MAP1S

microtubule associated protein 1S

Basic information

Region (hg38): 19:17719242-17734513

Previous symbols: [ "C19orf5", "VCY2IP1", "BPY2IP1" ]

Links

ENSG00000130479 ∙ NCBI:55201 ∙ OMIM:607573 ∙ HGNC:15715 ∙ Uniprot:Q66K74 ∙ 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 MAP1S gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MAP1S 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					1	1
missense			76	7		83
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	76	7	1

Variants in MAP1S

This is a list of pathogenic ClinVar variants found in the MAP1S region.

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

Position	Type	Phenotype	Significance	ClinVar
19-17719515-G-A		not specified	Likely benign (Aug 15, 2023)
19-17719524-G-C		not specified	Uncertain significance (Dec 14, 2021)
19-17719525-G-T		not specified	Uncertain significance (Sep 16, 2021)
19-17719534-C-G		not specified	Uncertain significance (Jun 05, 2023)
19-17719542-A-G		not specified	Uncertain significance (Oct 24, 2023)
19-17719597-A-T		not specified	Uncertain significance (Feb 28, 2024)
19-17720965-G-T		not specified	Uncertain significance (May 26, 2022)
19-17720992-G-A		not specified	Uncertain significance (Dec 17, 2023)
19-17720998-G-C		not specified	Uncertain significance (Aug 02, 2023)
19-17724142-C-A		not specified	Uncertain significance (May 22, 2024)
19-17724146-C-T		not specified	Uncertain significance (Mar 29, 2023)
19-17724165-C-T		not specified	Uncertain significance (Dec 16, 2023)
19-17724170-G-A		not specified	Uncertain significance (Aug 15, 2023)
19-17725869-C-T		not specified	Likely benign (Dec 28, 2022)
19-17725906-C-G		not specified	Uncertain significance (May 11, 2022)
19-17725965-G-A		not specified	Uncertain significance (Jun 10, 2024)
19-17726261-C-T		not specified	Uncertain significance (Jun 29, 2023)
19-17726342-G-T		not specified	Uncertain significance (May 24, 2023)
19-17726343-G-A		not specified	Uncertain significance (Oct 12, 2022)
19-17726352-A-G		not specified	Uncertain significance (Apr 04, 2024)
19-17726390-G-A		not specified	Uncertain significance (Dec 20, 2023)
19-17726415-C-T		not specified	Uncertain significance (Mar 14, 2023)
19-17726417-G-A		not specified	Uncertain significance (Oct 26, 2022)
19-17726433-G-A		not specified	Uncertain significance (May 05, 2023)
19-17726505-G-A		not specified	Uncertain significance (Jan 23, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MAP1S	protein_coding	protein_coding	ENST00000324096	7	15275

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.420	0.580	125722	0	24	125746	0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.535	633	672	0.942	0.0000482	6469
Missense in Polyphen		180	253.96	0.70878		2710
Synonymous	-2.27	374	322	1.16	0.0000250	2407
Loss of Function	3.76	6	27.1	0.221	0.00000150	310

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000187	0.000182
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000480	0.0000462
European (Non-Finnish)	0.000119	0.000114
Middle Eastern	0.00	0.00
South Asian	0.000137	0.000131
Other	0.000335	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Microtubule-associated protein that mediates aggregation of mitochondria resulting in cell death and genomic destruction (MAGD). Plays a role in anchoring the microtubule organizing center to the centrosomes. Binds to DNA. Plays a role in apoptosis. Involved in the formation of microtubule bundles (By similarity). {ECO:0000250, ECO:0000269|PubMed:15899810, ECO:0000269|PubMed:17234756}.

Recessive Scores

• pRec: 0.129

Haploinsufficiency Scores

• pHI: 0.150
• hipred: Y
• hipred_score: 0.594
• ghis: 0.475

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.675

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Map1s
• Phenotype: 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); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); cellular phenotype; muscle phenotype

Gene ontology

• Biological process: microtubule cytoskeleton organization;microtubule bundle formation;DNA metabolic process;autophagy;apoptotic process;nervous system development;axonogenesis;brain development;regulation of chromatin disassembly;dendrite development;regulation of microtubule depolymerization;mitochondrion transport along microtubule;neuron projection morphogenesis
• Cellular component: nucleus;nucleolus;spindle;cytosol;microtubule;microtubule associated complex;cell junction;dendrite;cell projection;neuronal cell body;synapse;perinuclear region of cytoplasm
• Molecular function: DNA binding;actin binding;deoxyribonuclease activity;protein binding;microtubule binding;tubulin binding;identical protein binding;beta-tubulin binding;actin filament binding