CECR2 p.Pro1323=
c.3969G>A · rs146231898 · VCV731818
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.25%, 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 -2.2 | GERP -2.6 |
| Overall | ||
| CADD | 0.207 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.25%
African / African-American · 940/75,022 alleles
Filtering AF
1.19%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.16%
Overall
0.0716%
1,156/1,613,952 alleles · low-frequency
exomes 607/1,461,704 · genomes 549/152,248 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.25% | 80 |
| Admixed American | 0.095% | 1,053 |
| Remaining individualsnot grpmax-eligible | 0.0752% | 1,329 |
| Middle Eastern | 0.033% | 3,031 |
| European (non-Finnish) | 0.00873% | 11,455 |
| East Asian | 0.00669% | 14,957 |
| South Asian | 0.00439% | 22,772 |
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
- CECR2
- Protein
- p.Pro1323=
- Coding
- c.3969G>A
- MANE Select
- NM_001290047
- dbSNP
- rs146231898
- Type
- single nucleotide variant
- Location
- chr22:17549256 (GRCh38)
- Gene constraint
- LOEUF 0.259 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 50.01 · 3 PDB
Similar variants
- CECR2 c.955-8C>T Benign ★★ same type
- CECR2 p.Ala743Val Benign ★★ same type
- CECR2 p.Ala847= Benign ★★ same type
- CECR2 p.His738= Benign ★★ same type
- CECR2 p.Leu301Val Benign ★★ same type
- CECR2 p.Pro1063= Benign ★★ same type
- CECR2 p.Pro682Thr Likely benign ★★ same type
- CECR2 p.Ser1437= 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/cecr2-p-pro1323 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown