CTDSP2

CTD small phosphatase 2, the group of CTD family phosphatases|MicroRNA protein coding host genes

Basic information

Region (hg38): 12:57819927-57846729

Links

ENSG00000175215 ∙ NCBI:10106 ∙ OMIM:608711 ∙ HGNC:17077 ∙ Uniprot:O14595 ∙ 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 CTDSP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CTDSP2 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			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			3			3
Total	0	0	12	1	0

Variants in CTDSP2

This is a list of pathogenic ClinVar variants found in the CTDSP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-57823627-C-G		not specified	Uncertain significance (Oct 07, 2024)
12-57823632-G-A		CTDSP2-related disorder	Likely benign (Nov 06, 2020)
12-57823637-C-T		not specified	Uncertain significance (Apr 04, 2024)
12-57823650-G-A		CTDSP2-related disorder	Likely benign (Nov 06, 2020)
12-57823671-G-T		CTDSP2-related disorder	Likely benign (Nov 06, 2020)
12-57823700-T-G		not specified	Uncertain significance (Oct 06, 2021)
12-57823973-C-A		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
12-57824043-C-T		not specified	Uncertain significance (Oct 09, 2024)
12-57824059-G-A		not specified	Uncertain significance (Dec 12, 2024)
12-57824266-T-A		not specified	Uncertain significance (May 08, 2023)
12-57826355-G-A			Likely benign (Jun 23, 2018)
12-57827556-T-C		not specified	Uncertain significance (Nov 06, 2023)
12-57827557-A-G		not specified	Uncertain significance (Feb 27, 2025)
12-57827589-G-A		not specified	Uncertain significance (Oct 25, 2024)
12-57829464-G-T		not specified	Uncertain significance (Jun 04, 2024)
12-57829525-G-C		not specified	Uncertain significance (Nov 10, 2024)
12-57829560-C-A		not specified	Uncertain significance (Jul 22, 2024)
12-57829584-T-C		not specified	Uncertain significance (Aug 15, 2023)
12-57846413-G-A		not specified	Uncertain significance (Jun 16, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CTDSP2	protein_coding	protein_coding	ENST00000398073	8	26813

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.114	0.880	124857	0	7	124864	0.0000280

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.51	107	161	0.666	0.00000913	1761
Missense in Polyphen		23	60.721	0.37878		693
Synonymous	0.796	56	64.1	0.873	0.00000365	537
Loss of Function	2.43	4	13.7	0.291	5.81e-7	165

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000442	0.0000441
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
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. May contribute to the development of sarcomas. {ECO:0000269|PubMed:12721286, ECO:0000269|PubMed:15681389}.
• Pathway: TGF-Ncore;XBP1(S) activates chaperone genes;BMP receptor signaling;Coregulation of Androgen receptor activity;Regulation of cytoplasmic and nuclear SMAD2/3 signaling (Consensus)

Recessive Scores

• pRec: 0.154

Intolerance Scores

• loftool: 0.464
• rvis_EVS: -0.23
• rvis_percentile_EVS: 36.86

Haploinsufficiency Scores

• pHI: 0.495
• hipred: Y
• hipred_score: 0.529
• ghis: 0.612

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.968

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ctdsp2
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); 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: negative regulation of protein phosphorylation;regulation of transcription by RNA polymerase II;protein dephosphorylation;IRE1-mediated unfolded protein response;negative regulation of G1/S transition of mitotic cell cycle
• Cellular component: nucleoplasm
• Molecular function: phosphoprotein phosphatase activity;protein binding;RNA polymerase II CTD heptapeptide repeat phosphatase activity;metal ion binding