MAP1S

protein-coding

microtubule associated protein 1S

Gene summary

Enables DNA binding activity; WD40-repeat domain binding activity; and cytoskeletal protein binding activity. Involved in metaphase chromosome alignment; microtubule cytoskeleton organization; and neuron projection morphogenesis. Located in several cellular components, including microtubule cytoskeleton; nuclear lumen; and perinuclear region of cytoplasm. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

C19orf5
VCY2IP1
BPY2IP1

MANE transcript

NM_018174.6

Inheritance

—

ClinVar variants

U:217B:17

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.22

Max pathogenic AF

—

Genomic locus

chr19:17,719,242-17,734,513

External References & Databases

Ensembl (ENSG00000130479)

Transcript & Mutation Effects

hg38 • Region Span ~15.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to MAP1S variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 219

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018174.6. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			6 clinvar		1 clinvar	7
missense			207 clinvar	16 clinvar		223
nonsense			2 clinvar			2
start loss			1 clinvar			1
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	217	16	1	234

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 30 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018174.6	RefSeq	NP_060644.4	7	MANE Select
ENST00000324096.9	Ensembl	ENSP00000325313.3	7	MANE Select
NM_001308363.2	RefSeq	NP_001295292.1	7	Standard
ENST00000544059.2	Ensembl	ENSP00000439243.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

microtubule cytoskeleton organization
microtubule bundle formation
DNA metabolic process
autophagy
apoptotic process

Molecular Function

DNA binding
actin binding
deoxyribonuclease activity
protein binding
microtubule binding

Cellular Component

nucleus
nucleolus
spindle
cytosol
microtubule

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000324096
Coding exons: 7
Length: 15275
Individuals with no LoFs: 125722
Homozygous LoFs: 0
Heterozygous LoFs: 24
Defined: 125746
p: 0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.535	633	672	0.942	0.0000482	6469
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.00012	rare
Latino/Admixed American	0.000059	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.000048	0.000046	rare
European (Non-Finnish)	0.00012	0.00011	rare
South Asian	0.00014	0.00013	rare
Other	0.00034	0.00033	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.675

Gene Damage Prediction

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