CTDSPL2

CTD small phosphatase like 2, the group of CTD family phosphatases

Basic information

Region (hg38): 15:44427622-44529038

Links

ENSG00000137770 ∙ NCBI:51496 ∙ OMIM:618739 ∙ HGNC:26936 ∙ Uniprot:Q05D32 ∙ 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 CTDSPL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CTDSPL2 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			18		1	19
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	0	2

Variants in CTDSPL2

This is a list of pathogenic ClinVar variants found in the CTDSPL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-44459037-C-G		not specified	Uncertain significance (Aug 02, 2023)
15-44459049-CA-C			Uncertain significance (May 26, 2022)
15-44459068-A-C		not specified	Uncertain significance (Mar 06, 2023)
15-44459069-C-T		not specified	Uncertain significance (Nov 07, 2023)
15-44459105-G-T		not specified	Uncertain significance (Dec 07, 2021)
15-44459109-A-G		not specified	Uncertain significance (Sep 25, 2024)
15-44459153-G-A		not specified	Uncertain significance (Sep 09, 2021)
15-44459162-T-C		not specified	Uncertain significance (May 27, 2022)
15-44484268-T-G		not specified	Uncertain significance (Mar 20, 2024)
15-44484269-A-G		not specified	Uncertain significance (Jul 26, 2024)
15-44484290-T-A		not specified	Uncertain significance (Dec 03, 2021)
15-44486575-A-G		not specified	Uncertain significance (Oct 09, 2024)
15-44486619-T-G		not specified	Uncertain significance (Oct 07, 2024)
15-44490802-C-G		not specified	Uncertain significance (Nov 15, 2024)
15-44490806-A-G			Benign (Mar 29, 2018)
15-44490808-G-A		not specified	Uncertain significance (Sep 14, 2022)
15-44490834-G-A		not specified	Uncertain significance (Mar 01, 2024)
15-44490903-G-C		not specified	Uncertain significance (Jun 30, 2022)
15-44490906-T-A		not specified	Uncertain significance (Aug 04, 2024)
15-44490970-C-G		not specified	Uncertain significance (Jun 18, 2024)
15-44490978-C-T		not specified	Uncertain significance (Jul 12, 2023)
15-44490985-T-G		not specified	Uncertain significance (Aug 23, 2021)
15-44490988-C-G		not specified	Uncertain significance (Mar 31, 2023)
15-44490999-G-A			Uncertain significance (Jul 06, 2021)
15-44496419-C-T			Benign (Mar 29, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CTDSPL2	protein_coding	protein_coding	ENST00000260327	12	101805

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000338	125096	0	1	125097	0.00000400

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.20	149	246	0.605	0.0000129	3024
Missense in Polyphen		12	70.447	0.17034		905
Synonymous	0.816	76	85.6	0.888	0.00000440	882
Loss of Function	4.67	1	27.3	0.0366	0.00000148	340

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000621	0.0000621
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable phosphatase. {ECO:0000250}.

Recessive Scores

• pRec: 0.114

Intolerance Scores

• loftool: 0.0922
• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.66

Haploinsufficiency Scores

• pHI: 0.205
• hipred: Y
• hipred_score: 0.673
• ghis: 0.673

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.519

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ctdspl2
• Phenotype: adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype; 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: protein dephosphorylation;negative regulation of BMP signaling pathway;positive regulation of protein export from nucleus
• Cellular component: nucleoplasm
• Molecular function: phosphoprotein phosphatase activity