Is JAG2 p.Ile652= (c.1956C>T) pathogenic?

JAG2 p.Ile652= (c.1956C>T) is classified Likely benign in JAG2 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-05-09). Ultra-rare (popmax 0.0137%, amr); Associated with JAG2-related disorder.

What condition is associated with JAG2 p.Ile652= (c.1956C>T)?

JAG2 p.Ile652= (c.1956C>T) is associated with JAG2-related disorder (ClinVar).

How common is JAG2 p.Ile652= (c.1956C>T) in the general population?

JAG2 p.Ile652= (c.1956C>T) is ultra-rare (popmax 0.0137%, amr) (gnomAD).

JAG2 p.Ile652=

c.1956C>T · rs775456413 · VCV3041750

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0137%, amr)

Conditions

JAG2-related disorder

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 -2.3	GERP -4.3
Overall
CADD	7.579	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0137% Admixed American · 8/58,402 alleles

Filtering AF 0.00677% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00494%

Overall 0.00131% 21/1,598,876 alleles · ultra-rare exomes 18/1,446,588 · genomes 3/152,288 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0137%	7,300
South Asian	0.00451%	22,181
African / African-American	0.00267%	37,404
Remaining individualsnot grpmax-eligible	0.00162%	61,846
European (non-Finnish)	0.000511%	195,582

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.Ile652=
Coding: c.1956C>T
MANE Select: NM_002226
dbSNP: rs775456413
Type: single nucleotide variant
Location: chr14:105148809 (GRCh38)
Gene constraint: LOEUF 0.495 · pLI 0.91 (gnomAD)
Structure: AlphaFold pLDDT 72.90 · 3 PDB
Residue 652: the egf-like 11; calcium-binding domain; a UniProt-annotated variant site (in lgmdr27)

Full JAG2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

JAG2-related disorder

Similar variants

JAG2 p.Arg979Cys Uncertain significance ★★ ⚠ same condition
JAG2 p.Gly530Arg Uncertain significance ★ ⚠ same condition
JAG2 p.Val1103Leu Uncertain significance ★ ⚠ same condition
JAG2 c.1382-6C>T Likely benign same condition
JAG2 c.1429-6G>A Likely benign same condition
JAG2 c.1429-7C>T Likely benign same condition
JAG2 c.1603-7C>T Likely benign same condition
JAG2 c.1753+8G>A Likely benign 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/jag2-p-ile652 (accessed [today's date]).

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