CBLL2 p.Arg389=
c.1167G>A · rs75062800 · VCV780686
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.21%, 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 -0.34 | GERP -0.56 |
| Overall | ||
| CADD | 0.433 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.21%
African / African-American · 1,833/57,170 alleles
Filtering AF
3.08%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.03%
Overall
0.169%
2,047/1,210,083 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.21% | 31 |
| Middle Eastern | 0.253% | 396 |
| Remaining individualsnot grpmax-eligible | 0.206% | 486 |
| Admixed American | 0.127% | 789 |
| East Asian | 0.0296% | 3,377 |
| South Asian | 0.0106% | 9,469 |
| European (non-Finnish) | 0.00346% | 28,880 |
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
- CBLL2
- Protein
- p.Arg389=
- Coding
- c.1167G>A
- MANE Select
- NM_152577
- dbSNP
- rs75062800
- Type
- single nucleotide variant
- Location
- chrX:22274158 (GRCh38)
- Structure
- AlphaFold pLDDT 55.14
- Residue 389
- the 'disordered' region
Similar variants
- CBLL2 p.Leu215= Benign ★★ same type
- CBLL2 p.Ala283Val Uncertain significance ★ ⚠ same type
- CBLL2 p.Arg108Gly Uncertain significance ★ ⚠ same type
- CBLL2 p.Arg310His Conflicting classifications of pathogenicity ★ ⚠ same type
- CBLL2 p.Arg341His Uncertain significance ★ ⚠ same type
- CBLL2 p.Arg424Gln Uncertain significance ★ ⚠ same type
- CBLL2 p.Arg95Cys Uncertain significance ★ ⚠ same type
- CBLL2 p.Arg95His 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/cbll2-p-arg389 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown