DNTT

DNA nucleotidylexotransferase, the group of DNA polymerases

Basic information

Region (hg38): 10:96304409-96338564

Links

ENSG00000107447 ∙ NCBI:1791 ∙ OMIM:187410 ∙ HGNC:2983 ∙ Uniprot:P04053 ∙ 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 DNTT gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DNTT 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	2	3
missense			26	3	1	30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					1	1
Total	0	0	26	4	4

Variants in DNTT

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

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

Position	Type	Phenotype	Significance	ClinVar
10-96304532-G-A		not specified	Uncertain significance (Jul 11, 2023)
10-96304639-C-A		not specified	Uncertain significance (Dec 27, 2023)
10-96304683-G-T		not specified	Uncertain significance (Nov 14, 2023)
10-96304707-C-G			Benign (Aug 09, 2018)
10-96304709-G-A			Benign (Feb 13, 2018)
10-96318387-C-T		not specified	Uncertain significance (Jan 31, 2024)
10-96318414-A-C		not specified	Uncertain significance (Apr 01, 2024)
10-96318417-C-T			Benign (Dec 31, 2019)
10-96318475-A-T		not specified	Uncertain significance (Aug 16, 2021)
10-96319270-A-G			Likely benign (Jul 31, 2018)
10-96319293-C-T		not specified	Uncertain significance (Dec 16, 2022)
10-96319302-C-G		not specified	Uncertain significance (Nov 18, 2022)
10-96319330-G-T		not specified	Uncertain significance (May 25, 2022)
10-96319378-C-T			Benign (Dec 31, 2019)
10-96320673-G-A		not specified	Likely benign (Jan 16, 2024)
10-96320691-C-T		not specified	Uncertain significance (Oct 16, 2024)
10-96320741-A-T		not specified	Uncertain significance (Dec 13, 2022)
10-96322696-G-T		not specified	Uncertain significance (Sep 26, 2023)
10-96322710-A-G			Benign (Mar 28, 2018)
10-96324272-A-T		not specified	Uncertain significance (Oct 30, 2023)
10-96324353-G-C			Likely benign (Aug 10, 2018)
10-96327477-A-G		not specified	Uncertain significance (Jun 18, 2021)
10-96327514-A-C		not specified	Uncertain significance (Oct 20, 2023)
10-96327524-G-A		not specified	Uncertain significance (Mar 19, 2024)
10-96327597-G-A		not specified	Uncertain significance (Nov 15, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DNTT	protein_coding	protein_coding	ENST00000371174	11	34237

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.95e-10	0.725	125654	1	90	125745	0.000362

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.466	314	292	1.08	0.0000165	3347
Missense in Polyphen		122	112.8	1.0816		1291
Synonymous	-0.0165	107	107	1.00	0.00000614	943
Loss of Function	1.50	19	27.5	0.690	0.00000146	327

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000731	0.000731
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000478	0.000475
Middle Eastern	0.000109	0.000109
South Asian	0.000330	0.000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Template-independent DNA polymerase which catalyzes the random addition of deoxynucleoside 5'-triphosphate to the 3'-end of a DNA initiator. One of the in vivo functions of this enzyme is the addition of nucleotides at the junction (N region) of rearranged Ig heavy chain and T-cell receptor gene segments during the maturation of B- and T-cells. {ECO:0000250|UniProtKB:P09838}.
• Pathway: Hematopoietic cell lineage - Homo sapiens (human);Non-homologous end-joining - Homo sapiens (human);Validated targets of C-MYC transcriptional repression;DNA-PK pathway in nonhomologous end joining (Consensus)

Recessive Scores

• pRec: 0.926

Intolerance Scores

• loftool: 0.900
• rvis_EVS: -0.29
• rvis_percentile_EVS: 33.42

Haploinsufficiency Scores

• pHI: 0.133
• hipred: Y
• hipred_score: 0.755
• ghis: 0.398

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.837

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dntt
• Phenotype: homeostasis/metabolism phenotype; normal phenotype; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); immune system phenotype

Gene ontology

• Biological process: DNA metabolic process;double-strand break repair via nonhomologous end joining;DNA modification;response to ATP;DNA biosynthetic process
• Cellular component: nuclear chromatin;euchromatin;nucleus;nucleoplasm;cytosol;nuclear matrix
• Molecular function: DNA binding;DNA-directed DNA polymerase activity;DNA nucleotidylexotransferase activity;protein binding;metal ion binding