CCER2 p.Thr76=
c.228C>T · VCV4807076
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.7%, 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 -4.6 | GERP -4.3 |
| Overall | ||
| CADD | 0.129 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.7%
African / African-American · 1,202/70,656 alleles
Filtering AF
1.62%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.59%
Overall
0.0866%
1,269/1,465,634 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.7% | 59 |
| Remaining individualsnot grpmax-eligible | 0.0632% | 1,582 |
| Admixed American | 0.0435% | 2,300 |
| Middle Eastern | 0.0178% | 5,618 |
| South Asian | 0.00418% | 23,945 |
| European (non-Finnish) | 0.000896% | 111,552 |
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.Thr76=
- Coding
- c.228C>T
- MANE Select
- NM_001243212
- Type
- single nucleotide variant
- Location
- chr19:38911046 (GRCh38)
- Gene constraint
- LOEUF 1.298 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 70.74
- Residue 76
- a UniProt-annotated variant site (found in patients with moyamoya disease; uncertain significance)
Similar variants
- CCER2 p.Glu33Asp Benign ★★ same type
- CCER2 c.102+7A>T Uncertain significance ★ same type
- CCER2 p.Ala121Gly Uncertain significance ★ ⚠ same type
- CCER2 p.Ala21Ser Uncertain significance ★ ⚠ same type
- CCER2 p.Arg123Leu Uncertain significance ★ ⚠ same type
- CCER2 p.Arg143Lys Uncertain significance ★ ⚠ same type
- CCER2 p.Arg195His Uncertain significance ★ ⚠ same type
- CCER2 p.Glu202Lys 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/ccer2-p-thr76 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown