SCAF4 p.Ser173=
c.519C>T · VCV4821639
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.105%, 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 -3.2 | GERP -4.8 |
| Overall | ||
| CADD | 3.176 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.105%
African / African-American · 79/75,028 alleles
Filtering AF
0.0866%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0797%
Overall
0.00979%
158/1,614,056 alleles · rare
exomes 97/1,461,776 · genomes 61/152,280 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.105% | 950 |
| Admixed American | 0.045% | 2,223 |
| Remaining individualsnot grpmax-eligible | 0.0256% | 3,906 |
| European (non-Finnish) | 0.00297% | 33,714 |
| South Asian | 0.0011% | 91,068 |
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
- SCAF4
- Protein
- p.Ser173=
- Coding
- c.519C>T
- MANE Select
- NM_020706
- Type
- single nucleotide variant
- Location
- chr21:31701857 (GRCh38)
- Gene constraint
- LOEUF 0.285 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 54.53 · 1 PDB
- Residue 173
- the 'disordered' region
Similar variants
- SCAF4 p.Arg447Ter Pathogenic ★★ same type
- 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-ser173 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown