MESP2 p.Ser261=
c.783G>T · rs1345819596 · VCV1571587
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/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.60 | acceptor gain · deltas |
|---|---|---|
| Pangolin | Δ0.39 | gain · loss 0.00 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 0.031 | GERP -4.2 |
| Overall | ||
| CADD | 17.2 | 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
- MESP2
- Protein
- p.Ser261=
- Coding
- c.783G>T
- MANE Select
- NM_001039958
- dbSNP
- rs1345819596
- Type
- single nucleotide variant
- Location
- chr15:89777140 (GRCh38)
- Gene constraint
- LOEUF 1.656 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 54.92
- Residue 261
- the 'disordered' region
Similar variants
- MESP2 p.Ser261Leu Uncertain significance ★ ⚠ same residue
- MESP2 p.Gly77Ter Pathogenic/Likely pathogenic ★★ same type
- MESP2 p.Gly81Ter Pathogenic/Likely pathogenic ★★ same type
- MESP2 p.Ser39Ter Pathogenic/Likely pathogenic ★★ same type
- MESP2 p.Ser42Ter Pathogenic/Likely pathogenic ★★ same type
- MESP2 p.Ser4Ter Pathogenic/Likely pathogenic ★★ same type
- MESP2 c.*107T>C Uncertain significance ★★ same type
- MESP2 p.Ala360Thr 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/mesp2-p-ser261 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown