 369
- a UniProt-annotated variant site (in lgmdr27); the egf-like 4 domain
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-phe369 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown