CCDC22 p.Val460=
c.1380C>T · rs1602675389 · VCV747951
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00347%, 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 -1.3 | GERP -3.4, phastCons 0.001 |
| Overall | ||
| CADD | 4.656 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00347%
African / African-American · 2/57,573 alleles
Filtering AF
0.000576%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000216%
Overall
0.000165%
2/1,210,716 alleles · very rare
exomes 2/1,097,691 · genomes 0/113,025 · 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
- CCDC22
- Protein
- p.Val460=
- Coding
- c.1380C>T
- MANE Select
- NM_014008
- dbSNP
- rs1602675389
- Type
- single nucleotide variant
- Location
- chrX:49248683 (GRCh38)
- Structure
- AlphaFold pLDDT 78.95 · 4 PDB
Similar variants
- CCDC22 p.Ala463Gly Uncertain significance ★★ ⚠ same type
- CCDC22 p.Arg107Cys Uncertain significance ★★ ⚠ same type
- CCDC22 p.Arg128Gln Uncertain significance ★★ ⚠ same type
- CCDC22 p.Arg135Gln Uncertain significance ★★ ⚠ same type
- CCDC22 p.Arg148Cys Uncertain significance ★★ ⚠ same type
- CCDC22 p.Arg245Gln Uncertain significance ★★ ⚠ same type
- CCDC22 p.Arg257His Uncertain significance ★★ ⚠ same type
- CCDC22 p.Arg379Cys 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/ccdc22-p-val460 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown