MAP6

microtubule associated protein 6

Basic information

Region (hg38): 11:75586917-75669038

Links

ENSG00000171533 ∙ NCBI:4135 ∙ OMIM:601783 ∙ HGNC:6868 ∙ Uniprot:Q96JE9 ∙ 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 MAP6 gene.

• Inborn genetic diseases (23 variants)
• not provided (7 variants)
• not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MAP6 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				3	2	5
missense			21	3	1	25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	21	6	4

Variants in MAP6

This is a list of pathogenic ClinVar variants found in the MAP6 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-75587161-C-T			Benign (Apr 04, 2018)
11-75587282-C-T		not specified	Likely benign (Sep 30, 2015)
11-75587424-C-T		not specified	Uncertain significance (Jun 06, 2023)
11-75587469-C-G		not specified	Uncertain significance (Oct 24, 2023)
11-75587499-G-T		not specified	Uncertain significance (Dec 03, 2021)
11-75587561-G-A		not specified	Likely benign (May 08, 2023)
11-75587703-A-G		not specified	Likely benign (May 25, 2022)
11-75587752-A-G			Benign (Nov 12, 2018)
11-75587919-C-T		not specified	Uncertain significance (Jun 02, 2023)
11-75588093-G-T		not specified	Uncertain significance (Aug 30, 2022)
11-75605876-C-T			Benign/Likely benign (Apr 01, 2023)
11-75605886-G-A		not specified	Likely benign (Jan 29, 2024)
11-75605894-T-C			Likely benign (Jan 01, 2023)
11-75605991-C-T		not specified	Uncertain significance (Feb 23, 2023)
11-75606128-G-A			Benign (Jun 20, 2021)
11-75608173-T-C		not specified	Uncertain significance (Nov 22, 2023)
11-75608306-A-G		not specified	Uncertain significance (Jan 26, 2022)
11-75667609-A-C		not specified	Uncertain significance (Sep 14, 2021)
11-75667629-A-C			Benign (Jun 09, 2021)
11-75667802-T-A		not specified	Uncertain significance (May 08, 2023)
11-75667808-C-T		not specified	Uncertain significance (Dec 14, 2021)
11-75667829-A-C		not specified	Uncertain significance (Aug 09, 2021)
11-75667925-G-C		not specified	Uncertain significance (Nov 15, 2021)
11-75667954-G-T		not specified	Uncertain significance (Nov 06, 2023)
11-75667960-C-G		not specified	Uncertain significance (Nov 08, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MAP6	protein_coding	protein_coding	ENST00000304771	4	82203

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.395	0.603	125741	0	7	125748	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.39	280	353	0.793	0.0000179	5182
Missense in Polyphen		74	119.8	0.61772		1891
Synonymous	1.00	120	135	0.890	0.00000750	1716
Loss of Function	2.67	3	13.6	0.220	5.89e-7	215

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000904	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.000218	0.000217
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in microtubule stabilization in many cell types, including neuronal cells (By similarity). Specifically has microtubule cold stabilizing activity (By similarity). Involved in dendrite morphogenesis and maintenance by regulating lysosomal trafficking via its interaction with TMEM106B (PubMed:24357581). Regulates KIF5A-mediated axonal cargo transport (By similarity). Regulates axonal growth during neuron polarization (By similarity). {ECO:0000250|UniProtKB:Q63560, ECO:0000269|PubMed:24357581}.

Recessive Scores

• pRec: 0.0730

Haploinsufficiency Scores

• pHI: 0.0655
• hipred: N
• hipred_score: 0.373
• ghis: 0.469

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.216

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Map6
• 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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)

Gene ontology

• Biological process: microtubule cytoskeleton organization;cytoskeleton-dependent intracellular transport;lysosome localization;dendrite morphogenesis;positive regulation of axonogenesis;regulation of microtubule cytoskeleton organization
• Cellular component: Golgi-associated vesicle;cis-Golgi network;microtubule;axon;dendrite;transport vesicle membrane;perinuclear region of cytoplasm
• Molecular function: protein binding;calmodulin binding;microtubule binding