CCER2 p.His220del
c.639CCA[7] · rs144792695 · VCV2796854
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.36%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.054 | GERP 0.77 |
| Overall | ||
| CADD | 8.125 | PHRED · no single calibrated threshold — expert panels disagree |
| Region caveats | ||
| Repeat context | tandem | (TGG)n simple repeat · ambiguous alignment · confidence, not pathogenicity |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.36%
East Asian · 549/40,510 alleles
Filtering AF
1.26%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.22%
Overall
0.155%
2,335/1,510,184 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 1.36% | 74 |
| South Asian | 0.587% | 170 |
| Middle Eastern | 0.289% | 346 |
| Remaining individualsnot grpmax-eligible | 0.25% | 401 |
| Admixed American | 0.109% | 914 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0991% | 1,009 |
| European (non-Finnish) | 0.0881% | 1,135 |
| African / African-American | 0.0826% | 1,211 |
| Finnishnot grpmax-eligible | 0.0347% | 2,878 |
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
- CCER2
- Protein
- p.His220del
- Coding
- c.639CCA[7]
- MANE Select
- NM_001243212
- dbSNP
- rs144792695
- Type
- Microsatellite
- Location
- chr19:38910612 (GRCh38)
- Gene constraint
- LOEUF 1.298 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 70.74
- Residue 220
- a UniProt-annotated variant site (found in patients with moyamoya disease; uncertain significance); a UniProt-annotated variant site (sequence variant); the 'disordered' region
Similar variants
- CCER2 p.His220_Gln221insHis Uncertain significance ★ same residue
- CCER2 p.Lys253del Uncertain significance ★ same type
- CCER2 p.His218_His220del Likely benign ★ 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/ccer2-p-his220del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown