MEF2A p.Val379=
c.1137T>C · rs199613639 · VCV3043823
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.112%, 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 -0.88 | phastCons 0.004 |
| Overall | ||
| CADD | 0.764 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.112%
European (non-Finnish) · 1,272/1,132,294 alleles
Filtering AF
0.107%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.105%
Overall
0.0889%
1,360/1,530,620 alleles · rare
exomes 1,257/1,378,350 · genomes 103/152,270 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.112% | 890 |
| Middle Eastern | 0.068% | 1,471 |
| Remaining individualsnot grpmax-eligible | 0.0539% | 1,854 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0436% | 2,294 |
| Admixed American | 0.0397% | 2,517 |
| African / African-American | 0.0206% | 4,855 |
| South Asian | 0.00612% | 16,328 |
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
- MEF2A
- Protein
- p.Val379=
- Coding
- c.1137T>C
- MANE Select
- NM_001319206
- dbSNP
- rs199613639
- Type
- single nucleotide variant
- Location
- chr15:99712390 (GRCh38)
- Gene constraint
- LOEUF 0.762 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 55.90 · 10 PDB
Similar variants
- MEF2A p.Asn261Ser Benign/Likely benign ★★ same type
- MEF2A p.Ile479Val Benign/Likely benign ★★ same type
- MEF2A p.Pro433= Benign ★★ same type
- MEF2A p.Pro277Leu Pathogenic ★ same type
- MEF2A c.610+2T>A Uncertain significance ★ same type
- MEF2A p.Ala502Thr Uncertain significance ★ same type
- MEF2A p.Arg409Trp Uncertain significance ★ same type
- MEF2A p.Arg411Cys 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/mef2a-p-val379 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown