MYO5B
Basic information
Region (hg38): 18:49822789-50195164
Links
Phenotypes
GenCC
Source:
- microvillus inclusion disease (Definitive), mode of inheritance: AR
- microvillus inclusion disease (Strong), mode of inheritance: AR
- microvillus inclusion disease (Supportive), mode of inheritance: AR
- progressive familial intrahepatic cholestasis type 1 (Supportive), mode of inheritance: AR
- microvillus inclusion disease (Strong), mode of inheritance: AR
- cholestasis, progressive familial intrahepatic, 10 (Strong), mode of inheritance: AR
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Diarrhea 2, with microvillus atrophy, with or without cholestasis; Cholestasis, progressive familial intrahepatic 10 | AR | Gastrointestinal; Renal | Individuals with Diarrhea 2, with microvillus atrophy, with or without cholestasis may require nutritional support with parenteral nutrition; Renal fanconi syndrome has been described, and appropriate care of related sequelae may be beneficial; Individuals with progressive familial intrahepatic cholestasis 10 or with cholestasis as part of Diarrhea 2, with microvillus atrophy. with or without cholestasis may benefit from medical management (eg, with ursodeoxycholic acid), but may require surgical intervention (eg, with biliary diversion); Liver transplant has been described | Gastrointestinal; Renal | 16800870; 19006234; 18724368; 21199752; 20186687; 22030065; 21206382; 22441677; 27532546; 28027573; 32304554; 33525641 |
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (29 variants)
- Congenital microvillous atrophy (10 variants)
- Cholestasis, progressive familial intrahepatic, 10 (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the MYO5B 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 | 288 | 14 | 310 | |||
missense | 500 | 21 | 15 | 542 | ||
nonsense | 16 | 21 | ||||
start loss | 0 | |||||
frameshift | 13 | 16 | ||||
inframe indel | 6 | |||||
splice donor/acceptor (+/-2bp) | 9 | |||||
splice region | 1 | 28 | 42 | 3 | 74 | |
non coding | 154 | 167 | 146 | 467 | ||
Total | 33 | 15 | 671 | 476 | 176 |
Highest pathogenic variant AF is 0.0000263
Variants in MYO5B
This is a list of pathogenic ClinVar variants found in the MYO5B region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
18-49822831-T-C | Congenital microvillous atrophy | Uncertain significance (Jan 13, 2018) | ||
18-49822927-G-A | Congenital microvillous atrophy | Uncertain significance (Mar 30, 2018) | ||
18-49823043-A-G | Congenital microvillous atrophy | Uncertain significance (Jan 12, 2018) | ||
18-49823048-C-A | Congenital microvillous atrophy | Uncertain significance (Jan 13, 2018) | ||
18-49823080-T-C | Congenital microvillous atrophy | Uncertain significance (Jan 12, 2018) | ||
18-49823090-C-G | Congenital microvillous atrophy | Uncertain significance (Jan 13, 2018) | ||
18-49823092-T-G | Congenital microvillous atrophy | Uncertain significance (Jan 12, 2018) | ||
18-49823103-C-G | Congenital microvillous atrophy | Benign (Jan 13, 2018) | ||
18-49823106-A-G | Congenital microvillous atrophy | Uncertain significance (Jan 15, 2018) | ||
18-49823107-T-C | Congenital microvillous atrophy | Uncertain significance (Jan 12, 2018) | ||
18-49823114-C-T | Congenital microvillous atrophy | Uncertain significance (Jan 12, 2018) | ||
18-49823120-T-G | Congenital microvillous atrophy | Uncertain significance (Jan 13, 2018) | ||
18-49823129-G-C | Congenital microvillous atrophy | Uncertain significance (Jan 13, 2018) | ||
18-49823130-A-G | Congenital microvillous atrophy | Uncertain significance (Jan 12, 2018) | ||
18-49823132-A-ACTTT | Diarrhea with Microvillus Atrophy | Uncertain significance (Jun 14, 2016) | ||
18-49823154-G-A | Congenital microvillous atrophy | Uncertain significance (Jan 13, 2018) | ||
18-49823156-A-G | Congenital microvillous atrophy | Uncertain significance (Jan 12, 2018) | ||
18-49823171-T-C | Congenital microvillous atrophy | Uncertain significance (Jan 13, 2018) | ||
18-49823176-A-AT | Diarrhea with Microvillus Atrophy | Uncertain significance (Jun 14, 2016) | ||
18-49823179-A-G | Congenital microvillous atrophy | Uncertain significance (Jan 12, 2018) | ||
18-49823189-C-T | Congenital microvillous atrophy | Uncertain significance (Jan 12, 2018) | ||
18-49823198-C-G | Congenital microvillous atrophy | Uncertain significance (Jan 12, 2018) | ||
18-49823198-C-T | Congenital microvillous atrophy | Benign (Jan 12, 2018) | ||
18-49823232-T-C | Congenital microvillous atrophy | Uncertain significance (Jan 13, 2018) | ||
18-49823251-G-A | Congenital microvillous atrophy | Uncertain significance (Jan 13, 2018) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
MYO5B | protein_coding | protein_coding | ENST00000285039 | 40 | 372281 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
3.38e-23 | 1.00 | 124735 | 0 | 112 | 124847 | 0.000449 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -0.616 | 1051 | 996 | 1.05 | 0.0000645 | 12201 |
Missense in Polyphen | 353 | 385.14 | 0.91655 | 4693 | ||
Synonymous | -1.68 | 440 | 397 | 1.11 | 0.0000253 | 3415 |
Loss of Function | 4.13 | 53 | 96.9 | 0.547 | 0.00000483 | 1186 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00114 | 0.00113 |
Ashkenazi Jewish | 0.000398 | 0.000397 |
East Asian | 0.00111 | 0.00106 |
Finnish | 0.000233 | 0.000232 |
European (Non-Finnish) | 0.000362 | 0.000362 |
Middle Eastern | 0.00111 | 0.00106 |
South Asian | 0.000556 | 0.000556 |
Other | 0.000495 | 0.000494 |
dbNSFP
Source:
- Function
- FUNCTION: May be involved in vesicular trafficking via its association with the CART complex. The CART complex is necessary for efficient transferrin receptor recycling but not for EGFR degradation. Required in a complex with RAB11A and RAB11FIP2 for the transport of NPC1L1 to the plasma membrane. Together with RAB11A participates in CFTR trafficking to the plasma membrane and TF (transferrin) recycling in nonpolarized cells. Together with RAB11A and RAB8A participates in epithelial cell polarization. Together with RAB25 regulates transcytosis. {ECO:0000269|PubMed:21206382, ECO:0000269|PubMed:21282656}.;
- Disease
- DISEASE: Diarrhea 2, with microvillus atrophy (DIAR2) [MIM:251850]: A disease characterized by onset of intractable life-threatening watery diarrhea during infancy. Two forms are recognized: early-onset microvillus inclusion disease with diarrhea beginning in the neonatal period, and late-onset, with first symptoms appearing after 3 or 4 months of life. {ECO:0000269|PubMed:18724368, ECO:0000269|PubMed:19006234, ECO:0000269|PubMed:20186687, ECO:0000269|PubMed:21206382, ECO:0000269|PubMed:24138727, ECO:0000269|PubMed:24892806}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.180
Intolerance Scores
- loftool
- 0.0862
- rvis_EVS
- -0.37
- rvis_percentile_EVS
- 28.21
Haploinsufficiency Scores
- pHI
- 0.247
- hipred
- Y
- hipred_score
- 0.706
- ghis
- 0.501
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.668
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | High | High | High |
Primary Immunodeficiency | High | High | High |
Cancer | High | High | High |
Mouse Genome Informatics
- Gene name
- Myo5b
- Phenotype
- homeostasis/metabolism phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); 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); growth/size/body region phenotype; digestive/alimentary phenotype;
Zebrafish Information Network
- Gene name
- myo5b
- Affected structure
- enterocyte
- Phenotype tag
- abnormal
- Phenotype quality
- columnar
Gene ontology
- Biological process
- renal water homeostasis;protein transport;vesicle-mediated transport;endosomal transport
- Cellular component
- myosin complex;cytoplasmic vesicle membrane;protein-containing complex;apical cortex;recycling endosome;extracellular exosome
- Molecular function
- microfilament motor activity;protein binding;calmodulin binding;ATP binding;Rab GTPase binding;actin filament binding