DCTPP1

dCTP pyrophosphatase 1

Basic information

Region (hg38): 16:30423615-30430030

Links

ENSG00000179958 ∙ NCBI:79077 ∙ OMIM:615840 ∙ HGNC:28777 ∙ Uniprot:Q9H773 ∙ 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 DCTPP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DCTPP1 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						0
missense			14	1		15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	1	0

Variants in DCTPP1

This is a list of pathogenic ClinVar variants found in the DCTPP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-30424283-C-T		not specified	Uncertain significance (Jun 10, 2024)
16-30424324-T-A		not specified	Uncertain significance (Sep 07, 2022)
16-30424342-C-T		not specified	Uncertain significance (Jul 13, 2021)
16-30424343-G-A		not specified	Uncertain significance (Feb 23, 2023)
16-30424370-G-A		not specified	Uncertain significance (Dec 02, 2024)
16-30424414-C-T		not specified	Likely benign (Oct 26, 2022)
16-30424415-G-A		not specified	Uncertain significance (Nov 11, 2024)
16-30424435-A-G		not specified	Uncertain significance (Sep 09, 2021)
16-30424436-C-T		not specified	Uncertain significance (Sep 18, 2024)
16-30424441-T-C		not specified	Uncertain significance (Dec 02, 2024)
16-30424460-G-A		not specified	Uncertain significance (Dec 15, 2022)
16-30424480-C-T		not specified	Uncertain significance (Aug 17, 2021)
16-30424490-G-T		not specified	Uncertain significance (Jun 26, 2023)
16-30424508-C-T		not specified	Uncertain significance (Mar 06, 2023)
16-30424520-C-T		not specified	Uncertain significance (Dec 11, 2023)
16-30429167-G-T		not specified	Likely benign (Oct 09, 2024)
16-30429917-G-A		not specified	Uncertain significance (Nov 09, 2023)
16-30429937-T-G		not specified	Uncertain significance (Oct 26, 2022)
16-30429944-C-A		not specified	Uncertain significance (Jan 04, 2022)
16-30429959-T-A		not specified	Uncertain significance (Jun 18, 2021)
16-30429976-G-A		not specified	Uncertain significance (Aug 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DCTPP1	protein_coding	protein_coding	ENST00000319285	3	6457

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.461	0.516	125724	0	23	125747	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.198	112	106	1.05	0.00000664	1081
Missense in Polyphen		36	38.459	0.93607		424
Synonymous	-0.479	46	42.1	1.09	0.00000225	372
Loss of Function	1.81	1	5.66	0.177	3.13e-7	57

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000327	0.000304
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000141	0.000141
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Hydrolyzes deoxynucleoside triphosphates (dNTPs) to the corresponding nucleoside monophosphates. Has a strong preference for dCTP and its analogs including 5-iodo-dCTP and 5-methyl-dCTP for which it may even have a higher efficiency. May protect DNA or RNA against the incorporation of these genotoxic nucleotide analogs through their catabolism. {ECO:0000269|PubMed:24467396}.
• Pathway: Pyrimidine metabolism - Homo sapiens (human);Pyrimidine metabolism;Metabolism of nucleotides;Interconversion of nucleotide di- and triphosphates;Metabolism (Consensus)

Recessive Scores

• pRec: 0.124

Intolerance Scores

• loftool: 0.382
• rvis_EVS: 0.24
• rvis_percentile_EVS: 68.98

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.369
• ghis: 0.573

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.817

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dctpp1

Gene ontology

• Biological process: dCTP catabolic process;nucleoside triphosphate catabolic process;DNA protection;dTTP catabolic process;protein homotetramerization
• Cellular component: nucleus;mitochondrion;cytosol
• Molecular function: magnesium ion binding;protein binding;pyrimidine deoxyribonucleotide binding;identical protein binding;nucleoside-triphosphate diphosphatase activity;dCTP diphosphatase activity