MAP1B
microtubule associated protein 1B, the group of Protein phosphatase 1 regulatory subunits
Basic information
Region (hg38): 5:72107234-72209565
Links
Phenotypes
GenCC
Source:
- periventricular nodular heterotopia 9 (Strong), mode of inheritance: AD
- periventricular nodular heterotopia (Supportive), mode of inheritance: AD
- periventricular nodular heterotopia 9 (Strong), mode of inheritance: AD
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Periventricular nodular heterotopia 9; Deafness, autosomal dominant 83 | AD | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Audiologic/Otolaryngologic; Neurologic | 29738522; 30150678; 31317654; 33268592 |
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn_genetic_diseases (239 variants)
- not_provided (203 variants)
- MAP1B-related_disorder (105 variants)
- Periventricular_nodular_heterotopia_9 (66 variants)
- Hearing_loss,_autosomal_dominant_83 (21 variants)
- not_specified (16 variants)
- Periventricular_nodular_heterotopia (7 variants)
- Cognitive_impairment (3 variants)
- White_matter_deficit (3 variants)
- Hypoplasia_of_the_corpus_callosum (3 variants)
- Autism_spectrum_disorder (2 variants)
- Pyloric_stenosis (1 variants)
- Neurodevelopmental_disorder (1 variants)
- Periventricular_cysts (1 variants)
- Chromosome_5Q14.3_deletion_syndrome,_distal (1 variants)
- Metopic_synostosis (1 variants)
- Global_developmental_delay (1 variants)
- Attention_deficit_hyperactivity_disorder (1 variants)
- EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)
- Hypotonia (1 variants)
- Abnormal_facial_shape (1 variants)
- Macrocephaly (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the MAP1B gene is commonly pathogenic or not. These statistics are base on transcript: NM_000005909.5. 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 | 65 | 12 | 77 | |||
| missense | 359 | 62 | 431 | |||
| nonsense | 18 | |||||
| start loss | 0 | |||||
| frameshift | 10 | 11 | 24 | |||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 19 | 21 | 363 | 127 | 20 |
Highest pathogenic variant AF is 0.00006381289
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| MAP1B | protein_coding | protein_coding | ENST00000296755 | 7 | 102335 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 9.78e-10 | 125736 | 0 | 11 | 125747 | 0.0000437 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.51 | 1051 | 1.31e+3 | 0.804 | 0.0000695 | 16127 |
| Missense in Polyphen | 296 | 399.3 | 0.7413 | 5032 | ||
| Synonymous | -0.0515 | 522 | 521 | 1.00 | 0.0000316 | 4927 |
| Loss of Function | 7.72 | 5 | 79.1 | 0.0632 | 0.00000476 | 1092 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000180 | 0.000180 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000352 | 0.0000352 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Facilitates tyrosination of alpha-tubulin in neuronal microtubules (By similarity). Phosphorylated MAP1B may play a role in the cytoskeletal changes that accompany neurite extension. Possibly MAP1B binds to at least two tubulin subunits in the polymer, and this bridging of subunits might be involved in nucleating microtubule polymerization and in stabilizing microtubules. Acts as a positive cofactor in DAPK1-mediated autophagic vesicle formation and membrane blebbing. {ECO:0000250, ECO:0000269|PubMed:18195017}.;
- Pathway
- Regulation of Microtubule Cytoskeleton;Netrin-mediated signaling events;Reelin signaling pathway;Lissencephaly gene (LIS1) in neuronal migration and development
(Consensus)
Recessive Scores
- pRec
- 0.373
Intolerance Scores
- loftool
- 0.253
- rvis_EVS
- -2.22
- rvis_percentile_EVS
- 1.35
Haploinsufficiency Scores
- pHI
- 0.928
- hipred
- Y
- hipred_score
- 0.824
- ghis
- 0.574
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.718
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Map1b
- Phenotype
- reproductive 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); limbs/digits/tail phenotype; vision/eye phenotype; growth/size/body region 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); homeostasis/metabolism phenotype; cellular phenotype;
Zebrafish Information Network
- Gene name
- map1b
- Affected structure
- neural tube
- Phenotype tag
- abnormal
- Phenotype quality
- increased width
Gene ontology
- Biological process
- microtubule cytoskeleton organization;microtubule bundle formation;neuron migration;axonogenesis;cellular process;dendrite development;regulation of microtubule depolymerization;negative regulation of intracellular transport;positive regulation of axon extension;mitochondrion transport along microtubule;axon extension;establishment of monopolar cell polarity
- Cellular component
- photoreceptor outer segment;cytosol;microtubule;microtubule associated complex;plasma membrane;postsynaptic density;cell junction;axon;dendrite;somatodendritic compartment;cell projection;neuronal cell body;dendritic spine;synapse;apical dendrite;basal dendrite;hippocampal mossy fiber
- Molecular function
- actin binding;structural molecule activity;protein binding;microtubule binding;tubulin binding