CTPS2

CTP synthase 2, the group of Glutamine amidotransferase class 1 domain containing|MicroRNA protein coding host genes

Basic information

Region (hg38): X:16587999-16712936

Links

ENSG00000047230 ∙ NCBI:56474 ∙ OMIM:300380 ∙ HGNC:2520 ∙ Uniprot:Q9NRF8 ∙ 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 CTPS2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CTPS2 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	2
missense			10	1	1	12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding			2	1		3
Total	0	0	12	3	2

Variants in CTPS2

This is a list of pathogenic ClinVar variants found in the CTPS2 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-16609606-C-G			Benign (Apr 05, 2018)
X-16609616-G-C		not specified	Uncertain significance (Jan 16, 2024)
X-16617186-C-T		not specified	Uncertain significance (Jul 15, 2021)
X-16617220-A-C		not specified	Likely benign (Mar 22, 2023)
X-16620284-C-T		not specified	Uncertain significance (Jun 07, 2023)
X-16639224-T-C		not specified	Uncertain significance (May 06, 2024)
X-16651149-G-A			Likely benign (Dec 01, 2022)
X-16654406-G-A		not specified	Uncertain significance (Dec 20, 2023)
X-16654457-G-A		not specified	Uncertain significance (Jun 10, 2024)
X-16654475-A-C		not specified	Uncertain significance (Apr 06, 2023)
X-16670674-A-G		not specified	Likely benign (Feb 27, 2024)
X-16678417-C-T		not specified	Uncertain significance (Apr 12, 2023)
X-16678424-C-G		CYTIDINE 5-PRIME TRIPHOSPHATE SYNTHETASE 2 deficiency	Benign (Feb 08, 2022)
X-16683156-C-T		not specified	Conflicting classifications of pathogenicity (Apr 17, 2024)
X-16689454-C-A		not specified	Uncertain significance (Apr 12, 2022)
X-16689565-C-T		not specified • Laterality defects, autosomal dominant	Uncertain significance (Jun 29, 2023)
X-16691598-G-T		not specified	Uncertain significance (Jun 27, 2022)
X-16691610-C-T		not specified	Uncertain significance (Feb 23, 2023)
X-16693148-G-A		not specified	Uncertain significance (Apr 06, 2023)
X-16698965-T-G		not specified	Uncertain significance (Mar 07, 2023)
X-16698991-G-A		not specified	Uncertain significance (May 24, 2024)
X-16699083-G-A			Likely benign (Nov 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CTPS2	protein_coding	protein_coding	ENST00000443824	17	124934

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.819	0.181	125740	3	4	125747	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.59	116	225	0.515	0.0000169	3870
Missense in Polyphen		30	105.98	0.28308		1771
Synonymous	0.604	79	86.1	0.917	0.00000719	1090
Loss of Function	3.70	4	23.2	0.172	0.00000169	415

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000760	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000725	0.0000544
Finnish	0.000125	0.0000924
European (Non-Finnish)	0.0000382	0.0000264
Middle Eastern	0.0000725	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the ATP-dependent amination of UTP to CTP with either L-glutamine or ammonia as the source of nitrogen. Constitutes the rate-limiting enzyme in the synthesis of cytosine nucleotides. {ECO:0000269|PubMed:10899599, ECO:0000269|PubMed:16179339}.
• Pathway: Pyrimidine metabolism - Homo sapiens (human);Pyrimidine metabolism;UTP and CTP dephosphorylation I;UTP and CTP <i>de novo</i> biosynthesis;Metabolism of nucleotides;Interconversion of nucleotide di- and triphosphates;UTP and CTP dephosphorylation II;Metabolism;superpathway of pyrimidine ribonucleotides <i>de novo</i> biosynthesis;Pyrimidine nucleotides nucleosides metabolism;superpathway of pyrimidine deoxyribonucleotides <i>de novo</i> biosynthesis (Consensus)

Recessive Scores

• pRec: 0.161

Intolerance Scores

• loftool: 0.311
• rvis_EVS: -0.18
• rvis_percentile_EVS: 39.95

Haploinsufficiency Scores

• pHI: 0.489
• hipred: Y
• hipred_score: 0.802
• ghis: 0.571

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.846

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ctps2
• Phenotype: normal phenotype

Gene ontology

• Biological process: pyrimidine nucleotide metabolic process;CTP biosynthetic process;glutamine metabolic process;nucleobase-containing small molecule interconversion;pyrimidine nucleobase biosynthetic process;'de novo' CTP biosynthetic process
• Cellular component: cytoplasm;cytosol;cytoophidium
• Molecular function: CTP synthase activity;protein binding;ATP binding;identical protein binding