CSDE1 p.Pro249Leu
c.746C>T · VCV3378322
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
AlphaMissense
ambiguous
0.4395 · ACMG-weighted
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| AlphaMissense | 0.4395 | ambiguous |
|---|---|---|
| REVEL | 0.454 | indeterminate |
| SaProt | LLR -11.69 | damaging |
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 12 | GERP 2.6, phastCons 1 |
| Regional constraint | o/e 0.64 | unconstrained · MANE · 3,722 bp · p 6.9e-09 · regional, not allelic |
| Overall | ||
| CADD | 29.6 | PHRED · no single calibrated threshold — expert panels disagree |
AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- CSDE1
- Protein
- p.Pro249Leu
- Coding
- c.746C>T
- MANE Select
- NM_001007553
- Type
- single nucleotide variant
- Location
- chr1:114733823 (GRCh38)
- Gene constraint
- LOEUF 0.295 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 80.05 · 5 PDB
- Residue 249
- an α-helix
Similar variants
- CSDE1 p.Ala765Thr Uncertain significance ★★ ⚠ same type
- CSDE1 p.Arg132His Uncertain significance ★★ ⚠ same type
- CSDE1 p.Glu335Gly Uncertain significance ★★ ⚠ same type
- CSDE1 c.2053-4T>C Benign/Likely benign ★★ same type
- CSDE1 c.2350-5C>A Benign/Likely benign ★★ same type
- CSDE1 p.Phe699= Benign/Likely benign ★★ same type
- CSDE1 p.Ser75= Benign ★★ same type
- CSDE1 c.500+1G>C 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/csde1-p-pro249leu (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown