SCRIB p.Phe571=
c.1713C>T · rs73373194 · VCV768271
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 5.79%, afr) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.37 | acceptor gain · deltas |
|---|---|---|
| Pangolin | Δ0.24 | gain · loss 0.08 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP -4 | GERP -2.9 |
| Overall | ||
| CADD | 9.398 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
5.79%
African / African-American · 4,341/75,024 alleles
Filtering AF
5.64%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 5.58%
Overall
0.302%
4,873/1,612,044 alleles · common
exomes 2,449/1,459,728 · genomes 2,424/152,316 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 5.79% | 17 |
| Remaining individualsnot grpmax-eligible | 0.301% | 332 |
| Admixed American | 0.295% | 339 |
| Middle Eastern | 0.189% | 528 |
| European (non-Finnish) | 0.0123% | 8,134 |
| South Asian | 0.0121% | 8,273 |
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
- SCRIB
- Protein
- p.Phe571=
- Coding
- c.1713C>T
- MANE Select
- NM_182706
- dbSNP
- rs73373194
- Type
- single nucleotide variant
- Location
- chr8:143809011 (GRCh38)
- Gene constraint
- LOEUF 0.684 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 52.33 · 42 PDB
- Residue 571
- the 'sufficient for targeting to adherens junction and to inhibit cell proliferation' region; the 'disordered' region
Similar variants
- SCRIB c.3120+10C>G Benign/Likely benign ★★ same type
- SCRIB c.504-9C>T Benign ★★ same type
- SCRIB p.Ala1488= Likely benign ★★ same type
- SCRIB p.Arg492= Benign ★★ same type
- SCRIB p.Asn647= Benign/Likely benign ★★ same type
- SCRIB p.Leu254= Benign ★★ same type
- SCRIB p.Pro1343= Benign ★★ same type
- SCRIB p.Pro1592Leu Likely benign ★★ 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/scrib-p-phe571 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown