JARID2 p.Ser563=
c.1689C>T · rs116734338 · VCV738933
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.405%, afr)
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 -7 | GERP -3.5 |
| Overall | ||
| CADD | 6.544 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.405%
African / African-American · 303/74,906 alleles
Filtering AF
0.367%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.352%
Overall
0.0242%
388/1,601,744 alleles · rare
exomes 203/1,449,372 · genomes 185/152,372 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.405% | 247 |
| Admixed American | 0.0504% | 1,984 |
| Remaining individualsnot grpmax-eligible | 0.042% | 2,380 |
| East Asian | 0.0112% | 8,912 |
| South Asian | 0.00223% | 44,864 |
| European (non-Finnish) | 0.00188% | 53,260 |
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.Ser563=
- Coding
- c.1689C>T
- MANE Select
- NM_004973
- dbSNP
- rs116734338
- Type
- single nucleotide variant
- Location
- chr6:15496914 (GRCh38)
- Gene constraint
- LOEUF 0.202 · pLI 1.00 · ClinGen HI 2/3 (gnomAD)
- Structure
- AlphaFold pLDDT 62.74 · 17 PDB
- Residue 563
- 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-ser563 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown