MEGF10 p.Arg613=
c.1839G>A · rs199930517 · VCV262066
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 4.8 | GERP -0.48, phastCons 1 |
| Overall | ||
| CADD | 13.37 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Remaining individualsnot grpmax-eligible | 0.0372% | 2,690 |
| European (non-Finnish)grpmax | 0.0265% | 3,770 |
| African / African-American | 0.00671% | 14,898 |
| Admixed American | 0.00172% | 58,306 |
| South Asian | 0.00113% | 88,404 |
Remaining individuals shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.
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
- MEGF10
- Protein
- p.Arg613=
- Coding
- c.1839G>A
- MANE Select
- NM_001256545
- dbSNP
- rs199930517
- Type
- single nucleotide variant
- Location
- chr5:127433508 (GRCh38)
- Gene constraint
- LOEUF 0.707 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 70.73
- Residue 613
- the 'necessary for interaction with ap2m1, self-assembly and formation of the irregular, mosaic-like adhesion pattern' region
Disease context
MEGF10-related myopathy — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Early-onset myopathy-areflexia-respiratory distress-dysphagia syndrome (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Infancy, Neonatal
Similar variants
- MEGF10 c.2104+1G>T Likely pathogenic ★★ same condition
- MEGF10 p.Cys774Arg Pathogenic/Likely pathogenic ★★ same condition
- MEGF10 p.Glu398Ter Pathogenic/Likely pathogenic ★★ same condition
- MEGF10 c.1426+5G>T Uncertain significance ★★ same condition
- MEGF10 c.*1170G>A Uncertain significance ★★ same condition
- MEGF10 p.Ala171Thr Uncertain significance ★★ ⚠ same condition
- MEGF10 p.Ala171Val Uncertain significance ★★ ⚠ same condition
- MEGF10 p.Ala219Val Uncertain significance ★★ ⚠ 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/megf10-p-arg613 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown