MEF2C p.Asp100=
c.300C>T · rs1561876666 · VCV590110
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00133%, afr)
Conditions
1
Inborn genetic diseases
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 1.6 | GERP -1.6, phastCons 1 |
| Overall | ||
| CADD | 6.921 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00133%
African / African-American · 1/74,932 alleles
Overall
6.2e-05%
1/1,613,888 alleles · very rare
exomes 0/1,461,676 · genomes 1/152,212 · 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
- MEF2C
- Protein
- p.Asp100=
- Coding
- c.300C>T
- MANE Select
- NM_002397
- dbSNP
- rs1561876666
- Type
- single nucleotide variant
- Location
- chr5:88761287 (GRCh38)
- Gene constraint
- LOEUF 0.212 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 56.80
- Residue 100
- the 'disordered' region
Similar variants
- MEF2C c.638-2A>C Pathogenic ★★ same condition
- MEF2C p.Arg189Ter Pathogenic/Likely pathogenic ★★ same condition
- MEF2C p.Leu38Pro Pathogenic ★★ same condition
- MEF2C p.Gly185Ser Uncertain significance ★★ ⚠ same condition
- MEF2C p.Met12Val Uncertain significance ★★ ⚠ same condition
- MEF2C p.Pro219Thr Uncertain significance ★★ ⚠ same condition
- MEF2C p.Ala103= Likely benign ★★ same condition
- MEF2C p.Asn214= Benign/Likely benign ★★ 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-asp100 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown