CTDP1

CTD phosphatase subunit 1, the group of CTD family phosphatases

Basic information

Region (hg38): 18:79679803-79754503

Links

ENSG00000060069 ∙ NCBI:9150 ∙ OMIM:604927 ∙ HGNC:2498 ∙ Uniprot:Q9Y5B0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• congenital cataracts-facial dysmorphism-neuropathy syndrome (Definitive), mode of inheritance: AR
• congenital cataracts-facial dysmorphism-neuropathy syndrome (Supportive), mode of inheritance: AR
• congenital cataracts-facial dysmorphism-neuropathy syndrome (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Congenital cataracts, facial dysmorphism, and neuropathy	AR	Endocrine; Pharmacogenomic; Renal	In Hypogonadotropic hypogonadism, surveillance in adolescence related to sexual maturation is indicated, as is monitoring of bone mineral density in order to allow early detection and treatment of disease; In the instance of anesthesia, monitoring is indicated, (eg, for severe complications such as stridor, pulmonary edema, malignant hyperthermia, and seizures); Individuals may suffer severe rhabdomyolysis related to viral infections, and awareness may allow rapid management	Cardiovascular; Endocrine; Musculoskeletal; Neurologic; Ophthalmologic; Renal	10439962; 10360766; 10442556; 14517542; 16194727; 16939648; 20301787; 21824574

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CTDP1 gene.

• Congenital cataracts-facial dysmorphism-neuropathy syndrome (1 variants)
• Charcot-Marie-Tooth disease (1 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CTDP1 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	125	17	144
missense			181	22	9	212
nonsense			3			3
start loss						0
frameshift			3			3
inframe indel			1		1	2
splice donor/acceptor (+/-2bp)			1			1
splice region			6	14	6	26
non coding	1		1	82	39	123
Total	1	0	192	229	66

Variants in CTDP1

This is a list of pathogenic ClinVar variants found in the CTDP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-79679844-G-T			Benign (Jun 29, 2018)
18-79679899-G-C			Likely benign (Nov 02, 2020)
18-79679914-C-T			Likely benign (May 17, 2019)
18-79679943-C-T		CTDP1-related disorder	Likely benign (Oct 29, 2021)
18-79679953-G-A			Likely benign (Jan 15, 2024)
18-79679953-G-T			Uncertain significance (Mar 18, 2022)
18-79679961-C-A			Benign (Jan 22, 2024)
18-79679961-C-T			Uncertain significance (Jul 30, 2022)
18-79679974-T-G			Likely benign (Sep 05, 2023)
18-79679975-C-T			Uncertain significance (Oct 13, 2022)
18-79679981-G-C			Uncertain significance (Feb 09, 2022)
18-79679989-C-T			Likely benign (May 03, 2022)
18-79679990-C-T		not specified	Uncertain significance (Feb 13, 2024)
18-79679992-G-A			Likely benign (Apr 24, 2023)
18-79679993-A-C			Uncertain significance (Mar 04, 2022)
18-79679995-G-A			Likely benign (Mar 01, 2023)
18-79679998-G-A			Likely benign (Dec 22, 2023)
18-79680005-G-A			Uncertain significance (Jun 05, 2024)
18-79680005-G-T			Uncertain significance (Feb 09, 2022)
18-79680007-C-T			Likely benign (Sep 08, 2023)
18-79680018-G-T		not specified	Uncertain significance (Jul 25, 2023)
18-79680020-C-T			Uncertain significance (Jul 29, 2022)
18-79680024-G-A		not specified	Uncertain significance (Aug 30, 2023)
18-79680025-G-C			Likely benign (Jan 18, 2024)
18-79680028-C-G			Likely benign (Feb 25, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CTDP1	protein_coding	protein_coding	ENST00000299543	13	74710

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000600	0.999	125729	0	19	125748	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.996	501	568	0.882	0.0000403	6141
Missense in Polyphen		171	249.17	0.68626		2750
Synonymous	-1.50	293	262	1.12	0.0000220	1950
Loss of Function	3.86	13	39.0	0.333	0.00000237	432

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000867	0.0000867
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00	0.00
Finnish	0.000185	0.000185
European (Non-Finnish)	0.0000807	0.0000791
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Processively dephosphorylates 'Ser-2' and 'Ser-5' of the heptad repeats YSPTSPS in the C-terminal domain of the largest RNA polymerase II subunit. This promotes the activity of RNA polymerase II. Plays a role in the exit from mitosis by dephosphorylating crucial mitotic substrates (USP44, CDC20 and WEE1) that are required for M-phase-promoting factor (MPF)/CDK1 inactivation. {ECO:0000269|PubMed:22692537}.
• Disease: DISEASE: Congenital cataracts, facial dysmorphism, and neuropathy (CCFDN) [MIM:604168]: An autosomal recessive developmental disorder characterized by a complex clinical phenotype with seemingly unrelated features involving multiple organs and systems. Developmental abnormalities include congenital cataracts and microcorneae, hypomyelination of the peripheral nervous system, impaired physical growth, delayed early motor and intellectual development, facial dysmorphism and hypogonadism. Central nervous system involvement, with cerebral and spinal cord atrophy, may be the result of disrupted development with superimposed degenerative changes. Affected individuals are prone to severe rhabdomyolysis after viral infections and to serious complications related to general anesthesia (such as pulmonary edema and epileptic seizures). {ECO:0000269|PubMed:14517542}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Disease;Formation of the HIV-1 Early Elongation Complex;Gene expression (Transcription);Formation of HIV-1 elongation complex containing HIV-1 Tat;Tat-mediated elongation of the HIV-1 transcript;Abortive elongation of HIV-1 transcript in the absence of Tat;HIV Transcription Elongation;HIV elongation arrest and recovery;Formation of HIV elongation complex in the absence of HIV Tat;Pausing and recovery of HIV elongation;Generic Transcription Pathway;Tat-mediated HIV elongation arrest and recovery;Pausing and recovery of Tat-mediated HIV elongation;Transcription of the HIV genome;Late Phase of HIV Life Cycle;HIV Life Cycle;HIV Infection;RNA Polymerase II Pre-transcription Events;Formation of RNA Pol II elongation complex ;RNA Polymerase II Transcription;Infectious disease;RNA Polymerase II Transcription Elongation;TP53 Regulates Transcription of DNA Repair Genes;Transcriptional Regulation by TP53;Formation of the Early Elongation Complex (Consensus)

Recessive Scores

• pRec: 0.230

Intolerance Scores

• loftool: 0.251
• rvis_EVS: -0.84
• rvis_percentile_EVS: 11.48

Haploinsufficiency Scores

• pHI: 0.118
• hipred: Y
• hipred_score: 0.749
• ghis: 0.543

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.955

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ctdp1

Zebrafish Information Network

• Gene name: ctdp1
• Affected structure: head
• Phenotype tag: abnormal
• Phenotype quality: pointed

Gene ontology

• Biological process: transcription by RNA polymerase II;transcription elongation from RNA polymerase II promoter;protein dephosphorylation;exit from mitosis;positive regulation by host of viral transcription;cell division;negative regulation of cell growth involved in cardiac muscle cell development;dephosphorylation of RNA polymerase II C-terminal domain
• Cellular component: spindle pole;nucleus;nucleoplasm;cytoplasm;centrosome;spindle;midbody;protein-containing complex;intracellular membrane-bounded organelle;spindle midzone
• Molecular function: TFIIF-class transcription factor complex binding;phosphoprotein phosphatase activity;protein binding;RNA polymerase II CTD heptapeptide repeat phosphatase activity;Tat protein binding