CTDSP1

protein-coding

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

Gene summary

This gene encodes a member of the small C-terminal domain phosphatase (SCP) family of nuclear phosphatases. These proteins play a role in transcriptional regulation through specific dephosphorylation of phosphoserine 5 within tandem heptapeptide repeats of the C-terminal domain of RNA polymerase II. The encoded protein plays a role in neuronal gene silencing in non-neuronal cells, and may also inhibit osteoblast differentiation. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Oct 2011]

MANE transcript

NM_021198.3

Inheritance

—

ClinVar variants

U:42B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr2:218,397,136-218,405,941

External References & Databases

Ensembl (ENSG00000144579)

Transcript & Mutation Effects

hg38 • Region Span ~8.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CTDSP1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 36

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_021198.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous					1 clinvar	1
missense			40 clinvar		1 clinvar	41
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	42	0	2	44

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 49 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_021198.3	RefSeq	NP_067021.1	7	MANE Select
ENST00000273062.7	Ensembl	ENSP00000273062.2	7	MANE Select
NM_001206878.2	RefSeq	NP_001193807.1	7	Standard
NM_001400268.1	RefSeq	NP_001387197.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

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

Molecular Function

phosphoprotein phosphatase activity
protein binding
RNA polymerase II CTD heptapeptide repeat phosphatase activity
metal ion binding

Cellular Component

nucleus
nucleoplasm
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000273062
Coding exons: 7
Length: 7686
Individuals with no LoFs: 124585
Homozygous LoFs: 0
Heterozygous LoFs: 1
Defined: 124586
p: 0.00000401

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.15	127	169	0.751	0.0000110	1683
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000089	0.0000089	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.129

Intolerance Scores

LoFtool: 0.479
RVIS EVS: 0.06
RVIS percentile EVS: 58.53

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.983

Gene Damage Prediction

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