CCDC88A p.Thr210=
c.630T>G · rs772724179 · VCV1628495
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, mid)
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 3 | GERP -4.4, phastCons 1 |
| Overall | ||
| CADD | 9.444 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
Middle Eastern · 1/6,058 alleles
Filtering AF
0.00438%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00313%
Overall
0.00268%
43/1,606,448 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0165% | 6,058 |
| South Asian | 0.00882% | 11,340 |
| Remaining individualsnot grpmax-eligible | 0.00644% | 15,535 |
| European (non-Finnish) | 0.00256% | 39,135 |
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.Thr210=
- Coding
- c.630T>G
- MANE Select
- NM_001365480
- dbSNP
- rs772724179
- Type
- single nucleotide variant
- Location
- chr2:55355749 (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-thr210 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown