MEF2C p.Arg413=
c.1239C>A · rs2546727379 · VCV3002134
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
neurodevelopmental disorder with hypotonia, stereotypic hand movements, and impaired language
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.075 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 8.7 | GERP 0.82, phastCons 1 |
| Overall | ||
| CADD | 11.9 | 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
- MEF2C
- Protein
- p.Arg413=
- Coding
- c.1239C>A
- MANE Select
- NM_002397
- dbSNP
- rs2546727379
- Type
- single nucleotide variant
- Location
- chr5:88722787 (GRCh38)
- Gene constraint
- LOEUF 0.212 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 56.80
- Residue 413
- the 'disordered' region
Similar variants
- MEF2C c.638-1G>A Pathogenic/Likely pathogenic ★★ same condition
- MEF2C c.638-2A>C Pathogenic ★★ same condition
- MEF2C c.965-2A>G Pathogenic ★★ same condition
- MEF2C c.-26C>T Pathogenic ★★ same condition
- MEF2C c.-8C>T Pathogenic ★★ same condition
- MEF2C p.Arg15Cys Pathogenic/Likely pathogenic ★★ same condition
- MEF2C p.Arg15His Pathogenic/Likely pathogenic ★★ same condition
- MEF2C p.Arg15Pro Pathogenic ★★ same condition
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/mef2c-p-arg413 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown