MAP2

protein-coding

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

Gene summary

This gene encodes a protein that belongs to the microtubule-associated protein family. The proteins of this family are thought to be involved in microtubule assembly, which is an essential step in neurogenesis. The products of similar genes in rat and mouse are neuron-specific cytoskeletal proteins that are enriched in dentrites, implicating a role in determining and stabilizing dentritic shape during neuron development. A number of alternatively spliced variants encoding distinct isoforms have been described. [provided by RefSeq, Jan 2010]

MANE transcript

NM_001375505.1

Inheritance

—

ClinVar variants

U:217B:37

Top phenotype

MAP2-associated Neurodevelopmental Disorder

gnomAD constraint

pLI —, LoF o/e 0.03

Max pathogenic AF

—

Genomic locus

chr2:209,424,047-209,734,147

External References & Databases

Ensembl (ENSG00000078018)

Transcript & Mutation Effects

hg38 • Region Span ~310.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to MAP2 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 210

not providedTotal: 39

MAP2-associated Neurodevelopmental DisorderTotal: 1

Rett syndromeTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001375505.1. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	13 clinvar	6 clinvar	21
missense			205 clinvar	13 clinvar	5 clinvar	223
nonsense						0
start loss						0
frameshift			6 clinvar			6
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	217	26	11	254

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 168 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001375505.1	RefSeq	NP_001362434.1	12	MANE Select
ENST00000682079.1	Ensembl	ENSP00000507035.1	12	MANE Select
NM_001039538.2	RefSeq	NP_001034627.1	11	Standard
NM_001363910.2	RefSeq	NP_001350839.1	12	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Taxane Pathway, Pharmacokinetics
Melatonin metabolism and effects
MAPK Cascade
Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways
LKB1 signaling events

Biological Process

microtubule cytoskeleton organization
microtubule bundle formation
axonogenesis
dendrite development
central nervous system neuron development

Molecular Function

dystroglycan binding
structural molecule activity
protein binding
calmodulin binding
microtubule binding

Cellular Component

nucleolus
cytoplasm
cytosol
microtubule
microtubule associated complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000360351
Coding exons: 12
Length: 310061
Individuals with no LoFs: 125547
Homozygous LoFs: 0
Heterozygous LoFs: 2
Defined: 125549
p: 0.00000797

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.884	885	962	0.920	0.0000486	11944
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000027	0.000018	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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.;

Recessive Scores

pRec: 0.255

Intolerance Scores

LoFtool: 0.316
RVIS EVS: -1.31
RVIS percentile EVS: 4.82

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.714

Gene Damage Prediction

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