MAP2

microtubule associated protein 2, the group of A-kinase anchoring proteins

Basic information

Region (hg38): 2:209424046-209734147

Links

ENSG00000078018 ∙ NCBI:4133 ∙ OMIM:157130 ∙ HGNC:6839 ∙ Uniprot:P11137 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MAP2 gene.

• Inborn genetic diseases (49 variants)
• not provided (31 variants)
• not specified (1 variants)
• Rett syndrome (1 variants)
• MAP2-associated Neurodevelopmental Disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MAP2 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				13	5	18
missense			47	7	7	61
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					2	2
non coding						0
Total	0	0	48	20	12

Variants in MAP2

This is a list of pathogenic ClinVar variants found in the MAP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-209653183-C-T		not specified	Uncertain significance (Jul 09, 2021)
2-209653194-A-G			Likely benign (May 22, 2018)
2-209653223-C-T		not specified	Uncertain significance (Nov 02, 2023)
2-209653224-G-A			Likely benign (Oct 10, 2018)
2-209653275-C-T			Likely benign (Mar 29, 2018)
2-209653287-A-G			Likely benign (Jul 02, 2018)
2-209653298-G-A		not specified	Uncertain significance (Jan 07, 2022)
2-209653333-G-A			Benign (Dec 31, 2019)
2-209678673-G-C		not specified	Uncertain significance (Apr 05, 2023)
2-209692696-G-A			Benign (Dec 31, 2018)
2-209692706-A-G			Benign (Dec 31, 2019)
2-209692781-C-A		not specified	Uncertain significance (Oct 10, 2023)
2-209692904-T-G		not specified	Uncertain significance (Jun 05, 2023)
2-209692909-G-A		not specified	Uncertain significance (May 25, 2022)
2-209692982-C-T		not specified	Likely benign (Aug 16, 2022)
2-209693021-T-C		not specified	Uncertain significance (Mar 13, 2023)
2-209693045-T-G		not specified	Uncertain significance (Oct 26, 2022)
2-209693101-T-C		not specified	Uncertain significance (May 27, 2022)
2-209693258-A-G		not specified	Uncertain significance (Jun 10, 2022)
2-209693262-T-G		not specified	Uncertain significance (Dec 20, 2023)
2-209693272-A-G		not specified	Likely benign (Aug 23, 2021)
2-209693307-G-A		not specified	Uncertain significance (Dec 07, 2023)
2-209693345-A-G		not specified	Uncertain significance (Feb 15, 2023)
2-209693389-G-T			Benign (Dec 31, 2019)
2-209693410-G-T			Benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MAP2	protein_coding	protein_coding	ENST00000360351	12	310061

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	8.30e-9	125547	0	2	125549	0.00000797

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.884	885	962	0.920	0.0000486	11944
Missense in Polyphen		333	428.52	0.7771		5291
Synonymous	-0.583	367	353	1.04	0.0000187	3627
Loss of Function	6.95	2	60.1	0.0333	0.00000298	857

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000265	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: The exact function of MAP2 is unknown but MAPs may stabilize the microtubules against depolymerization. They also seem to have a stiffening effect on microtubules.
• Pathway: Taxane Pathway, Pharmacokinetics;Melatonin metabolism and effects;MAPK Cascade;Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways;LKB1 signaling events (Consensus)

Recessive Scores

• pRec: 0.255

Intolerance Scores

• loftool: 0.316
• rvis_EVS: -1.31
• rvis_percentile_EVS: 4.82

Haploinsufficiency Scores

• pHI: 0.286
• hipred: Y
• hipred_score: 0.594
• ghis: 0.607

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.714

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Map2
• Phenotype: endocrine/exocrine gland phenotype; growth/size/body region phenotype; 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); 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)

Gene ontology

• Biological process: microtubule cytoskeleton organization;microtubule bundle formation;axonogenesis;dendrite development;central nervous system neuron development;establishment of cell polarity;negative regulation of axon extension;regulation of microtubule polymerization;negative regulation of microtubule polymerization;neuron projection development;dendrite morphogenesis;cellular response to organic substance;positive regulation of anterograde dense core granule transport;regulation of organelle transport along microtubule;positive regulation of anterograde synaptic vesicle transport;regulation of cellular protein localization;negative regulation of microtubule binding;negative regulation of microtubule motor activity
• Cellular component: nucleolus;cytoplasm;cytosol;microtubule;microtubule associated complex;postsynaptic density;dendrite;dendrite cytoplasm;nuclear periphery;neuron projection;neuronal cell body;axon initial segment;dendritic shaft;axon hillock;dendritic growth cone;main axon;dendritic branch;basal dendrite;CA3 pyramidal cell dendrite;primary dendrite;distal dendrite;apical distal dendrite;dendritic filopodium;proximal dendrite;proximal neuron projection
• Molecular function: dystroglycan binding;structural molecule activity;protein binding;calmodulin binding;microtubule binding;tau protein binding