MBD4 p.Pro31=
c.93G>A · VCV4104655
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.56e-05%, nfe)
Conditions
1
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -3.2 | GERP -4.4 |
| Overall | ||
| CADD | 2.373 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.56e-05%
European (non-Finnish) · 1/1,167,878 alleles
Overall
6.29e-05%
1/1,589,352 alleles · very rare
exomes 1/1,437,074 · genomes 0/152,278 · 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.Pro31=
- Coding
- c.93G>A
- MANE Select
- NM_001276270
- Type
- single nucleotide variant
- Location
- chr3:129439741 (GRCh38)
- Gene constraint
- LOEUF 1.023 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 60.67 · 19 PDB
- Residue 31
- the 'disordered' region
Similar variants
- MBD4 p.Pro31Ser Uncertain significance ★ ⚠ same residue
- MBD4 p.Pro31Ala Uncertain significance ★ ⚠ same residue
- 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
- MBD4 p.Arg400Ter 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-pro31 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown