MAP4

microtubule associated protein 4

Basic information

Region (hg38): 3:47850690-48089272

Links

ENSG00000047849 ∙ NCBI:4134 ∙ OMIM:157132 ∙ HGNC:6862 ∙ Uniprot:P27816 ∙ 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 MAP4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MAP4 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				14	3	17
missense			58	7	7	72
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding				4	1	5
Total	0	0	58	25	11

Variants in MAP4

This is a list of pathogenic ClinVar variants found in the MAP4 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-47852796-T-C		MAP4-related disorder	Benign (Apr 11, 2019)
3-47852834-C-T		MAP4-related disorder	Likely benign (Sep 17, 2024)
3-47852865-C-T			Likely benign (Jul 01, 2022)
3-47852890-C-T		MAP4-related disorder	Likely benign (Dec 05, 2022)
3-47853229-G-A		not specified	Uncertain significance (Sep 10, 2024)
3-47853249-G-A		not specified	Uncertain significance (May 05, 2023)
3-47853257-G-A		MAP4-related disorder	Likely benign (Sep 05, 2019)
3-47853294-G-A		not specified	Likely benign (Jan 06, 2023)
3-47853313-G-C		not specified	Uncertain significance (Nov 03, 2023)
3-47853323-C-T		MAP4-related disorder	Likely benign (May 24, 2019)
3-47853325-G-C		not specified	Uncertain significance (Jun 30, 2024)
3-47853328-G-A		not specified	Uncertain significance (May 09, 2023)
3-47853334-C-T		not specified	Uncertain significance (Dec 21, 2023)
3-47853343-C-G		not specified	Uncertain significance (Jan 11, 2023)
3-47855286-C-T		not specified	Uncertain significance (Aug 26, 2022)
3-47867251-C-G		not specified	Uncertain significance (Jul 07, 2022)
3-47867325-G-A		MAP4-related disorder	Likely benign (Jun 01, 2024)
3-47869220-C-T		MAP4-related disorder	Likely benign (Feb 09, 2023)
3-47869221-G-T		not specified	Uncertain significance (Sep 26, 2022)
3-47869238-A-G		MAP4-related disorder	Likely benign (Mar 25, 2019)
3-47869248-G-A		not specified	Uncertain significance (Feb 10, 2023)
3-47869253-G-A		MAP4-related disorder	Likely benign (Jul 25, 2019)
3-47869283-C-G		not specified	Uncertain significance (Apr 15, 2024)
3-47869287-C-T		not specified	Uncertain significance (Aug 15, 2023)
3-47869294-T-C		not specified	Uncertain significance (Apr 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MAP4	protein_coding	protein_coding	ENST00000360240	18	238588

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.848	0.152	125724	0	23	125747	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.690	577	626	0.922	0.0000317	7442
Missense in Polyphen		139	170.97	0.81302		2130
Synonymous	0.722	226	240	0.941	0.0000134	2407
Loss of Function	4.81	8	41.4	0.193	0.00000194	578

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000354	0.000354
Ashkenazi Jewish	0.00	0.00
East Asian	0.000238	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.0000543	0.0000527
Middle Eastern	0.000238	0.000217
South Asian	0.0000800	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Non-neuronal microtubule-associated protein. Promotes microtubule assembly. {ECO:0000269|PubMed:10791892}.
• Pathway: Taxane Pathway, Pharmacokinetics;Splicing factor NOVA regulated synaptic proteins (Consensus)

Recessive Scores

• pRec: 0.147

Intolerance Scores

• loftool: 0.146
• rvis_EVS: 0.41
• rvis_percentile_EVS: 76.56

Haploinsufficiency Scores

• pHI: 0.108
• hipred: N
• hipred_score: 0.273
• ghis: 0.473

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.838

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Map4
• Phenotype: normal phenotype

Gene ontology

• Biological process: microtubule cytoskeleton organization;mitotic spindle organization;neuron projection development;microtubule sliding;establishment of spindle orientation;cell division;negative regulation of non-motile cilium assembly
• Cellular component: cytosol;microtubule;microtubule associated complex;plasma membrane;axoneme;postsynaptic density;microtubule cytoskeleton;axon;neuron projection;mitotic spindle
• Molecular function: RNA binding;structural molecule activity;protein binding;microtubule binding