NUSAP1

nucleolar and spindle associated protein 1

Basic information

Region (hg38): 15:41320794-41381050

Links

ENSG00000137804 ∙ NCBI:51203 ∙ OMIM:612818 ∙ HGNC:18538 ∙ Uniprot:Q9BXS6 ∙ 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 NUSAP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NUSAP1 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			16	3		19
nonsense		1				1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			7	1		8
Total	0	1	23	5	0

Variants in NUSAP1

This is a list of pathogenic ClinVar variants found in the NUSAP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-41331951-G-C		not specified	Uncertain significance (Aug 10, 2021)
15-41332258-C-A		not specified	Uncertain significance (Apr 09, 2024)
15-41332407-G-A		not specified	Uncertain significance (Dec 22, 2023)
15-41332425-C-T		not specified	Uncertain significance (Nov 27, 2023)
15-41332447-A-G		not specified	Uncertain significance (Apr 20, 2023)
15-41332492-T-G		not specified	Uncertain significance (May 27, 2022)
15-41332504-A-T		not specified	Uncertain significance (Mar 18, 2024)
15-41332524-G-A		not specified	Uncertain significance (Dec 21, 2022)
15-41332527-C-T		not specified	Likely benign (Sep 16, 2021)
15-41332530-C-T		not specified	Uncertain significance (Nov 09, 2021)
15-41349099-A-G		not specified	Uncertain significance (Jan 19, 2024)
15-41349124-T-G			Likely benign (Apr 01, 2022)
15-41349227-G-T		not specified	Uncertain significance (Nov 18, 2022)
15-41351022-C-A		not specified	Uncertain significance (Jun 26, 2023)
15-41351052-G-T		not specified	Uncertain significance (Dec 21, 2023)
15-41351082-C-A		not specified	Uncertain significance (Jul 12, 2022)
15-41351098-G-T		not specified	Uncertain significance (Jan 18, 2023)
15-41351102-C-A		not specified	Uncertain significance (Jan 24, 2023)
15-41351121-T-A		not specified	Uncertain significance (Apr 07, 2022)
15-41356056-G-A		not specified	Uncertain significance (Dec 20, 2023)
15-41356123-C-T		not specified	Uncertain significance (Apr 08, 2024)
15-41358159-G-C		not specified	Uncertain significance (Mar 08, 2024)
15-41365430-G-A		not specified	Uncertain significance (Feb 22, 2023)
15-41365502-G-A		not specified	Likely benign (Jun 03, 2022)
15-41365535-G-A		not specified	Uncertain significance (Sep 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NUSAP1	protein_coding	protein_coding	ENST00000559596	11	48357

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0457	0.953	124873	0	19	124892	0.0000761

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.628	190	216	0.880	0.0000111	2845
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000157	0.000155
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000715	0.0000707
Middle Eastern	0.00	0.00
South Asian	0.000199	0.000196
Other	0.000165	0.000165

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.620
• hipred: N
• hipred_score: 0.145
• ghis: 0.593

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.882

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nusap1
• 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); embryo phenotype; growth/size/body region phenotype; cellular phenotype

Zebrafish Information Network

• Gene name: nusap1
• Affected structure: post-vent region
• Phenotype tag: abnormal
• Phenotype quality: increased curvature

Gene ontology

• Biological process: mitotic sister chromatid segregation;mitotic cytokinesis;mitotic chromosome condensation;establishment of mitotic spindle localization;positive regulation of mitotic nuclear division
• Cellular component: chromosome;nucleolus;cytoplasm;spindle microtubule;mitotic spindle
• Molecular function: DNA binding;RNA binding;protein binding;microtubule binding