CC2D1A p.Arg13=
c.37A>C · VCV3713252
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0373%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 5.9 | GERP 0.6, phastCons 1 |
| Overall | ||
| CADD | 16.38 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0373%
Middle Eastern · 2/5,358 alleles
Filtering AF
0.00662%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00268%
Overall
0.000463%
7/1,512,106 alleles · ultra-rare
exomes 7/1,359,956 · genomes 0/152,150 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0373% | 2,679 |
| Remaining individualsnot grpmax-eligible | 0.00341% | 29,336 |
| South Asian | 0.00123% | 81,428 |
| European (non-Finnish) | 0.000177% | 566,290 |
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.Arg13=
- Coding
- c.37A>C
- MANE Select
- NM_017721
- Type
- single nucleotide variant
- Location
- chr19:13906478 (GRCh38)
- Gene constraint
- LOEUF 0.649 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 74.71 · 1 PDB
Similar variants
- CC2D1A p.Arg13Lys Uncertain significance ★ ⚠ same residue
- 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
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-arg13 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown