ORC4 p.Ser293=
c.879G>T · rs542121583 · VCV2103108
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.79 | GERP -3.4, phastCons 0.013 |
| Overall | ||
| CADD | 1.989 | PHRED · no single calibrated threshold — expert panels disagree |
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
- ORC4
- Protein
- p.Ser293=
- Coding
- c.879G>T
- MANE Select
- NM_181741
- dbSNP
- rs542121583
- Type
- single nucleotide variant
- Location
- chr2:147939219 (GRCh38)
- Gene constraint
- LOEUF 1.532 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 86.12 · 15 PDB
Similar variants
- ORC4 p.Ser293Trp Uncertain significance ★ ⚠ same residue
- ORC4 p.Ser208Ter Pathogenic/Likely pathogenic ★★ same type
- ORC4 p.Tyr174Cys Pathogenic/Likely pathogenic ★★ same type
- ORC4 p.Ala375Pro Uncertain significance ★★ ⚠ same type
- ORC4 p.Arg116Lys Uncertain significance ★★ ⚠ same type
- ORC4 p.Arg148Gln Uncertain significance ★★ ⚠ same type
- ORC4 p.Arg213Gln Uncertain significance ★★ same type
- ORC4 p.Arg25His 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/orc4-p-ser293 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown