SF1 p.Pro480=
c.1440G>A · rs1592451188 · VCV3160785
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00242%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.158 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -4.8 | GERP -2.9 |
| Overall | ||
| CADD | 6.482 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00242%
South Asian · 2/82,510 alleles
Filtering AF
0.000402%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000217%
Overall
0.000772%
12/1,554,614 alleles · very rare
exomes 10/1,402,594 · genomes 2/152,020 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00242% | 41,255 |
| East Asian | 0.00228% | 43,880 |
| Admixed American | 0.00191% | 52,490 |
| European (non-Finnish) | 0.000697% | 143,572 |
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.Pro480=
- Coding
- c.1440G>A
- MANE Select
- NM_004630
- dbSNP
- rs1592451188
- Type
- single nucleotide variant
- Location
- chr11:64767042 (GRCh38)
- Gene constraint
- LOEUF 0.22 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 65.28 · 10 PDB
- Residue 480
- the 'disordered' region
Similar variants
- SF1 p.Pro480Leu 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-pro480 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown