Is JARID2 p.Pro248= (c.744C>T) pathogenic?

JARID2 p.Pro248= (c.744C>T) is classified Likely benign in JARID2 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-05-02). Ultra-rare (popmax 0.0133%, afr); Associated with JARID2-related disorder.

What condition is associated with JARID2 p.Pro248= (c.744C>T)?

JARID2 p.Pro248= (c.744C>T) is associated with JARID2-related disorder (ClinVar).

How common is JARID2 p.Pro248= (c.744C>T) in the general population?

JARID2 p.Pro248= (c.744C>T) is ultra-rare (popmax 0.0133%, afr) (gnomAD).

JARID2 p.Pro248=

c.744C>T · rs147119452 · VCV3056803

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0133%, afr)

Conditions

JARID2-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 -0.66	GERP -1.8, phastCons 0.005
Overall
CADD	11.96	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0133% African / African-American · 10/75,052 alleles

Filtering AF 0.00722% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00549%

Overall 0.00124% 20/1,614,216 alleles · ultra-rare exomes 13/1,461,892 · genomes 7/152,324 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0133%	7,505
Remaining individualsnot grpmax-eligible	0.0048%	20,834
Admixed American	0.00333%	30,013
European (non-Finnish)	0.000424%	236,009

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: JARID2
Protein: p.Pro248=
Coding: c.744C>T
MANE Select: NM_004973
dbSNP: rs147119452
Type: single nucleotide variant
Location: chr6:15487380 (GRCh38)
Gene constraint: LOEUF 0.202 · pLI 1.00 · ClinGen HI 2/3 (gnomAD)
Structure: AlphaFold pLDDT 62.74 · 17 PDB
Residue 248: the 'disordered' region

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

Disease context

JARID2-related disorder

Similar variants

JARID2 p.Pro248Leu Uncertain significance ★ ⚠ same residue
JARID2 p.Arg311Gly Uncertain significance ★★ ⚠ same condition
JARID2 p.Thr1043Ser Uncertain significance ★★ ⚠ same condition
JARID2 p.Asn1194Ser Uncertain significance ★ ⚠ same condition
JARID2 p.Leu163Pro Uncertain significance ★ ⚠ same condition
JARID2 p.Lys131Asn Uncertain significance ★ ⚠ same condition
JARID2 p.Lys775Glu Uncertain significance ★ ⚠ same condition
JARID2 p.Pro843Leu Uncertain significance ★ ⚠ 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/jarid2-p-pro248 (accessed [today's date]).

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