SCARF2 p.Cys80=
c.240C>T · rs138431734 · VCV1176005
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.14%, mid)
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 0.33 | GERP -2.4, phastCons 0.95 |
| Overall | ||
| CADD | 7.264 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.14%
Middle Eastern · 69/6,036 alleles
Filtering AF
0.927%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.847%
Overall
0.0661%
1,056/1,597,688 alleles · low-frequency
exomes 961/1,445,424 · genomes 95/152,264 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 1.14% | 87 |
| Ashkenazi Jewishnot grpmax-eligible | 0.922% | 108 |
| Remaining individualsnot grpmax-eligible | 0.158% | 632 |
| Admixed American | 0.109% | 915 |
| South Asian | 0.0509% | 1,963 |
| European (non-Finnish) | 0.042% | 2,380 |
| African / African-American | 0.0187% | 5,349 |
| Finnishnot grpmax-eligible | 0.00977% | 10,234 |
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.Cys80=
- Coding
- c.240C>T
- MANE Select
- NM_182895
- dbSNP
- rs138431734
- Type
- single nucleotide variant
- Location
- chr22:20431839 (GRCh38)
- Gene constraint
- LOEUF 0.992 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 64.63
- Residue 80
- a disulfide bond; the egf-like 1 domain
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-cys80 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown