CCER2 p.Thr257=
c.771G>A · VCV3708630
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0412%, amr)
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 0.049 | GERP -3.8, phastCons 0.001 |
| Overall | ||
| CADD | 10.65 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0412%
Admixed American · 21/50,962 alleles
Filtering AF
0.0275%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0231%
Overall
0.00508%
78/1,535,388 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0412% | 2,427 |
| East Asian | 0.0195% | 5,116 |
| Remaining individualsnot grpmax-eligible | 0.0167% | 5,998 |
| Middle Eastern | 0.0167% | 6,006 |
| European (non-Finnish) | 0.00296% | 33,728 |
| African / African-American | 0.00274% | 36,515 |
| South Asian | 0.00238% | 42,032 |
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.Thr257=
- Coding
- c.771G>A
- MANE Select
- NM_001243212
- Type
- single nucleotide variant
- Location
- chr19:38909266 (GRCh38)
- Gene constraint
- LOEUF 1.298 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 70.74
- Residue 257
- the 'disordered' region
Similar variants
- CCER2 p.Thr257Met Uncertain significance ★ ⚠ same residue
- 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
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-thr257 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown