ESCO2 p.Arg9=
c.27G>A · rs2486624257 · VCV1969115
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 | <0.2 | all four deltas below 0.2 · G>T here scores Δ0.45 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 4.5 | GERP -0.46, phastCons 1 |
| Overall | ||
| CADD | 9.752 | 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
- ESCO2
- Protein
- p.Arg9=
- Coding
- c.27G>A
- MANE Select
- NM_001017420
- dbSNP
- rs2486624257
- Type
- single nucleotide variant
- Location
- chr8:27775541 (GRCh38)
- Gene constraint
- LOEUF 1.013 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 58.81
Similar variants
- ESCO2 p.Arg9Lys Uncertain significance ★★ ⚠ same residue
- ESCO2 c.1013+1G>A Likely pathogenic ★★ same type
- ESCO2 c.1131+1G>A Pathogenic ★★ same type
- ESCO2 c.1131+1G>T Pathogenic ★★ same type
- ESCO2 c.1132-7A>G Pathogenic/Likely pathogenic ★★ same type
- ESCO2 c.1353+1G>A Likely pathogenic ★★ same type
- ESCO2 c.1353+1G>T Likely pathogenic ★★ same type
- ESCO2 p.Arg169Ter 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/esco2-p-arg9 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown