CR2 p.Val896=
c.2688G>T · rs1250358980 · VCV789557
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
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 0.26 | GERP -3.4, phastCons 0.91 |
| Overall | ||
| CADD | 2.76 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- CR2
- Protein
- p.Val896=
- Coding
- c.2688G>T
- MANE Select
- NM_001006658
- dbSNP
- rs1250358980
- Type
- single nucleotide variant
- Location
- chr1:207475188 (GRCh38)
- Gene constraint
- LOEUF 0.871 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.18 · 9 PDB
- Residue 896
- the sushi 14 domain
Similar variants
- CR2 p.Val896Ala Uncertain significance ★ ⚠ same residue
- CR2 c.1225+1G>C Pathogenic ★★ same type
- CR2 c.3089-1G>A Likely pathogenic ★★ same type
- CR2 p.Arg142Ter Pathogenic/Likely pathogenic ★★ same type
- CR2 p.Arg368Ter Pathogenic/Likely pathogenic ★★ same type
- CR2 p.Arg392Ter Pathogenic/Likely pathogenic ★★ same type
- CR2 p.Arg840Ter Pathogenic/Likely pathogenic ★★ same type
- CR2 p.Cys154Ter Pathogenic ★★ 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/cr2-p-val896 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown