CC2D1A p.Asp516=
c.1548C>T · rs375858581 · VCV2815495
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0174%, afr)
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 -9.7 | GERP -4.6 |
| Overall | ||
| CADD | 0.286 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0174%
African / African-American · 13/74,918 alleles
Filtering AF
0.0103%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00813%
Overall
0.00173%
28/1,614,006 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0174% | 5,763 |
| Admixed American | 0.00833% | 12,001 |
| South Asian | 0.00329% | 30,364 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,239 |
| East Asian | 0.00223% | 44,888 |
| European (non-Finnish) | 0.000339% | 295,004 |
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.Asp516=
- Coding
- c.1548C>T
- MANE Select
- NM_017721
- dbSNP
- rs375858581
- Type
- single nucleotide variant
- Location
- chr19:13920829 (GRCh38)
- Gene constraint
- LOEUF 0.649 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 74.71 · 1 PDB
Similar variants
- CC2D1A p.Asp516Asn 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-asp516 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown