JARID2 p.Ser1024=
c.3072C>T · VCV4973819
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.145%, eas)
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 -0.31 | GERP -3.6, phastCons 0.15 |
| Overall | ||
| CADD | 10.64 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.145%
East Asian · 65/44,856 alleles
Filtering AF
0.117%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.106%
Overall
0.00601%
97/1,614,132 alleles · rare
exomes 77/1,461,874 · genomes 20/152,258 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.145% | 690 |
| Remaining individualsnot grpmax-eligible | 0.0272% | 3,677 |
| African / African-American | 0.00933% | 10,721 |
| South Asian | 0.0022% | 45,537 |
| European (non-Finnish) | 0.000508% | 196,671 |
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.Ser1024=
- Coding
- c.3072C>T
- MANE Select
- NM_004973
- Type
- single nucleotide variant
- Location
- chr6:15512327 (GRCh38)
- Gene constraint
- LOEUF 0.202 · pLI 1.00 · ClinGen HI 2/3 (gnomAD)
- Structure
- AlphaFold pLDDT 62.74 · 17 PDB
- Residue 1024
- the jmjc 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-ser1024 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown