PROS1 p.Glu55fs
c.162del · VCV4540905
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 2 of 15 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 7.5 | GERP 1.9, phastCons 1 |
| Region caveats | ||
| Repeat context | seg dup | · reads may not map uniquely · confidence, not pathogenicity |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- PROS1
- Protein
- p.Glu55fs
- Coding
- c.162del
- MANE Select
- NM_000313
- Type
- Deletion
- Location
- chr3:93927322 (GRCh38)
- Gene constraint
- LOEUF 0.53 · pLI 0.75 (gnomAD)
- Structure
- AlphaFold pLDDT 83.06 · 3 PDB
- Residue 55
- a modified residue (4-carboxyglutamate); the gla domain
Similar variants
- PROS1 p.Lys84fs Pathogenic ★★ same type
- PROS1 p.Lys674fs Uncertain significance ★★ same type
- PROS1 c.1323_1323+1del Likely pathogenic ★ same type
- PROS1 c.344_346+7del Likely pathogenic ★ same type
- PROS1 p.Ala24fs Likely pathogenic ★ same type
- PROS1 p.Asn659fs Pathogenic ★ same type
- PROS1 p.Asp176fs Pathogenic ★ same type
- PROS1 p.Gln51fs Pathogenic ★ 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/pros1-p-glu55fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown