CC2D2A p.Arg627=
c.1881G>A · rs1718228986 · VCV1284871
Benign/Likely benign
No assertion criteria
Classification
Benign/Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 8.49e-05%, nfe)
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 -1.3 | GERP -2.8 |
| Overall | ||
| CADD | 1.341 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.49e-05%
European (non-Finnish) · 1/1,177,916 alleles
Overall
6.86e-05%
1/1,456,882 alleles · very rare
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
- CC2D2A
- Protein
- p.Arg627=
- Coding
- c.1881G>A
- MANE Select
- NM_001378615
- dbSNP
- rs1718228986
- Type
- single nucleotide variant
- Location
- chr4:15538015 (GRCh38)
- Gene constraint
- LOEUF 0.854 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 69.46
- Residue 627
- the 'disordered' region
Similar variants
- CC2D2A p.Arg627Gln Uncertain significance ★★ ⚠ same residue
- CC2D2A p.Arg627Trp Uncertain significance ★★ ⚠ same residue
- CC2D2A c.1017+1G>A Pathogenic/Likely pathogenic ★★ same type
- CC2D2A c.1149+1G>A Pathogenic/Likely pathogenic ★★ same type
- CC2D2A c.123+2T>G Likely pathogenic ★★ same type
- CC2D2A c.1359+1G>A Pathogenic/Likely pathogenic ★★ same type
- CC2D2A c.1359+1G>C Likely pathogenic ★★ same type
- CC2D2A c.1466+1G>A Likely pathogenic ★★ 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/cc2d2a-p-arg627 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown