DCTD

dCMP deaminase

Basic information

Region (hg38): 4:182890060-182917936

Links

ENSG00000129187 ∙ NCBI:1635 ∙ OMIM:607638 ∙ HGNC:2710 ∙ Uniprot:P32321 ∙ 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 DCTD gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DCTD 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			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	0	1

Variants in DCTD

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

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

Position	Type	Phenotype	Significance	ClinVar
4-182891408-C-G		not specified	Uncertain significance (Jan 26, 2022)
4-182891418-G-A		not specified	Uncertain significance (Aug 05, 2023)
4-182891439-A-C		not specified	Uncertain significance (Sep 20, 2022)
4-182893041-C-A		not specified	Uncertain significance (Sep 23, 2023)
4-182893080-C-T		not specified	Uncertain significance (Oct 12, 2022)
4-182893091-T-C		not specified	Uncertain significance (May 29, 2024)
4-182894559-A-T		not specified	Uncertain significance (Aug 23, 2021)
4-182894595-C-G			Benign (Mar 30, 2018)
4-182914940-T-A		not specified	Uncertain significance (Apr 09, 2024)
4-182914986-T-A		not specified	Uncertain significance (Feb 10, 2022)
4-182915019-C-A		not specified	Uncertain significance (Aug 14, 2023)
4-182915043-C-T		not specified	Uncertain significance (Dec 14, 2023)
4-182915497-G-C		not specified	Uncertain significance (Jan 29, 2024)
4-182915501-G-C		not specified	Uncertain significance (Aug 13, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DCTD	protein_coding	protein_coding	ENST00000357067	6	27877

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000709	0.769	125712	0	36	125748	0.000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.176	107	112	0.953	0.00000652	1271
Missense in Polyphen		36	42.744	0.84222		495
Synonymous	0.458	39	42.8	0.911	0.00000293	316
Loss of Function	1.01	6	9.32	0.644	3.92e-7	126

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000124	0.000120
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000195	0.000193
Middle Eastern	0.000218	0.000217
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Supplies the nucleotide substrate for thymidylate synthetase.
• Pathway: Pyrimidine metabolism - Homo sapiens (human);Pyrimidine Metabolism;UMP Synthase Deiciency (Orotic Aciduria);Gemcitabine Action Pathway;MNGIE (Mitochondrial Neurogastrointestinal Encephalopathy);Gemcitabine Metabolism Pathway;Beta Ureidopropionase Deficiency;Dihydropyrimidinase Deficiency;Pyrimidine metabolism;Metabolism of nucleotides;Interconversion of nucleotide di- and triphosphates;Metabolism;Pyrimidine nucleotides nucleosides metabolism;pyrimidine deoxyribonucleotides biosynthesis from CTP (Consensus)

Recessive Scores

• pRec: 0.241

Intolerance Scores

• loftool: 0.659
• rvis_EVS: -0.32
• rvis_percentile_EVS: 31.46

Haploinsufficiency Scores

• pHI: 0.208
• hipred: N
• hipred_score: 0.466
• ghis: 0.681

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.677

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dctd

Gene ontology

• Biological process: pyrimidine nucleotide metabolic process;dUMP biosynthetic process;dTMP biosynthetic process;nucleobase-containing small molecule interconversion
• Cellular component: cytoplasm;cytosol
• Molecular function: dCMP deaminase activity;protein binding;zinc ion binding;identical protein binding