Is JARID2 p.Pro884= (c.2652C>G) pathogenic?

JARID2 p.Pro884= (c.2652C>G) is classified Likely benign in JARID2 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-03-07). Absent from gnomAD v4.1.

How common is JARID2 p.Pro884= (c.2652C>G) in the general population?

JARID2 p.Pro884= (c.2652C>G) is absent from gnomAD v4.1 (gnomAD).

JARID2 p.Pro884=

c.2652C>G · VCV4973815

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP -6.1	GERP -3.6
Overall
CADD	0.731	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: JARID2
Protein: p.Pro884=
Coding: c.2652C>G
MANE Select: NM_004973
Type: single nucleotide variant
Location: chr6:15507246 (GRCh38)
Gene constraint: LOEUF 0.202 · pLI 1.00 · ClinGen HI 2/3 (gnomAD)
Structure: AlphaFold pLDDT 62.74 · 17 PDB
Residue 884: the jmjc domain

Full JARID2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

JARID2 p.Ala265Pro Uncertain significance ★★ ⚠ same type
JARID2 p.Ala844Pro Uncertain significance ★★ ⚠ same type
JARID2 p.Arg311Gly Uncertain significance ★★ ⚠ same type
JARID2 p.Asn1155Tyr Uncertain significance ★★ ⚠ same type
JARID2 p.Asn171Asp Uncertain significance ★★ ⚠ same type
JARID2 p.Asn383Ser Uncertain significance ★★ ⚠ same type
JARID2 p.Glu186Gln Uncertain significance ★★ ⚠ same type
JARID2 p.His514Arg 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/jarid2-p-pro884 (accessed [today's date]).

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