CC2D1A p.Ser473=
c.1419G>A · rs373165331 · VCV2894957
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0329%, mid)
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 -0.68 | GERP -4.7 |
| Overall | ||
| CADD | 1.156 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0329%
Middle Eastern · 2/6,072 alleles
Filtering AF
0.00626%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00469%
Overall
0.0018%
29/1,611,152 alleles · ultra-rare
exomes 20/1,459,382 · genomes 9/151,770 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0329% | 3,036 |
| African / African-American | 0.0121% | 8,295 |
| East Asian | 0.0112% | 8,950 |
| Admixed American | 0.00336% | 29,797 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,336 |
| Finnishnot grpmax-eligible | 0.00157% | 63,724 |
| European (non-Finnish) | 0.000763% | 130,988 |
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.Ser473=
- Coding
- c.1419G>A
- MANE Select
- NM_017721
- dbSNP
- rs373165331
- Type
- single nucleotide variant
- Location
- chr19:13920619 (GRCh38)
- Gene constraint
- LOEUF 0.649 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 74.71 · 1 PDB
- Residue 473
- the 'disordered' region
Similar variants
- CC2D1A p.Ser473Leu 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-ser473 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown