MBTD1
Basic information
Region (hg38): 17:51177425-51260163
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (41 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the MBTD1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000017643.3. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 41 | 41 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 41 | 0 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| MBTD1 | protein_coding | protein_coding | ENST00000586178 | 15 | 82739 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 9.56e-7 | 125686 | 0 | 1 | 125687 | 0.00000398 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.45 | 150 | 325 | 0.462 | 0.0000164 | 4136 |
| Missense in Polyphen | 31 | 106.48 | 0.29114 | 1351 | ||
| Synonymous | 0.847 | 99 | 110 | 0.897 | 0.00000609 | 1140 |
| Loss of Function | 5.76 | 0 | 38.6 | 0.00 | 0.00000218 | 458 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Putative Polycomb group (PcG) protein. PcG proteins maintain the transcriptionally repressive state of genes, probably via a modification of chromatin, rendering it heritably changed in its expressibility (By similarity). Specifically binds to monomethylated and dimethylated 'Lys-20' on histone H4. {ECO:0000250, ECO:0000269|PubMed:19841675}.;
- Disease
- DISEASE: Note=A chromosomal aberration involving MBTD1 is a cause of acute poorly differentiated myeloid leukemia. Translocation (10;17)(p15;q21) with ZMYND11. {ECO:0000269|PubMed:23915195}.;
- Pathway
- Mesodermal Commitment Pathway
(Consensus)
Recessive Scores
- pRec
- 0.0830
Intolerance Scores
- loftool
- 0.119
- rvis_EVS
- 0.06
- rvis_percentile_EVS
- 58.53
Haploinsufficiency Scores
- pHI
- 0.360
- hipred
- Y
- hipred_score
- 0.731
- ghis
- 0.541
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.943
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Mbtd1
- Phenotype
- craniofacial phenotype; skeleton phenotype; liver/biliary system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype;
Gene ontology
- Biological process
- chromatin organization;regulation of transcription, DNA-templated;embryonic skeletal system development
- Cellular component
- nucleus
- Molecular function
- zinc ion binding;methylated histone binding