CCM2 p.Lys10=
c.30G>A · rs1583819255 · VCV662968
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 3 submitters
gnomAD v4.1
Not reported
no allele count reported in gnomAD v4.1 (AN 1,307,216)
Conditions
1
cerebral cavernous malformation 2
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.23 | donor gain · deltas |
|---|---|---|
| Pangolin | Δ0.52 | loss · gain 0.06 · SpliceAI calls gain · independent |
| Constraint at this position | ||
| Conservation | phyloP 3.5 | GERP -0.61, phastCons 0.76 |
| Overall | ||
| CADD | 20.8 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 1,307,216). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- CCM2
- Protein
- p.Lys10=
- Coding
- c.30G>A
- MANE Select
- NM_031443
- dbSNP
- rs1583819255
- Type
- single nucleotide variant
- Location
- chr7:45000363 (GRCh38)
- Gene constraint
- LOEUF 0.753 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 67.48 · 8 PDB
- Residue 10
- the 'disordered' region
Similar variants
- CCM2 p.Lys10Asn Uncertain significance ★ ⚠ same residue
- CCM2 c.289-1G>A Pathogenic/Likely pathogenic ★★ same condition
- CCM2 c.30+1G>A Pathogenic ★★ same condition
- CCM2 c.472+1G>C Pathogenic/Likely pathogenic ★★ same condition
- CCM2 c.473-1G>T Pathogenic ★★ same condition
- CCM2 c.745+1G>T Pathogenic ★★ same condition
- CCM2 p.Arg19Ter Pathogenic ★★ same condition
- CCM2 p.Arg57Ter Pathogenic/Likely pathogenic ★★ 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/ccm2-p-lys10 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown