CD46 p.Cys256=
c.768C>T · rs751844358 · VCV2881514
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00659%, sas)
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 -3.3 | GERP -3.1 |
| Overall | ||
| CADD | 3.071 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00659%
South Asian · 6/91,072 alleles
Filtering AF
0.00286%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00195%
Overall
0.000753%
11/1,461,294 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00659% | 15,179 |
| East Asian | 0.00223% | 44,854 |
| European (non-Finnish) | 0.000339% | 294,870 |
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
- CD46
- Protein
- p.Cys256=
- Coding
- c.768C>T
- MANE Select
- NM_172351
- dbSNP
- rs751844358
- Type
- single nucleotide variant
- Location
- chr1:207767107 (GRCh38)
- Gene constraint
- LOEUF 0.763 · pLI 0.04 (gnomAD)
- Structure
- AlphaFold pLDDT 82.38 · 7 PDB
- Residue 256
- a β-strand; a disulfide bond; the sushi 4 domain
Similar variants
- CD46 p.Cys256Ter Pathogenic ★ same residue
- CD46 p.Cys256Arg Uncertain significance ★ ⚠ same residue
- CD46 c.1082+2T>A Pathogenic ★★ same type
- CD46 c.286+1G>C Pathogenic/Likely pathogenic ★★ same type
- CD46 c.286+2T>G Pathogenic/Likely pathogenic ★★ same type
- CD46 c.287-2A>G Pathogenic/Likely pathogenic ★★ same type
- CD46 p.Arg229Ter Pathogenic/Likely pathogenic ★★ same type
- CD46 p.Arg59Ter Pathogenic/Likely 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/cd46-p-cys256 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown