MESP2 p.Gln53=
c.159G>A · rs2141774049 · VCV1583926
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000524%, 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 0.43 | GERP -0.15 |
| Overall | ||
| CADD | 6.131 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000524%
European (non-Finnish) · 6/1,145,756 alleles
Filtering AF
0.000188%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000124%
Overall
0.000391%
6/1,533,360 alleles · very rare
exomes 6/1,381,008 · genomes 0/152,352 · 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
- MESP2
- Protein
- p.Gln53=
- Coding
- c.159G>A
- MANE Select
- NM_001039958
- dbSNP
- rs2141774049
- Type
- single nucleotide variant
- Location
- chr15:89776516 (GRCh38)
- Gene constraint
- LOEUF 1.656 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 54.92
- Residue 53
- the 'disordered' region
Similar variants
- MESP2 p.Gln53Ter 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-gln53 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown