RAD21 p.Val602=
c.1806T>A · VCV3609451
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0379%, eas)
Conditions
1
Cornelia de Lange syndrome 4
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 2.5 | GERP 0.24, phastCons 1 |
| Overall | ||
| CADD | 6.496 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0379%
East Asian · 17/44,884 alleles
Filtering AF
0.0241%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0197%
Overall
0.00105%
17/1,614,108 alleles · ultra-rare
exomes 16/1,461,808 · genomes 1/152,300 · joint denominator
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
- RAD21
- Protein
- p.Val602=
- Coding
- c.1806T>A
- MANE Select
- NM_006265
- Type
- single nucleotide variant
- Location
- chr8:116847590 (GRCh38)
- Gene constraint
- LOEUF 0.341 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 61.49 · 37 PDB
- Residue 602
- a UniProt-annotated variant site (in cdls4); an α-helix
Similar variants
- RAD21 c.144+1G>A Pathogenic ★★ same condition
- RAD21 p.Arg478Ter Pathogenic/Likely pathogenic ★★ same condition
- RAD21 p.Arg65Ter Pathogenic/Likely pathogenic ★★ same condition
- RAD21 p.Gln436Ter Pathogenic/Likely pathogenic ★★ same condition
- RAD21 p.Gly408Ter Pathogenic ★★ same condition
- RAD21 p.Ala410Thr Uncertain significance ★★ ⚠ same condition
- RAD21 p.Arg404Lys Uncertain significance ★★ ⚠ same condition
- RAD21 p.Arg569His 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/rad21-p-val602 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown