ESCO2 p.Ser244=
c.732T>C · rs764226665 · VCV1145978
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00178%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.7 | GERP 1.8, phastCons 0.97 |
| Overall | ||
| CADD | 8.204 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00178%
European (non-Finnish) · 21/1,179,350 alleles
Filtering AF
0.00114%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000971%
Overall
0.00137%
22/1,610,904 alleles · very rare
exomes 22/1,458,706 · genomes 0/152,198 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00178% | 56,160 |
| Admixed American | 0.00169% | 59,270 |
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.Ser244=
- Coding
- c.732T>C
- MANE Select
- NM_001017420
- dbSNP
- rs764226665
- Type
- single nucleotide variant
- Location
- chr8:27777040 (GRCh38)
- Gene constraint
- LOEUF 1.013 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 58.81
- Residue 244
- a modified residue (phosphoserine)
Similar variants
- 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
- ESCO2 p.Arg552Ter Pathogenic/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/esco2-p-ser244 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown