CC2D1A p.Ala283=
c.849C>T · VCV4941134
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00449%, eas)
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 -5.6 | GERP -4.4 |
| Overall | ||
| CADD | 4.513 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00449%
East Asian · 2/44,506 alleles
Filtering AF
0.00146%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00123%
Overall
0.00187%
30/1,603,046 alleles · very rare
exomes 28/1,450,906 · genomes 2/152,140 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00449% | 22,253 |
| European (non-Finnish) | 0.00213% | 47,022 |
| Admixed American | 0.00173% | 57,950 |
| Remaining individualsnot grpmax-eligible | 0.00162% | 61,878 |
| African / African-American | 0.00134% | 74,690 |
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
- CC2D1A
- Protein
- p.Ala283=
- Coding
- c.849C>T
- MANE Select
- NM_017721
- Type
- single nucleotide variant
- Location
- chr19:13918170 (GRCh38)
- Gene constraint
- LOEUF 0.649 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 74.71 · 1 PDB
Similar variants
- CC2D1A c.2225+1G>A Likely pathogenic ★★ same type
- CC2D1A c.2454+1G>A Likely pathogenic ★★ same type
- CC2D1A c.2710+1G>A Likely pathogenic ★★ same type
- CC2D1A c.61-2A>G Likely pathogenic ★★ same type
- CC2D1A c.748+1G>T Pathogenic ★★ same type
- CC2D1A c.1941-6C>T Uncertain significance ★★ same type
- CC2D1A c.2073+5G>T Uncertain significance ★★ same type
- CC2D1A c.946+6A>G 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/cc2d1a-p-ala283 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown