CCDC88A p.Lys343=
c.1029G>A · rs113785488 · VCV730855
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.04%, afr)
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 1.4 | GERP 0.16, phastCons 1 |
| Overall | ||
| CADD | 9.91 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.04%
African / African-American · 775/74,536 alleles
Filtering AF
0.979%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.955%
Overall
0.0857%
1,371/1,600,570 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.04% | 96 |
| Middle Eastern | 0.299% | 335 |
| Admixed American | 0.219% | 457 |
| Remaining individualsnot grpmax-eligible | 0.181% | 553 |
| European (non-Finnish) | 0.0277% | 3,610 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0239% | 4,175 |
| South Asian | 0.00681% | 14,682 |
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.Lys343=
- Coding
- c.1029G>A
- MANE Select
- NM_001365480
- dbSNP
- rs113785488
- Type
- single nucleotide variant
- Location
- chr2:55346187 (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-lys343 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown