PYROXD1 p.Pro45del
c.133_135del · rs1555137914 · VCV2074705
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no gnomAD frequency available for this variant
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 4.2 | GERP 0.41, phastCons 1 |
Population frequency
dbSNP / gnomAD
No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- PYROXD1
- Protein
- p.Pro45del
- Coding
- c.133_135del
- MANE Select
- NM_024854
- dbSNP
- rs1555137914
- Type
- Deletion
- Location
- chr12:21440414 (GRCh38)
- Gene constraint
- LOEUF 1.107 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 88.64 · 2 PDB
- Residue 45
- a β-strand
Similar variants
- PYROXD1 p.Cys111fs Pathogenic/Likely pathogenic ★★ same type
- PYROXD1 p.Val298fs Pathogenic/Likely pathogenic ★★ same type
- RECQL p.Arg644_Lys645del Uncertain significance ★★ same type
- RECQL p.Lys643del Uncertain significance ★★ same type
- RECQL p.Thr566del Uncertain significance ★★ same type
- RECQL c.1797+14_1797+17del Benign/Likely benign ★★ same type
- RECQL c.1798-5del Benign ★★ same type
- PYROXD1 c.1254+1del Likely 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/pyroxd1-p-pro45del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown