HMG20B
Basic information
Region (hg38): 19:3572776-3579088
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the HMG20B gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 12 | 12 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 12 | 0 | 0 |
Variants in HMG20B
This is a list of pathogenic ClinVar variants found in the HMG20B region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 19-3573708-G-A | not specified | Uncertain significance (Jul 08, 2022) | ||
| 19-3574384-C-G | not specified | Uncertain significance (Oct 14, 2023) | ||
| 19-3574575-A-T | not specified | Uncertain significance (Apr 23, 2024) | ||
| 19-3576276-G-C | not specified | Uncertain significance (Nov 08, 2022) | ||
| 19-3576606-G-C | not specified | Uncertain significance (Jul 20, 2021) | ||
| 19-3576984-A-T | not specified | Uncertain significance (Aug 16, 2022) | ||
| 19-3577027-G-T | not specified | Uncertain significance (Feb 17, 2022) | ||
| 19-3577032-A-G | not specified | Uncertain significance (Jan 03, 2024) | ||
| 19-3577039-C-G | not specified | Uncertain significance (Dec 20, 2021) | ||
| 19-3577045-A-T | not specified | Uncertain significance (Dec 01, 2022) | ||
| 19-3577071-G-A | not specified | Uncertain significance (Jan 19, 2022) | ||
| 19-3578005-G-A | not specified | Uncertain significance (Nov 18, 2022) | ||
| 19-3578046-G-A | not specified | Uncertain significance (Apr 26, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| HMG20B | protein_coding | protein_coding | ENST00000333651 | 9 | 6312 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.691 | 0.309 | 124635 | 0 | 3 | 124638 | 0.0000120 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.23 | 121 | 213 | 0.569 | 0.0000146 | 2023 |
| Missense in 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 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000290 | 0.0000290 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000183 | 0.0000177 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
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.;
- Pathway
- Factors involved in megakaryocyte development and platelet production;HDACs deacetylate histones;Chromatin modifying enzymes;Hemostasis;Chromatin organization
(Consensus)
Intolerance Scores
- loftool
- 0.589
- rvis_EVS
- -0.21
- rvis_percentile_EVS
- 38.28
Haploinsufficiency Scores
- pHI
- 0.547
- hipred
- Y
- hipred_score
- 0.629
- ghis
- 0.637
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.980
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Hmg20b
- Phenotype
Gene ontology
- Biological process
- regulation of transcription by RNA polymerase II;cell cycle;blood coagulation;histone deacetylation;negative regulation of protein sumoylation;skeletal muscle cell differentiation;positive regulation of neuron differentiation
- Cellular component
- nucleoplasm;chromosome;nuclear body
- Molecular function
- DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;histone deacetylase activity;protein binding;protein heterodimerization activity