MECP2 p.Arg20Ser
c.60A>C · rs2522549346 · VCV2430069
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no allele count reported in gnomAD v4.1 (AN 1,025,784)
Conditions
1
Developmental disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.435 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 7.1 | GERP 1.1, phastCons 1 |
| Regional constraint | o/e 1.06 | unconstrained · MANE · 65 kb · p 0.54 · regional, not allelic |
| Overall | ||
| CADD | 25.8 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 1,025,784). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- MECP2
- Protein
- p.Arg20Ser
- Coding
- c.60A>C
- MANE Select
- NM_001110792
- dbSNP
- rs2522549346
- Type
- single nucleotide variant
- Location
- chrX:154097606 (GRCh38)
- Structure
- AlphaFold pLDDT 57.25 · 11 PDB
- Residue 20
- the 'disordered' region
Similar variants
- MECP2 p.Arg20fs Pathogenic ★ same residue
- MECP2 p.Ser362_Ser438del Uncertain significance ★ same condition
- MECP2 c.414-3C>G Pathogenic ★★★ same type
- MECP2 c.62+1G>A Pathogenic ★★★ same type
- MECP2 c.62+2T>G Pathogenic ★★★ same type
- MECP2 p.Ala143Asp Pathogenic ★★★ same type
- MECP2 p.Ala291Val Likely pathogenic ★★★ ⚠ same type
- MECP2 p.Arg127His 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/mecp2-p-arg20ser (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown