CECR2 p.Arg894=
c.2682C>T · rs768595444 · VCV740092
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00833%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -11 | GERP -3.5 |
| Overall | ||
| CADD | 0.385 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00833%
Admixed American · 5/59,994 alleles
Filtering AF
0.00323%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00207%
Overall
0.000806%
13/1,613,772 alleles · very rare
exomes 11/1,461,610 · genomes 2/152,162 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00833% | 11,999 |
| East Asian | 0.00669% | 14,957 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,230 |
| Finnishnot grpmax-eligible | 0.00156% | 64,022 |
| European (non-Finnish) | 0.00017% | 589,918 |
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.Arg894=
- Coding
- c.2682C>T
- MANE Select
- NM_001290047
- dbSNP
- rs768595444
- Type
- single nucleotide variant
- Location
- chr22:17542825 (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.Pro1323= Benign ★★ same type
- CECR2 p.Pro682Thr 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/cecr2-p-arg894 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown