HMG20B
protein-codinghigh mobility group 20B, the group of Non-canonical high mobility group
Gene summary
Predicted to enable DNA binding activity. Predicted to be involved in regulation of gene expression. Predicted to act upstream of or within negative regulation of protein sumoylation; positive regulation of neuron differentiation; and skeletal muscle cell differentiation. Located in nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~6.3 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to HMG20B variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_006339.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 45 | 1 | 46 | |||
| nonsense | 2 | 2 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 49 | 1 | 0 | 50 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_006330.2 | 9 | MANE Select | |
| Ensembl | ENSP00000328269.6 | 9 | MANE Select | |
| Ensembl | ENSP00000262949.7 | 7 | Standard | |
| Ensembl | ENSP00000410924.1 | 7 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Factors involved in megakaryocyte development and platelet production
- HDACs deacetylate histones
- Chromatin modifying enzymes
- Hemostasis
- Chromatin organization
Biological Process
- regulation of transcription by RNA polymerase II
- cell cycle
- blood coagulation
- histone deacetylation
- negative regulation of protein sumoylation
Molecular Function
- DNA-binding transcription factor activity, RNA polymerase II-specific
- DNA binding
- histone deacetylase activity
- protein binding
- protein heterodimerization activity
Cellular Component
- nucleoplasm
- chromosome
- nuclear body
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000333651
- Coding exons
- 9
- Length
- 6312
- Individuals with no LoFs
- 124635
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 3
- Defined
- 124638
- p
- 0.0000120
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.23 | 121 | 213 | 0.569 | 0.0000146 | 2023 |
| Missense (PolyPhen) | 24 | 72.736 | 0.32996 | 670 | ||
| Synonymous | -0.964 | 104 | 92.2 | 1.13 | 0.00000665 | 598 |
| Loss of Function | 3.14 | 3 | 16.9 | 0.177 | 7.28e-7 | 201 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000018 | 0.000018 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Required for correct progression through G2 phase of the cell cycle and entry into mitosis. Required for RCOR1/CoREST mediated repression of neuronal specific gene promoters.;
Intolerance Scores
- LoFtool
- 0.589
- RVIS EVS
- -0.21
- RVIS percentile EVS
- 38.28
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.980
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |