SCARF2 p.Pro583=
c.1749G>T · VCV3631318
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.064%, 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 -1.9 | GERP -1.7 |
| Overall | ||
| CADD | 5.121 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.064%
African / African-American · 47/73,408 alleles
Filtering AF
0.0495%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0443%
Overall
0.00345%
53/1,534,148 alleles · ultra-rare
exomes 23/1,381,844 · genomes 30/152,304 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.064% | 1,562 |
| Remaining individualsnot grpmax-eligible | 0.00836% | 11,958 |
| Admixed American | 0.00198% | 50,520 |
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
- SCARF2
- Protein
- p.Pro583=
- Coding
- c.1749G>T
- MANE Select
- NM_182895
- Type
- single nucleotide variant
- Location
- chr22:20426227 (GRCh38)
- Gene constraint
- LOEUF 0.992 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 64.63
- Residue 583
- the 'disordered' region
Similar variants
- SCARF2 p.Ala12Ser Uncertain significance ★★ ⚠ same type
- SCARF2 p.Ala627Val Uncertain significance ★★ ⚠ same type
- SCARF2 p.Ala854Thr Uncertain significance ★★ ⚠ same type
- SCARF2 p.Arg860Lys Uncertain significance ★★ ⚠ same type
- SCARF2 p.Asp378Glu Uncertain significance ★★ ⚠ same type
- SCARF2 p.Asp830Asn Uncertain significance ★★ ⚠ same type
- SCARF2 p.Glu581Gln Uncertain significance ★★ ⚠ same type
- SCARF2 p.Glu853Gly 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/scarf2-p-pro583 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown