SF1 p.Pro479=
c.1437G>A · rs1223525577 · VCV3160784
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00361%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.044 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -1.3 | GERP -2.9, phastCons 0.001 |
| Overall | ||
| CADD | 6.392 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00361%
South Asian · 3/83,152 alleles
Filtering AF
0.000958%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000466%
Overall
0.000321%
5/1,557,166 alleles · very rare
exomes 5/1,405,062 · genomes 0/152,104 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00361% | 27,717 |
| European (non-Finnish) | 0.000174% | 574,871 |
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
- SF1
- Protein
- p.Pro479=
- Coding
- c.1437G>A
- MANE Select
- NM_004630
- dbSNP
- rs1223525577
- Type
- single nucleotide variant
- Location
- chr11:64767045 (GRCh38)
- Gene constraint
- LOEUF 0.22 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 65.28 · 10 PDB
- Residue 479
- the 'disordered' region
Similar variants
- SF1 p.Pro479Leu Uncertain significance ★ ⚠ same residue
- SF1 c.31+105G>A Uncertain significance ★ same type
- SF1 c.31+111C>G Uncertain significance ★ same type
- SF1 c.31+112C>T Uncertain significance ★ same type
- SF1 c.31+123C>T Uncertain significance ★ same type
- SF1 c.31+12C>A Uncertain significance ★ same type
- SF1 c.31+138G>A Uncertain significance ★ same type
- SF1 c.31+139G>C 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/sf1-p-pro479 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown