CCDC88C p.Arg464=
c.1392C>A · rs1892343786 · VCV2987472
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000172%, 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 2.2 | GERP -0.47, phastCons 1 |
| Overall | ||
| CADD | 8.316 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000172%
European (non-Finnish) · 2/1,164,704 alleles
Filtering AF
2.9e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.00014%
2/1,432,488 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
- CCDC88C
- Protein
- p.Arg464=
- Coding
- c.1392C>A
- MANE Select
- NM_001080414
- dbSNP
- rs1892343786
- Type
- single nucleotide variant
- Location
- chr14:91321255 (GRCh38)
- Gene constraint
- LOEUF 0.759 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 65.69
- Residue 464
- a UniProt-annotated variant site (in sca40; no effect on subcellular location; increases activation of the jnk signaling pathway; induces apoptosis)
Similar variants
- CCDC88C p.Arg464Cys Uncertain significance ★★ ⚠ same residue
- CCDC88C p.Arg464His Uncertain significance ★★ ⚠ same residue
- 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
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-arg464 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown