SBF1 p.Pro1300=
c.3900C>G · rs776621303 · VCV1645841
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
very rare (popmax 0.000728%, nfe)
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 7.4 | GERP 2.2, phastCons 1 |
| Overall | ||
| CADD | 11.48 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000728%
European (non-Finnish) · 8/1,099,444 alleles
Filtering AF
0.000313%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000226%
Overall
0.000556%
8/1,439,560 alleles · very rare
exomes 7/1,287,390 · genomes 1/152,170 · joint denominator
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
- SBF1
- Protein
- p.Pro1300=
- Coding
- c.3900C>G
- MANE Select
- NM_002972
- dbSNP
- rs776621303
- Type
- single nucleotide variant
- Location
- chr22:50457038 (GRCh38)
- Gene constraint
- LOEUF 0.381 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 74.72
- Residue 1300
- the myotubularin phosphatase domain; the 'disordered' region
Similar variants
- SBF1 c.3826+1G>A Pathogenic/Likely pathogenic ★★ same type
- SBF1 p.Met417Val Pathogenic/Likely pathogenic ★★ ⚠ same type
- SBF1 c.1431+6A>T Uncertain significance ★★ same type
- SBF1 c.1636+4C>T Uncertain significance ★★ same type
- SBF1 c.1899+3G>A Uncertain significance ★★ same type
- SBF1 c.2643+6C>T Uncertain significance ★★ same type
- SBF1 c.279+3C>T Uncertain significance ★★ same type
- SBF1 c.3904+6G>A 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/sbf1-p-pro1300 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown