MAP6
Basic information
Region (hg38): 11:75586918-75669038
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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 | 5 | |||||
missense | 24 | 29 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 1 | |||||
Total | 0 | 0 | 24 | 7 | 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) | ||
11-75587436-C-T | not specified | Uncertain significance (Mar 18, 2024) | ||
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) | |||
11-75667702-C-T | not specified | Uncertain significance (Apr 23, 2024) | ||
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) |
GnomAD
Source:
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:
- 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