DNASE1L1

deoxyribonuclease 1 like 1

Basic information

Region (hg38): X:154401235-154412112

Previous symbols: [ "DNL1L" ]

Links

ENSG00000013563 ∙ NCBI:1774 ∙ OMIM:300081 ∙ HGNC:2957 ∙ Uniprot:P49184 ∙ 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 DNASE1L1 gene.

• 3-Methylglutaconic aciduria type 2 (46 variants)
• not provided (17 variants)
• Cardiovascular phenotype (13 variants)
• not specified (8 variants)
• Inborn genetic diseases (6 variants)
• Left ventricular noncompaction cardiomyopathy (3 variants)
• Endocardial fibroelastosis (3 variants)
• Primary dilated cardiomyopathy (2 variants)
• Cardiomyopathy (1 variants)
• Dilated cardiomyopathy 3B (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DNASE1L1 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				4	1	5
missense			5	1		6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region			2	2		4
non coding	3	5	19	23	3	53
Total	3	5	25	28	4

Variants in DNASE1L1

This is a list of pathogenic ClinVar variants found in the DNASE1L1 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-154403031-C-T		not specified	Likely benign (May 09, 2022)
X-154403136-G-A		not specified	Uncertain significance (Dec 21, 2022)
X-154403190-C-T		not specified	Uncertain significance (Mar 24, 2023)
X-154403308-G-A			Likely benign (Aug 01, 2022)
X-154403583-G-A			Likely benign (Jan 01, 2023)
X-154404839-C-T			Likely benign (Mar 01, 2023)
X-154405018-C-G			Benign (Jul 26, 2017)
X-154405081-T-C		not specified	Uncertain significance (Sep 14, 2023)
X-154405446-G-T		not specified	Uncertain significance (Apr 09, 2022)
X-154405479-T-C			Likely benign (Feb 01, 2023)
X-154405550-G-A		not specified	Uncertain significance (Sep 13, 2023)
X-154411725-G-G		Left ventricular noncompaction cardiomyopathy • Endocardial fibroelastosis • 3-Methylglutaconic aciduria type 2 • Dilated cardiomyopathy 3B	Benign (Jun 14, 2016)
X-154411756-G-C		Primary dilated cardiomyopathy • Left ventricular noncompaction cardiomyopathy • Endocardial fibroelastosis • 3-Methylglutaconic aciduria type 2	Benign/Likely benign (Jan 12, 2018)
X-154411792-C-T			Benign (Mar 03, 2015)
X-154411807-C-T		not specified	Likely benign (Sep 12, 2016)
X-154411825-G-C			Benign (Mar 03, 2015)
X-154411827-C-T		not specified	Likely benign (Mar 08, 2011)
X-154411840-G-A		Cardiovascular phenotype	Uncertain significance (May 31, 2022)
X-154411844-A-G		3-Methylglutaconic aciduria type 2	Uncertain significance (Aug 15, 2022)
X-154411846-G-A		3-Methylglutaconic aciduria type 2	Uncertain significance (Dec 09, 2023)
X-154411856-G-T		not specified • 3-Methylglutaconic aciduria type 2 • Cardiovascular phenotype	Uncertain significance (Jun 16, 2022)
X-154411861-G-T		3-Methylglutaconic aciduria type 2	Uncertain significance (Jul 09, 2021)
X-154411860-A-AGTGGC			Pathogenic (Nov 03, 2021)
X-154411867-G-T		3-Methylglutaconic aciduria type 2	Likely benign (Jan 17, 2024)
X-154411870-C-G		3-Methylglutaconic aciduria type 2 • Cardiovascular phenotype	Uncertain significance (Sep 06, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DNASE1L1	protein_coding	protein_coding	ENST00000369809	7	10871

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.388	0.603	125723	1	2	125726	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.693	111	134	0.831	0.0000118	1948
Missense in Polyphen		31	50.457	0.61438		691
Synonymous	-1.46	75	60.5	1.24	0.00000544	634
Loss of Function	2.20	2	9.19	0.218	6.93e-7	140

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000365	0.0000365
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000245	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Neutrophil degranulation;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.286

Intolerance Scores

• loftool: 0.302
• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.66

Haploinsufficiency Scores

• pHI: 0.190
• hipred: N
• hipred_score: 0.201
• ghis: 0.500

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dnase1l1
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: DNA catabolic process, endonucleolytic;DNA metabolic process;DNA catabolic process;neutrophil degranulation
• Cellular component: extracellular region;nucleus;endoplasmic reticulum;specific granule lumen
• Molecular function: DNA binding;deoxyribonuclease I activity;deoxyribonuclease activity