MAP1A

protein-coding

microtubule associated protein 1A

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 product of this gene is a precursor polypeptide that presumably undergoes proteolytic processing to generate the final MAP1A heavy chain and LC2 light chain. Expression of this gene is almost exclusively in the brain. Studies of the rat microtubule-associated protein 1A gene suggested a role in early events of spinal cord development. [provided by RefSeq, Jul 2008]

Previous symbols:

MAP1L

MANE transcript

NM_002373.6

Inheritance

—

ClinVar variants

P:1U:407B:34

Top phenotype

MAP1A-related disorder

gnomAD constraint

pLI —, LoF o/e 0.11

Max pathogenic AF

—

Genomic locus

chr15:43,510,958-43,531,620

External References & Databases

Ensembl (ENSG00000166963)

Transcript & Mutation Effects

hg38 • Region Span ~20.7 kb

Loading mutation effect viewer...

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 MAP1A variants in ClinVar

5 Conditions Cataloged

not specifiedTotal: 405

not providedTotal: 20

MAP1A-related disorderTotal: 20

Neurodevelopmental disorderTotal: 1

Inborn genetic diseasesTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_002373.6. 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				9 clinvar	1 clinvar	10
missense			396 clinvar	22 clinvar	2 clinvar	420
nonsense			2 clinvar			2
start loss						0
frameshift	1 clinvar		9 clinvar			10
splice donor/acceptor (+/-2bp)						0
Total	1	0	407	31	3	442

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 6 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_002373.6	RefSeq	NP_002364.5	3	MANE Select
ENST00000300231.6	Ensembl	ENSP00000300231.5	3	MANE Select
NM_001411089.1	RefSeq	NP_001398018.1	7	Standard
ENST00000382031.5	Ensembl	ENSP00000371462.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

microtubule cytoskeleton organization
axonogenesis
memory
associative learning
dendrite development

Molecular Function

actin binding
structural molecule activity
protein binding
microtubule binding
cytoskeletal adaptor activity

Cellular Component

cytoplasm
cytosol
microtubule
microtubule associated complex
axon

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000300231
Coding exons: 3
Length: 20663
Individuals with no LoFs: 124826
Homozygous LoFs: 0
Heterozygous LoFs: 21
Defined: 124847
p: 0.0000841

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.01	1297	1.52e+3	0.855	0.0000843	18093
Missense (PolyPhen)		525	686.3	0.76497		8311
Synonymous	1.41	551	595	0.926	0.0000312	5897
Loss of Function	7.45	9	81.6	0.110	0.00000445	1091

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.00013	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000056	0.000056	rare
Finnish	0.000093	0.000093	rare
European (Non-Finnish)	0.000099	0.000097	rare
South Asian	0.000098	0.000098	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Structural protein involved in the filamentous cross- bridging between microtubules and other skeletal elements.;

Recessive Scores

pRec: 0.194

Intolerance Scores

LoFtool: 0.367
RVIS EVS: 1.16
RVIS percentile EVS: 92.61

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.353

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High