CLSPN

claspin

Basic information

Region (hg38): 1:35720218-35769978

Links

ENSG00000092853

∙ NCBI:63967 ∙ OMIM:605434 ∙ HGNC:19715 ∙ Uniprot:Q9HAW4 ∙ 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 CLSPN gene.

not_specified (155 variants)
not_provided (4 variants)
Myoepithelial_tumor (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLSPN gene is commonly pathogenic or not. These statistics are base on transcript: NM_000022111.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				2 clinvar	1 clinvar	3
missense			151 clinvar	6 clinvar		157
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	151	8	1

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLSPN	protein_coding	protein_coding	ENST00000318121	25	49750

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00259	0.997	125591	0	157	125748	0.000624

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.854	616	679	0.908	0.0000337	8905
Missense in Polyphen		173	213.18	0.81152		2822
Synonymous	-0.0902	248	246	1.01	0.0000123	2393
Loss of Function	5.61	19	69.4	0.274	0.00000381	890

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00448	0.00445
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000121	0.000109
Finnish	0.00255	0.00254
European (Non-Finnish)	0.000142	0.000141
Middle Eastern	0.000121	0.000109
South Asian	0.000196	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Required for checkpoint mediated cell cycle arrest in response to inhibition of DNA replication or to DNA damage induced by both ionizing and UV irradiation. Adapter protein which binds to BRCA1 and the checkpoint kinase CHEK1 and facilitates the ATR- dependent phosphorylation of both proteins. Can also bind specifically to branched DNA structures and may associate with S- phase chromatin following formation of the pre-replication complex (pre-RC). This may indicate a role for this protein as a sensor which monitors the integrity of DNA replication forks. {ECO:0000269|PubMed:12766152, ECO:0000269|PubMed:15096610, ECO:0000269|PubMed:15190204, ECO:0000269|PubMed:15226314, ECO:0000269|PubMed:15707391}.;
Pathway: HDR through Homologous Recombination (HR) or Single Strand Annealing (SSA);DNA Repair;DNA Double-Strand Break Repair;Homology Directed Repair;Post-translational protein modification;Metabolism of proteins;Activation of ATR in response to replication stress;G2/M Checkpoints;Cell Cycle Checkpoints;Apoptotic cleavage of cellular proteins;Apoptotic execution phase;Apoptosis;Programmed Cell Death;Ub-specific processing proteases;Deubiquitination;Cell Cycle;PLK1 signaling events;Processing of DNA double-strand break ends;ATR signaling pathway (Consensus)

Intolerance Scores

loftool: 0.701
rvis_EVS: 0.74
rvis_percentile_EVS: 86.38

Haploinsufficiency Scores

pHI: 0.451
hipred: Y
hipred_score: 0.794
ghis: 0.409

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2: S
essential_gene_gene_trap: E
gene_indispensability_pred: E
gene_indispensability_score: 0.680

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Clspn
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);

Gene ontology

Biological process: DNA damage checkpoint;DNA replication;DNA repair;mitotic G2 DNA damage checkpoint;protein deubiquitination;peptidyl-serine phosphorylation;activation of protein kinase activity;mitotic DNA replication checkpoint
Cellular component: nucleoplasm;Golgi apparatus
Molecular function: DNA binding;protein binding;anaphase-promoting complex binding