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.

not_specified (31 variants)
not_provided (2 variants)

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. These statistics are base on transcript: NM_000021198.3. 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					1 clinvar	1
missense			31 clinvar		1 clinvar	32
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	31	0	2

Loading clinvar variants...

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