JAG1 p.Pro1027=
c.3081G>A · rs766664730 · VCV1131407
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00668%, eas)
Conditions
2
Cardiovascular phenotype
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 | GERP -3.4 |
| Overall | ||
| CADD | 1.928 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00668%
East Asian · 3/44,886 alleles
Filtering AF
0.00267%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00236%
Overall
0.00328%
53/1,613,988 alleles · very rare
exomes 51/1,461,838 · genomes 2/152,150 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00668% | 14,962 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,622 |
| European (non-Finnish) | 0.00356% | 28,095 |
| African / African-American | 0.00267% | 37,450 |
| South Asian | 0.0022% | 45,538 |
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.Pro1027=
- Coding
- c.3081G>A
- MANE Select
- NM_000214
- dbSNP
- rs766664730
- Type
- single nucleotide variant
- Location
- chr20:10640901 (GRCh38)
- Gene constraint
- LOEUF 0.211 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 73.02 · 7 PDB
Similar variants
- JAG1 p.Pro1027Leu Uncertain significance ★ ⚠ same residue
- JAG1 c.1395+3A>G Pathogenic ★★ same condition
- JAG1 c.2113+1G>A Likely pathogenic ★★ same condition
- JAG1 c.2113+1G>T Pathogenic/Likely pathogenic ★★ same condition
- JAG1 c.2572+1G>T Pathogenic/Likely pathogenic ★★ same condition
- JAG1 c.439+1G>A Pathogenic ★★ same condition
- JAG1 c.886+1G>A Pathogenic ★★ same condition
- JAG1 c.886+3A>G 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-pro1027 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown