SCRIB p.Pro1343=
c.4029T>G · rs112399431 · VCV786130
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.23%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| REVEL | 0.002 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | Δ0.22 | acceptor loss, 11 bp away · masked 0 · deltas |
| Constraint at this position | ||
| Conservation | phyloP -5.2 | GERP -2.7 |
| Overall | ||
| CADD | 0.171 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.23%
African / African-American · 1,606/72,122 alleles
Filtering AF
2.14%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.1%
Overall
0.122%
1,850/1,516,056 alleles · low-frequency
exomes 843/1,363,966 · genomes 1,007/152,090 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.23% | 45 |
| Admixed American | 0.191% | 523 |
| Remaining individualsnot grpmax-eligible | 0.157% | 636 |
| Middle Eastern | 0.124% | 806 |
| European (non-Finnish) | 0.00449% | 22,274 |
| South Asian | 0.00129% | 77,586 |
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.Pro1343=
- Coding
- c.4029T>G
- MANE Select
- NM_182706
- dbSNP
- rs112399431
- Type
- single nucleotide variant
- Location
- chr8:143792856 (GRCh38)
- Gene constraint
- LOEUF 0.684 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 52.33 · 42 PDB
- Residue 1343
- 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.Phe571= 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-pro1343 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown