MAP1B

microtubule associated protein 1B, the group of Protein phosphatase 1 regulatory subunits

Basic information

Region (hg38): 5:72107233-72209565

Links

ENSG00000131711 ∙ NCBI:4131 ∙ OMIM:157129 ∙ HGNC:6836 ∙ Uniprot:P46821 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• 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: CGD

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 ClinVar and linked to the MAP1B gene.

• not provided (4 variants)
• Inborn genetic diseases (3 variants)
• 6 conditions (1 variants)
• Periventricular nodular heterotopia 9 (1 variants)
• Hearing loss, autosomal dominant 83;Periventricular nodular heterotopia 9 (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.

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				61	8	69
missense			166	40	9	215
nonsense	2	7	2			11
start loss			1			1
frameshift	7	7	2			16
inframe indel				2		2
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding			1	1		2
Total	9	14	172	104	17

Highest pathogenic variant AF is 0.00000657

Variants in MAP1B

This is a list of pathogenic ClinVar variants found in the MAP1B region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
5-72107531-G-C			Uncertain significance (Oct 09, 2022)
5-72107545-T-G		Periventricular nodular heterotopia 9	Uncertain significance (May 05, 2022)
5-72107548-T-C			Uncertain significance (Jan 28, 2022)
5-72107580-A-G		Inborn genetic diseases	Uncertain significance (Jun 27, 2023)
5-72107584-C-G		Inborn genetic diseases	Uncertain significance (Aug 11, 2021)
5-72107597-G-A		MAP1B-related disorder	Likely benign (Oct 28, 2019)
5-72107627-C-T		MAP1B-related disorder	Benign/Likely benign (Jul 12, 2019)
5-72107633-C-T		MAP1B-related disorder	Likely benign (Oct 12, 2021)
5-72107642-C-G			Uncertain significance (Jul 21, 2022)
5-72107682-C-T			Uncertain significance (Jul 01, 2022)
5-72107683-A-C			Uncertain significance (Aug 04, 2023)
5-72107706-A-G		Inborn genetic diseases	Conflicting classifications of pathogenicity (Mar 01, 2024)
5-72107707-T-C		Inborn genetic diseases	Uncertain significance (May 03, 2023)
5-72107723-G-A		MAP1B-related disorder	Benign/Likely benign (Mar 01, 2023)
5-72115704-G-A		MAP1B-related disorder	Uncertain significance (May 04, 2023)
5-72115706-T-A			Uncertain significance (Feb 26, 2023)
5-72115709-T-G			Uncertain significance (Aug 18, 2022)
5-72115748-C-T		Periventricular nodular heterotopia 9	Uncertain significance (Oct 31, 2023)
5-72115770-ACT-A		Periventricular nodular heterotopia 9	Likely pathogenic (Nov 24, 2023)
5-72183771-C-T			Likely benign (Jul 10, 2018)
5-72183772-G-A		MAP1B-related disorder	Benign (Dec 31, 2019)
5-72183803-CT-C			Uncertain significance (May 01, 2020)
5-72183825-G-C			Uncertain significance (Feb 14, 2023)
5-72186625-G-A			Uncertain significance (Apr 03, 2023)
5-72186637-T-C			Likely benign (Sep 10, 2018)

GnomAD

Source: gnomAD

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: dbNSFP

• 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