CTDSP1

CTD small phosphatase 1, the group of MicroRNA protein coding host genes|CTD family phosphatases

Basic information

Region (hg38): 2:218397136-218405941

Links

ENSG00000144579 ∙ NCBI:58190 ∙ OMIM:605323 ∙ HGNC:21614 ∙ Uniprot:Q9GZU7 ∙ 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 CTDSP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CTDSP1 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		1	17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	0	2

Variants in CTDSP1

This is a list of pathogenic ClinVar variants found in the CTDSP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-218400101-C-T		not specified	Uncertain significance (Apr 19, 2023)
2-218400123-C-G		not specified	Uncertain significance (Sep 07, 2022)
2-218400131-A-C		not specified	Uncertain significance (Oct 05, 2023)
2-218401638-C-G		not specified	Uncertain significance (Dec 06, 2021)
2-218401648-G-A		not specified	Uncertain significance (Apr 22, 2024)
2-218401656-C-G		not specified	Uncertain significance (Mar 08, 2024)
2-218401662-G-A			Benign (Jul 26, 2018)
2-218401663-C-T		not specified	Uncertain significance (May 14, 2024)
2-218401669-G-A		not specified	Uncertain significance (Jan 10, 2023)
2-218401670-C-T			Benign (Jul 26, 2018)
2-218401677-C-G		not specified	Uncertain significance (Jan 24, 2023)
2-218402386-T-C		not specified	Uncertain significance (Nov 07, 2022)
2-218403080-A-G		not specified	Uncertain significance (Jan 06, 2023)
2-218403262-A-G		not specified	Uncertain significance (Jan 18, 2022)
2-218403280-G-T		not specified	Uncertain significance (Aug 13, 2021)
2-218403313-C-T		not specified	Uncertain significance (Sep 16, 2021)
2-218403340-C-T		not specified	Uncertain significance (Mar 20, 2024)
2-218403359-G-A		not specified	Uncertain significance (Aug 29, 2023)
2-218404372-A-T		not specified	Uncertain significance (Jan 31, 2024)
2-218404376-G-A		not specified	Uncertain significance (Jun 11, 2024)
2-218404412-G-A		not specified	Uncertain significance (Apr 04, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CTDSP1	protein_coding	protein_coding	ENST00000273062	7	7686

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.993	0.00746	124585	0	1	124586	0.00000401

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.15	127	169	0.751	0.0000110	1683
Missense in Polyphen		23	69.991	0.32861		719
Synonymous	-2.35	96	70.9	1.35	0.00000463	533
Loss of Function	3.54	0	14.6	0.00	9.39e-7	138

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000889	0.00000889
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Preferentially catalyzes the dephosphorylation of 'Ser- 5' within the tandem 7 residue repeats in the C-terminal domain (CTD) of the largest RNA polymerase II subunit POLR2A. Negatively regulates RNA polymerase II transcription, possibly by controlling the transition from initiation/capping to processive transcript elongation. Recruited by REST to neuronal genes that contain RE-1 elements, leading to neuronal gene silencing in non-neuronal cells. {ECO:0000269|PubMed:12721286, ECO:0000269|PubMed:15681389}.
• Pathway: TGF-Ncore;miR-targeted genes in epithelium - TarBase;miR-targeted genes in squamous cell - TarBase;mir-124 predicted interactions with cell cycle and differentiation;EMT transition in Colorectal Cancer;BMP receptor signaling;Coregulation of Androgen receptor activity;Regulation of cytoplasmic and nuclear SMAD2/3 signaling (Consensus)

Recessive Scores

• pRec: 0.129

Intolerance Scores

• loftool: 0.479
• rvis_EVS: 0.06
• rvis_percentile_EVS: 58.53

Haploinsufficiency Scores

• pHI: 0.349
• hipred: Y
• hipred_score: 0.642
• ghis: 0.509

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.983

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ctdsp1
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype

Gene ontology

• Biological process: negative regulation of protein phosphorylation;regulation of transcription by RNA polymerase II;protein dephosphorylation;negative regulation of neuron differentiation;negative regulation of G1/S transition of mitotic cell cycle
• Cellular component: nucleus;nucleoplasm;extracellular exosome
• Molecular function: phosphoprotein phosphatase activity;protein binding;RNA polymerase II CTD heptapeptide repeat phosphatase activity;metal ion binding