JAG1 p.Phe94=
c.282C>T · rs772592163 · VCV337760
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00892%, eas)
Conditions
1
Isolated Nonsyndromic Congenital Heart Disease
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 2.2 | GERP 1.7, phastCons 1 |
| Overall | ||
| CADD | 11.44 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00892%
East Asian · 4/44,860 alleles
Filtering AF
0.00298%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0018%
Overall
0.000274%
4/1,460,846 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
- JAG1
- Protein
- p.Phe94=
- Coding
- c.282C>T
- MANE Select
- NM_000214
- dbSNP
- rs772592163
- Type
- single nucleotide variant
- Location
- chr20:10672806 (GRCh38)
- Gene constraint
- LOEUF 0.211 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 73.02 · 7 PDB
Disease context
Isolated Nonsyndromic Congenital Heart Disease
Similar variants
- JAG1 p.Arg184Cys Pathogenic/Likely pathogenic ★★ same condition
- JAG1 p.Arg184His Pathogenic/Likely pathogenic ★★ same condition
- JAG1 p.Arg235Ter Pathogenic ★★ same condition
- JAG1 p.Arg900Ter Pathogenic ★★ same condition
- JAG1 p.Cys768Ter Pathogenic ★★ same condition
- JAG1 p.Gln539Ter Pathogenic ★★ same condition
- JAG1 p.Glu1003Ter Pathogenic ★★ same condition
- JAG1 p.Gly386Arg 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/jag1-p-phe94 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown