CC2D2A p.Val693=
c.2079G>A · rs1348040937 · VCV740343
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0023%, eas)
Conditions
2
Joubert syndrome
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 0.85 | GERP -2.7, phastCons 1 |
| Overall | ||
| CADD | 8.855 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0023%
East Asian · 1/43,456 alleles
Overall
0.000189%
3/1,583,826 alleles · very rare
exomes 2/1,431,626 · genomes 1/152,200 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0023% | 43,456 |
| Remaining individualsnot grpmax-eligible | 0.00163% | 61,484 |
| African / African-American | 0.00135% | 74,222 |
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.Val693=
- Coding
- c.2079G>A
- MANE Select
- NM_001378615
- dbSNP
- rs1348040937
- Type
- single nucleotide variant
- Location
- chr4:15540912 (GRCh38)
- Gene constraint
- LOEUF 0.854 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 69.46
Similar variants
- CC2D2A p.Val693Met Uncertain significance ★ ⚠ same residue
- CC2D2A c.1017+1G>A Pathogenic/Likely pathogenic ★★ same condition
- CC2D2A c.123+2T>G Likely pathogenic ★★ same condition
- CC2D2A c.1359+1G>C Likely pathogenic ★★ same condition
- CC2D2A c.1466+1G>A Likely pathogenic ★★ same condition
- CC2D2A c.1466+2T>C Likely pathogenic ★★ same condition
- CC2D2A c.1608-2A>G Likely pathogenic ★★ same condition
- CC2D2A c.2004-17A>G 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/cc2d2a-p-val693 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown