Is JAG1 p.Arg2= (c.6T>G) pathogenic?

JAG1 p.Arg2= (c.6T>G) is classified Likely benign in JAG1 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-11-15). Absent from gnomAD v4.1; Associated with Cardiovascular phenotype.

What condition is associated with JAG1 p.Arg2= (c.6T>G)?

JAG1 p.Arg2= (c.6T>G) is associated with Cardiovascular phenotype (ClinVar).

How common is JAG1 p.Arg2= (c.6T>G) in the general population?

JAG1 p.Arg2= (c.6T>G) is absent from gnomAD v4.1 (gnomAD).

JAG1 p.Arg2=

c.6T>G · rs2514539114 · VCV1756635

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

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 2.6	GERP 0.34, phastCons 1
Overall
CADD	15.05	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: JAG1
Protein: p.Arg2=
Coding: c.6T>G
MANE Select: NM_000214
dbSNP: rs2514539114
Type: single nucleotide variant
Location: chr20:10673525 (GRCh38)
Gene constraint: LOEUF 0.211 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 73.02 · 7 PDB

Full JAG1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Cardiovascular phenotype — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

JAG1 p.Arg2His Uncertain significance ★★ ⚠ same residue
JAG1 p.Arg2Cys Uncertain significance ★ same residue
JAG1 p.Arg2Gly Uncertain significance ★ ⚠ same residue
JAG1 p.Arg2Leu Conflicting classifications of pathogenicity ★ ⚠ same residue
JAG1 p.Arg2Pro Uncertain significance ★ ⚠ same residue
JAG1 c.886+3A>G Likely pathogenic ★★ same condition
JAG1 p.Gln457Ter Pathogenic ★★ same condition
JAG1 p.Glu353Ter 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-arg2 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown