MBD4 p.Phe459fs
c.1376_1377del · VCV3642431
Pathogenic
Multiple submitters
Classification
Pathogenic
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 5 of 8 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 12 | GERP 2.1, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- MBD4
- Protein
- p.Phe459fs
- Coding
- c.1376_1377del
- MANE Select
- NM_001276270
- Type
- Deletion
- Location
- chr3:129433866 (GRCh38)
- Gene constraint
- LOEUF 1.023 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 60.67 · 19 PDB
- Residue 459
- 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); an α-helix
Similar variants
- MBD4 p.Phe459Leu Uncertain significance ★★ ⚠ same residue
- MBD4 p.Phe459Cys Uncertain significance ★ ⚠ same residue
- MBD4 p.Arg251fs Pathogenic ★★ same condition
- MBD4 p.Arg83fs Pathogenic ★★ same condition
- MBD4 p.Gln259_Ser260insTer Pathogenic ★★ same condition
- MBD4 p.Gln283fs Pathogenic ★★ same condition
- MBD4 p.Leu476fs Pathogenic ★★ same condition
- MBD4 p.Lys312fs 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/mbd4-p-phe459fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown