DUT

deoxyuridine triphosphatase

Basic information

Region (hg38): 15:48331011-48343373

Links

ENSG00000128951

∙ NCBI:1854 ∙ OMIM:601266 ∙ HGNC:3078 ∙ Uniprot:P33316 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

bone marrow failure and diabetes mellitus syndrome (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Bone marrow failure and diabetes mellitus syndrome	AR	Endocrine; Hematologic	The condition can involve bone marrow failure and early-onset diabetes mellitus, and awareness may allow early detection and management; BMT has been described as curative for bone marrow failure	Endocrine; Hematologic	28073829; 35611808; 35931051

ClinVar

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

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DUT 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 clinvar		1
missense			4 clinvar	1 clinvar		5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1 clinvar	1
Total	0	0	4	2	1

Variants in DUT

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

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

Position	Phenotype	Significance	ClinVar
15-48331673-T-C	not specified	Likely benign (Aug 17, 2021)	2245952
15-48331804-G-A	not specified	Benign (May 22, 2018)	1336417
15-48332285-C-T	High myopia	Uncertain significance (Dec 17, 2018)	623429
15-48332314-G-A		Likely benign (Nov 01, 2022)	2645309
15-48332391-G-C	not specified	Uncertain significance (May 15, 2023)	2538025
15-48334422-A-G	Bone marrow failure and diabetes mellitus syndrome	Pathogenic (Sep 22, 2022)	1706580
15-48341336-T-C	not specified	Uncertain significance (May 16, 2024)	3274109
15-48341523-G-C	not specified	Uncertain significance (Jun 06, 2023)	2545353
15-48341530-G-A	Bone marrow failure and diabetes mellitus syndrome	Uncertain significance (Apr 04, 2024)	3068241
15-48342037-G-A	not specified	Uncertain significance (Aug 12, 2024)	3505949
15-48342055-T-G	not specified	Uncertain significance (Jul 14, 2021)	2237387

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DUT	protein_coding	protein_coding	ENST00000331200	7	12363

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00127	0.866	125720	0	18	125738	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.16	94	131	0.716	0.00000659	1559
Missense in Polyphen		24	41.932	0.57235		474
Synonymous	0.972	44	53.0	0.830	0.00000277	534
Loss of Function	1.30	6	10.6	0.568	5.13e-7	134

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000130	0.000129
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000465	0.0000462
European (Non-Finnish)	0.000107	0.000106
Middle Eastern	0.00	0.00
South Asian	0.0000999	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: This enzyme is involved in nucleotide metabolism: it produces dUMP, the immediate precursor of thymidine nucleotides and it decreases the intracellular concentration of dUTP so that uracil cannot be incorporated into DNA. {ECO:0000269|PubMed:8805593}.;
Pathway: Pyrimidine metabolism - Homo sapiens (human);Drug metabolism - other enzymes - Homo sapiens (human);Pyrimidine Metabolism;UMP Synthase Deiciency (Orotic Aciduria);MNGIE (Mitochondrial Neurogastrointestinal Encephalopathy);Beta Ureidopropionase Deficiency;Dihydropyrimidinase Deficiency;Pyrimidine metabolism;pyrimidine deoxyribonucleotides <i>de novo</i> biosynthesis;mechanism of gene regulation by peroxisome proliferators via ppara;Metabolism of nucleotides;Interconversion of nucleotide di- and triphosphates;Metabolism;Pyrimidine metabolism;Pyrimidine nucleotides nucleosides metabolism;superpathway of pyrimidine deoxyribonucleotides <i>de novo</i> biosynthesis (Consensus)

Recessive Scores

pRec: 0.495

Haploinsufficiency Scores

pHI: 0.896
hipred: Y
hipred_score: 0.555
ghis: 0.674

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2: N
essential_gene_gene_trap: E
gene_indispensability_pred: N
gene_indispensability_score: 0.0277

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Dut
Phenotype

Gene ontology

Biological process: liver development;nucleobase-containing compound metabolic process;dUMP biosynthetic process;DNA replication;response to organic cyclic compound;nucleobase-containing small molecule interconversion;regulation of protein heterodimerization activity;dUTP catabolic process;protein homotrimerization;negative regulation of signaling receptor activity
Cellular component: nucleus;nucleoplasm;mitochondrion;cytosol;extracellular exosome
Molecular function: magnesium ion binding;RNA binding;dUTP diphosphatase activity;protein binding;receptor inhibitor activity;pyrimidine deoxyribonucleotide binding;peroxisome proliferator activated receptor binding