MBD4 p.Asp261=
c.783T>C · rs1559800907 · VCV2876542
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00446%, eas)
Conditions
2
Inborn genetic diseases
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 -2 | GERP -4.1 |
| Overall | ||
| CADD | 0.097 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00446%
East Asian · 2/44,882 alleles
Filtering AF
0.000739%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000276%
Overall
0.000124%
2/1,614,124 alleles · very rare
exomes 0/1,461,808 · genomes 2/152,316 · 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
- MBD4
- Protein
- p.Asp261=
- Coding
- c.783T>C
- MANE Select
- NM_001276270
- dbSNP
- rs1559800907
- Type
- single nucleotide variant
- Location
- chr3:129436861 (GRCh38)
- Gene constraint
- LOEUF 1.023 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 60.67 · 19 PDB
- Residue 261
- 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)
Similar variants
- MBD4 p.Asp261Asn Conflicting classifications of pathogenicity ★ ⚠ same residue
- MBD4 p.Asp261Gly Uncertain significance ★ ⚠ same residue
- MBD4 c.104+1G>A Likely pathogenic ★★ same condition
- MBD4 c.1544-1G>A Likely pathogenic ★★ same condition
- MBD4 c.1544-1G>T Pathogenic/Likely pathogenic ★★ same condition
- MBD4 c.1544-2A>G Likely pathogenic ★★ same condition
- MBD4 c.335+1G>A Likely pathogenic ★★ same condition
- MBD4 p.Arg181Ter 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-asp261 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown