MBD4 p.Arg486=
c.1456A>C · rs2530700773 · VCV3053345
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
MBD4-related disorder
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 4.6 | GERP 0.23, phastCons 1 |
| Overall | ||
| CADD | 16.46 | 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
- MBD4
- Protein
- p.Arg486=
- Coding
- c.1456A>C
- MANE Select
- NM_001276270
- dbSNP
- rs2530700773
- Type
- single nucleotide variant
- Location
- chr3:129433185 (GRCh38)
- Gene constraint
- LOEUF 1.023 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 60.67 · 19 PDB
- Residue 486
- a UniProt-annotated variant site (in tpds2; no mbd4 protein detected by immunohistochemical analysis in patient tumor tissue); a UniProt-annotated variant site (in uvm1); a UniProt-annotated variant site (in tpds2)
Disease context
MBD4-related disorder
Similar variants
- MBD4 c.1647+60C>T Likely benign same condition
- MED1 p.Arg249Pro Likely benign same condition
- MED1 p.Tyr102fs Uncertain significance same condition
- MBD4 c.104+1G>A Likely pathogenic ★★ same type
- MBD4 c.1544-1G>A Likely pathogenic ★★ same type
- MBD4 c.1544-1G>T Pathogenic/Likely pathogenic ★★ same type
- MBD4 c.1544-2A>G Likely pathogenic ★★ same type
- MBD4 c.335+1G>A Likely 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/mbd4-p-arg486 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown