CCDC88A p.Arg573=
c.1717C>A · rs866318133 · VCV2026873
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.54e-05%, nfe)
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 7.7 | GERP 0.21, phastCons 1 |
| Overall | ||
| CADD | 11.14 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.54e-05%
European (non-Finnish) · 1/1,171,014 alleles
Overall
0.000659%
1/151,812 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
- CCDC88A
- Protein
- p.Arg573=
- Coding
- c.1717C>A
- MANE Select
- NM_001365480
- dbSNP
- rs866318133
- Type
- single nucleotide variant
- Location
- chr2:55335104 (GRCh38)
- Gene constraint
- LOEUF 0.25 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 67.09 · 1 PDB
Similar variants
- CCDC88A p.Ala1536Thr Uncertain significance ★★ ⚠ same type
- CCDC88A p.Ala155Val Uncertain significance ★★ ⚠ same type
- CCDC88A p.Ala158Thr Uncertain significance ★★ ⚠ same type
- CCDC88A p.Ala1770Val Uncertain significance ★★ ⚠ same type
- CCDC88A p.Ala194Thr Uncertain significance ★★ ⚠ same type
- CCDC88A p.Ala72Thr Uncertain significance ★★ ⚠ same type
- CCDC88A p.Ala845Gly Uncertain significance ★★ ⚠ same type
- CCDC88A p.Arg1169His 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/ccdc88a-p-arg573 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown