NUSAP1

protein-coding

nucleolar and spindle associated protein 1

Gene summary

NUSAP1 is a nucleolar-spindle-associated protein that plays a role in spindle microtubule organization (Raemaekers et al., 2003 [PubMed 12963707]).[supplied by OMIM, Jun 2009]

MANE transcript

NM_016359.5

Inheritance

—

ClinVar variants

P:2U:68B:7

Top phenotype

Microcephaly, seizures, and developmental delay

gnomAD constraint

pLI —, LoF o/e 0.3

Max pathogenic AF

—

Genomic locus

chr15:41,320,794-41,381,050

External References & Databases

Ensembl (ENSG00000137804)

Transcript & Mutation Effects

hg38 • Region Span ~60.3 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 NUSAP1 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 65

not providedTotal: 4

Microcephaly, seizures, and developmental delayTotal: 1

NUSAP1-associated neurodevelopmental disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_016359.5. 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				1 clinvar		1
missense			62 clinvar	6 clinvar		68
nonsense		2 clinvar	2 clinvar			4
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	2	68	7	0	77

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 76 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_016359.5	RefSeq	NP_057443.2	11	MANE Select
ENST00000559596.6	Ensembl	ENSP00000453403.1	11	MANE Select
NM_001243142.2	RefSeq	NP_001230071.1	11	Standard
NM_001243143.2	RefSeq	NP_001230072.1	11	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
nusap1	Danio rerio	Structure: post-vent region Quality: increased curvature abnormal

Gene / Model

Organism

Observed Phenotype

nusap1

Danio rerio

Structure: post-vent region

Quality: increased curvature

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

mitotic sister chromatid segregation
mitotic cytokinesis
mitotic chromosome condensation
establishment of mitotic spindle localization
positive regulation of mitotic nuclear division

Molecular Function

DNA binding
RNA binding
protein binding
microtubule binding

Cellular Component

chromosome
nucleolus
cytoplasm
spindle microtubule
mitotic spindle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000559596
Coding exons: 11
Length: 48357
Individuals with no LoFs: 124873
Homozygous LoFs: 0
Heterozygous LoFs: 19
Defined: 124892
p: 0.0000761

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.628	190	216	0.880	0.0000111	2845
Missense (PolyPhen)		46	53.534	0.85926		818
Synonymous	-0.0794	78	77.1	1.01	0.00000390	824
Loss of Function	2.89	6	19.9	0.302	9.31e-7	286

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000066	0.000064	rare
Latino/Admixed American	0.000091	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000071	0.000071	rare
South Asian	0.00020	0.00020	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Microtubule-associated protein with the capacity to bundle and stabilize microtubules (By similarity). May associate with chromosomes and promote the organization of mitotic spindle microtubules around them. {ECO:0000250, ECO:0000269|PubMed:12963707}.;

Recessive Scores

pRec: 0.0908

Intolerance Scores

LoFtool: 0.952
RVIS EVS: 0.37
RVIS percentile EVS: 75.43

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.882

Gene Damage Prediction

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