ESCO2 p.Val294=
c.882T>C · rs752508730 · VCV1157812
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0034%, nfe)
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 5.9 | GERP 0.55, phastCons 1 |
| Overall | ||
| CADD | 5.089 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0034%
European (non-Finnish) · 40/1,177,164 alleles
Filtering AF
0.00256%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00226%
Overall
0.00248%
40/1,610,048 alleles · very rare
exomes 40/1,457,756 · genomes 0/152,292 · joint denominator
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- ESCO2
- Protein
- p.Val294=
- Coding
- c.882T>C
- MANE Select
- NM_001017420
- dbSNP
- rs752508730
- Type
- single nucleotide variant
- Location
- chr8:27780194 (GRCh38)
- Gene constraint
- LOEUF 1.013 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 58.81
- Residue 294
- the 'disordered' region
Similar variants
- PBK p.Ile294Val 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-val294 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown