MESP2 p.Val138=
c.414G>T · rs1249240936 · VCV1097078
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00148%, 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 1.9 | GERP -2.1, phastCons 1 |
| Overall | ||
| CADD | 9.433 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00148%
European (non-Finnish) · 17/1,145,076 alleles
Filtering AF
0.000904%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000739%
Overall
0.00118%
18/1,530,010 alleles · very rare
exomes 18/1,377,646 · genomes 0/152,364 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00148% | 67,357 |
| African / African-American | 0.00144% | 69,572 |
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.Val138=
- Coding
- c.414G>T
- MANE Select
- NM_001039958
- dbSNP
- rs1249240936
- Type
- single nucleotide variant
- Location
- chr15:89776771 (GRCh38)
- Gene constraint
- LOEUF 1.656 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 54.92
- Residue 138
- a UniProt-annotated variant site (in)
Similar variants
- MESP2 p.Val138Met Benign ★★ same residue
- MESP2 p.Val138Leu Uncertain significance ⚠ same residue
- MESP2 p.Val138fs Pathogenic ★ 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
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-val138 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown