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.

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.

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				2	1	3
missense			81	5		86
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	81	7	1

Variants in CLSPN

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

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

Position	Type	Phenotype	Significance	ClinVar
1-35736524-C-T		not specified	Likely benign (Nov 13, 2023)
1-35736567-G-A		not specified	Uncertain significance (Jan 16, 2025)
1-35736601-C-G		not specified	Uncertain significance (Jun 29, 2023)
1-35736990-C-T		not specified	Uncertain significance (Feb 04, 2025)
1-35736993-G-A		not specified	Uncertain significance (Sep 11, 2024)
1-35737358-C-G		not specified	Uncertain significance (Apr 18, 2023)
1-35737369-A-C		not specified	Uncertain significance (Apr 08, 2024)
1-35737382-A-G		not specified	Uncertain significance (Mar 05, 2025)
1-35737399-C-G		not specified	Uncertain significance (May 15, 2024)
1-35737403-A-G		not specified	Uncertain significance (Dec 12, 2024)
1-35737410-T-C		not specified	Likely benign (Mar 03, 2025)
1-35738037-T-C		not specified	Uncertain significance (Jan 10, 2023)
1-35738071-T-A		Myoepithelial tumor	Uncertain significance (Nov 01, 2022)
1-35738457-T-C		not specified	Uncertain significance (Nov 30, 2022)
1-35738568-T-C		not specified	Uncertain significance (Jun 30, 2024)
1-35739231-C-T		not specified	Uncertain significance (Sep 11, 2024)
1-35739426-C-T		not specified	Uncertain significance (May 13, 2024)
1-35739446-A-G		not specified	Uncertain significance (Jun 16, 2023)
1-35739465-C-T		not specified	Uncertain significance (Jun 17, 2024)
1-35739471-C-T		not specified	Uncertain significance (Sep 10, 2024)
1-35743189-T-A		not specified	Uncertain significance (Mar 11, 2022)
1-35743214-G-C		not specified	Uncertain significance (Nov 07, 2023)
1-35743465-T-C		not specified	Uncertain significance (Mar 17, 2023)
1-35743517-C-T		not specified	Uncertain significance (Sep 07, 2022)
1-35745457-G-A		not specified	Uncertain significance (Nov 16, 2021)

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