MAP1A

microtubule associated protein 1A

Basic information

Region (hg38): 15:43510957-43531620

Previous symbols: [ "MAP1L" ]

Links

ENSG00000166963 ∙ NCBI:4130 ∙ OMIM:600178 ∙ HGNC:6835 ∙ Uniprot:P78559 ∙ 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 MAP1A gene.

• Inborn genetic diseases (105 variants)
• not provided (12 variants)
• MAP1A-related condition (4 variants)
• Neurodevelopmental disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MAP1A 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				7	1	8
missense			105	4	1	110
nonsense			1			1
start loss						0
frameshift	1					1
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	1	0	107	11	2

Variants in MAP1A

This is a list of pathogenic ClinVar variants found in the MAP1A region.

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

Position	Type	Phenotype	Significance	ClinVar
15-43521483-G-A		not specified	Uncertain significance (May 18, 2022)
15-43521640-A-G		not specified	Uncertain significance (Feb 10, 2023)
15-43521859-C-T		not specified	Uncertain significance (Dec 13, 2023)
15-43521884-C-G		not specified	Uncertain significance (Nov 29, 2021)
15-43521922-G-A		not specified	Uncertain significance (Oct 12, 2022)
15-43521967-A-C		not specified	Uncertain significance (Jun 24, 2022)
15-43521971-A-C		not specified	Uncertain significance (Jun 24, 2022)
15-43521972-A-C		not specified	Uncertain significance (Jun 24, 2022)
15-43522243-A-G		not specified	Uncertain significance (Jul 17, 2023)
15-43522324-G-A		not specified	Uncertain significance (Dec 27, 2023)
15-43522342-G-A		not specified	Uncertain significance (Nov 18, 2022)
15-43522483-G-A		not specified	Uncertain significance (Sep 14, 2021)
15-43522486-A-G		not specified	Uncertain significance (Dec 20, 2023)
15-43522506-G-C		not specified	Uncertain significance (Feb 28, 2024)
15-43522820-G-T		not specified	Uncertain significance (Aug 28, 2023)
15-43522915-C-T		not specified	Uncertain significance (Feb 28, 2023)
15-43522919-A-G			Benign/Likely benign (Mar 01, 2023)
15-43522950-C-T		not specified	Uncertain significance (Jun 16, 2023)
15-43522977-C-G		not specified	Uncertain significance (Feb 03, 2022)
15-43523050-C-T		not specified	Uncertain significance (Dec 27, 2023)
15-43523092-G-T		not specified	Uncertain significance (Feb 05, 2024)
15-43523109-C-G		not specified	Uncertain significance (May 24, 2023)
15-43523127-A-G		Inborn genetic diseases	Uncertain significance (Jan 10, 2022)
15-43523173-G-C			Uncertain significance (Oct 21, 2021)
15-43523185-C-T		not specified	Uncertain significance (Oct 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MAP1A	protein_coding	protein_coding	ENST00000300231	3	20663

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	2.74e-7	124826	0	21	124847	0.0000841

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.01	1297	1.52e+3	0.855	0.0000843	18093
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000189	0.000187
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000556	0.0000556
Finnish	0.0000928	0.0000928
European (Non-Finnish)	0.0000995	0.0000971
Middle Eastern	0.0000556	0.0000556
South Asian	0.0000981	0.0000980
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.832
• hipred: N
• hipred_score: 0.328
• ghis: 0.580

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.353

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Map1a
• Phenotype: 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); hearing/vestibular/ear phenotype; cellular phenotype

Gene ontology

• Biological process: microtubule cytoskeleton organization;axonogenesis;memory;associative learning;dendrite development;regulation of microtubule depolymerization;negative regulation of proteasomal ubiquitin-dependent protein catabolic process;regulation of synaptic plasticity;voluntary musculoskeletal movement;neuron cellular homeostasis;anterograde axonal protein transport;retrograde axonal protein transport;negative regulation of protein localization to microtubule;positive regulation of cellular protein localization;neuron projection maintenance;positive regulation of protein localization to cell surface
• Cellular component: cytoplasm;cytosol;microtubule;microtubule associated complex;axon;dendrite;cell projection;neuron projection;neuronal cell body;axon initial segment;dendritic shaft;dendritic branch;synapse;primary dendrite;dendritic microtubule;axon cytoplasm
• Molecular function: actin binding;structural molecule activity;protein binding;microtubule binding;cytoskeletal adaptor activity;tubulin binding;tau protein binding