SCAF4 p.Arg447=
c.1339C>A · VCV3905769
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no allele count reported in gnomAD v4.1 (AN 1,496,112)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>A here scores Δ0.23 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 3.5 | GERP 2.1, phastCons 1 |
| Overall | ||
| CADD | 10.53 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 1,496,112). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- SCAF4
- Protein
- p.Arg447=
- Coding
- c.1339C>A
- MANE Select
- NM_020706
- Type
- single nucleotide variant
- Location
- chr21:31693468 (GRCh38)
- Gene constraint
- LOEUF 0.285 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 54.53 · 1 PDB
- Residue 447
- a UniProt-annotated variant site (in fzs; likely pathogenic); the 'disordered' region
Similar variants
- SCAF4 p.Arg447Ter Pathogenic ★★ same residue
- SCAF4 p.Arg475Ter Pathogenic ★★ same type
- SCAF4 p.Arg477Ter Pathogenic ★★ same type
- SCAF4 p.Arg491Ter Pathogenic/Likely pathogenic ★★ same type
- SOD1 p.Gly73Ser Likely pathogenic ★★ same type
- SCAF4 p.Arg71Gln Uncertain significance ★★ ⚠ same type
- SCAF4 p.Asn627Ser Uncertain significance ★★ ⚠ same type
- SCAF4 p.Lys635Glu 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/scaf4-p-arg447 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown