JARID2 p.Pro593=
c.1779G>A · VCV4533650
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0164%, mid)
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 -0.64 | GERP -3.5, phastCons 0.001 |
| Overall | ||
| CADD | 10.14 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0164%
Middle Eastern · 1/6,084 alleles
Filtering AF
0.00175%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00104%
Overall
0.00155%
25/1,613,856 alleles · ultra-rare
exomes 21/1,461,622 · genomes 4/152,234 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0164% | 6,084 |
| African / African-American | 0.00534% | 18,736 |
| South Asian | 0.0033% | 30,343 |
| Admixed American | 0.00167% | 59,996 |
| European (non-Finnish) | 0.00136% | 73,748 |
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.Pro593=
- Coding
- c.1779G>A
- MANE Select
- NM_004973
- Type
- single nucleotide variant
- Location
- chr6:15497004 (GRCh38)
- Gene constraint
- LOEUF 0.202 · pLI 1.00 · ClinGen HI 2/3 (gnomAD)
- Structure
- AlphaFold pLDDT 62.74 · 17 PDB
- Residue 593
- the jmjn domain
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-pro593 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown