CLASP2

cytoplasmic linker associated protein 2, the group of TOG domain containing

Basic information

Region (hg38): 3:33496245-33718356

Links

ENSG00000163539 ∙ NCBI:23122 ∙ OMIM:605853 ∙ HGNC:17078 ∙ Uniprot:O75122 ∙ 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 CLASP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLASP2 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				10	4	14
missense			43		5	48
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1	2		3
non coding			1	2	2	5
Total	0	0	44	12	11

Variants in CLASP2

This is a list of pathogenic ClinVar variants found in the CLASP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-33498666-C-G		not specified	Uncertain significance (Dec 20, 2022)
3-33501703-C-T		CLASP2-related disorder	Benign (Mar 26, 2019)
3-33501760-A-G		CLASP2-related disorder	Likely benign (Apr 26, 2019)
3-33510618-C-T			Likely benign (Apr 06, 2018)
3-33510655-T-A		not specified	Uncertain significance (Sep 22, 2023)
3-33510667-T-C		not specified	Uncertain significance (Aug 08, 2022)
3-33510734-C-G		not specified	Uncertain significance (Mar 22, 2022)
3-33517048-A-C		not specified	Uncertain significance (Dec 20, 2022)
3-33517081-T-C		CLASP2-related disorder	Benign (Oct 28, 2019)
3-33535234-G-A		CLASP2-related disorder	Likely benign (Sep 10, 2019)
3-33535337-G-A		not specified	Uncertain significance (Dec 11, 2023)
3-33535340-C-T		not specified	Uncertain significance (Jul 26, 2022)
3-33535343-G-A		not specified	Uncertain significance (Dec 14, 2022)
3-33535392-G-A		not specified	Uncertain significance (Jul 14, 2023)
3-33535444-C-T		CLASP2-related disorder	Likely benign (Jun 17, 2019)
3-33538797-C-T		not specified	Uncertain significance (Apr 26, 2023)
3-33538798-A-C		not specified	Uncertain significance (Jun 23, 2023)
3-33538839-C-T		not specified	Uncertain significance (Jun 02, 2023)
3-33538850-C-T		not specified	Uncertain significance (Nov 05, 2021)
3-33543456-T-C		CLASP2-related disorder	Likely benign (Sep 19, 2019)
3-33543517-G-A		CLASP2-related disorder	Benign (Mar 15, 2019)
3-33544715-T-C		not specified	Uncertain significance (Dec 27, 2023)
3-33544819-G-A		not specified	Uncertain significance (Jan 08, 2024)
3-33544831-G-A		not specified	Uncertain significance (Jan 08, 2024)
3-33559354-T-C		not specified	Uncertain significance (Jan 23, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLASP2	protein_coding	protein_coding	ENST00000468888	39	222112

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	5.49e-7	124640	0	14	124654	0.0000562

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.87	466	768	0.607	0.0000397	9745
Missense in Polyphen		210	397.48	0.52833		5163
Synonymous	0.134	263	266	0.990	0.0000129	2948
Loss of Function	7.49	10	84.2	0.119	0.00000507	1037

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000900	0.0000900
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000932	0.0000928
European (Non-Finnish)	0.0000751	0.0000708
Middle Eastern	0.00	0.00
South Asian	0.0000384	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Microtubule plus-end tracking protein that promotes the stabilization of dynamic microtubules (PubMed:26003921). Involved in the nucleation of noncentrosomal microtubules originating from the trans-Golgi network (TGN). Required for the polarization of the cytoplasmic microtubule arrays in migrating cells towards the leading edge of the cell. May act at the cell cortex to enhance the frequency of rescue of depolymerizing microtubules by attaching their plus-ends to cortical platforms composed of ERC1 and PHLDB2 (PubMed:16824950). This cortical microtubule stabilizing activity is regulated at least in part by phosphatidylinositol 3-kinase signaling. Also performs a similar stabilizing function at the kinetochore which is essential for the bipolar alignment of chromosomes on the mitotic spindle (PubMed:16866869, PubMed:16914514). Acts as a mediator of ERBB2- dependent stabilization of microtubules at the cell cortex. {ECO:0000269|PubMed:11290329, ECO:0000269|PubMed:15631994, ECO:0000269|PubMed:16824950, ECO:0000269|PubMed:16866869, ECO:0000269|PubMed:16914514, ECO:0000269|PubMed:17543864, ECO:0000269|PubMed:20937854, ECO:0000269|PubMed:26003921}.
• Pathway: Developmental Biology;Signal Transduction;Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal;Amplification of signal from the kinetochores;Mitotic Spindle Checkpoint;Cell Cycle Checkpoints;RHO GTPases Activate Formins;RHO GTPase Effectors;Signaling by Rho GTPases;Signaling by ROBO receptors;Mitotic Prometaphase;Separation of Sister Chromatids;Mitotic Anaphase;Mitotic Metaphase and Anaphase;Axon guidance;M Phase;Cell Cycle;Resolution of Sister Chromatid Cohesion;Role of ABL in ROBO-SLIT signaling;Cell Cycle, Mitotic (Consensus)

Recessive Scores

• pRec: 0.146

Haploinsufficiency Scores

• pHI: 0.484
• hipred: Y
• hipred_score: 0.800
• ghis: 0.634

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.606

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Clasp2
• Phenotype: cellular phenotype

Gene ontology

• Biological process: microtubule cytoskeleton organization;vesicle targeting;microtubule nucleation;negative regulation of microtubule depolymerization;Golgi organization;mitotic spindle organization;establishment or maintenance of cell polarity;exit from mitosis;regulation of gastrulation;positive regulation of epithelial cell migration;regulation of epithelial to mesenchymal transition;microtubule organizing center organization;regulation of microtubule polymerization or depolymerization;regulation of microtubule-based process;microtubule anchoring;positive regulation of exocytosis;cell division;negative regulation of stress fiber assembly;negative regulation of focal adhesion assembly;protein localization to plasma membrane;positive regulation of extracellular matrix disassembly;negative regulation of wound healing, spreading of epidermal cells;positive regulation of basement membrane assembly involved in embryonic body morphogenesis
• Cellular component: kinetochore;condensed chromosome kinetochore;cytoplasm;Golgi apparatus;trans-Golgi network;microtubule organizing center;kinetochore microtubule;cytosol;microtubule;cytoplasmic microtubule;plasma membrane;focal adhesion;cell cortex;membrane;cell leading edge;ruffle membrane;basal cortex;mitotic spindle
• Molecular function: dystroglycan binding;protein binding;microtubule binding;microtubule plus-end binding