CCDC88C p.Phe1024=
c.3072C>T · rs762288121 · VCV2900527
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00329%, sas)
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 2.4 | GERP 0.78, phastCons 0.99 |
| Overall | ||
| CADD | 5.793 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00329%
South Asian · 3/91,092 alleles
Filtering AF
0.000875%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000443%
Overall
0.000806%
13/1,613,822 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00329% | 30,364 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,232 |
| East Asian | 0.00223% | 44,886 |
| European (non-Finnish) | 0.000593% | 168,556 |
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.Phe1024=
- Coding
- c.3072C>T
- MANE Select
- NM_001080414
- dbSNP
- rs762288121
- Type
- single nucleotide variant
- Location
- chr14:91307161 (GRCh38)
- Gene constraint
- LOEUF 0.759 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 65.69
- Residue 1024
- the 'disordered' region
Similar variants
- CCDC88C p.Phe1024Leu 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
- CCDC88C c.3358-5G>A 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-phe1024 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown