CCDC88C p.Ser2005=
c.6015A>G · VCV4811951
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 8.48e-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 -9.1 | GERP -4 |
| Overall | ||
| CADD | 0.06 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.48e-05%
European (non-Finnish) · 1/1,179,836 alleles
Overall
6.21e-05%
1/1,611,496 alleles · very rare
exomes 0/1,459,302 · genomes 1/152,194 · joint denominator
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
- CCDC88C
- Protein
- p.Ser2005=
- Coding
- c.6015A>G
- MANE Select
- NM_001080414
- Type
- single nucleotide variant
- Location
- chr14:91272697 (GRCh38)
- Gene constraint
- LOEUF 0.759 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 65.69
- Residue 2005
- the 'disordered' region
Similar variants
- CCDC88C c.3358-2A>C Likely pathogenic ★★ same type
- CCDC88C c.4442-2A>G Likely pathogenic ★★ same type
- CCDC88C c.4768+1G>T Likely pathogenic ★★ same type
- CCDC88C p.Arg1701Ter Pathogenic/Likely pathogenic ★★ same type
- CCDC88C p.Arg312Ter Pathogenic ★★ same type
- CCDC88C p.Arg407Ter Pathogenic/Likely pathogenic ★★ same type
- CCDC88C c.3358-5G>A Uncertain significance ★★ same type
- CCDC88C p.Ala1102Thr 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/ccdc88c-p-ser2005 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown