CC2D1A p.Arg164=
c.490C>A · rs781491587 · VCV2753830
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00134%, 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 1.7 | GERP 1.3, phastCons 1 |
| Overall | ||
| CADD | 11.79 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00134%
African / African-American · 1/74,796 alleles
Overall
0.000657%
1/152,136 alleles · very rare
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.Arg164=
- Coding
- c.490C>A
- MANE Select
- NM_017721
- dbSNP
- rs781491587
- Type
- single nucleotide variant
- Location
- chr19:13913279 (GRCh38)
- Gene constraint
- LOEUF 0.649 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 74.71 · 1 PDB
Similar variants
- CC2D1A p.Arg164Trp Uncertain significance ★★ ⚠ same residue
- CC2D1A p.Arg164Gln 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
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-arg164 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown