DNASE1L2

deoxyribonuclease 1 like 2

Basic information

Region (hg38): 16:2235816-2238711

Links

ENSG00000167968 ∙ NCBI:1775 ∙ OMIM:602622 ∙ HGNC:2958 ∙ Uniprot:Q92874 ∙ 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 DNASE1L2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DNASE1L2 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			20			20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	0	0

Variants in DNASE1L2

This is a list of pathogenic ClinVar variants found in the DNASE1L2 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-2236888-C-G		not specified	Uncertain significance (Nov 25, 2024)
16-2236913-G-T		not specified	Uncertain significance (Nov 18, 2023)
16-2237066-T-C		not specified	Uncertain significance (Jul 12, 2022)
16-2237111-T-A		not specified	Uncertain significance (Nov 30, 2021)
16-2237118-G-C		not specified	Uncertain significance (Sep 09, 2024)
16-2237249-A-G		not specified	Uncertain significance (Jan 05, 2022)
16-2237267-G-A		not specified	Uncertain significance (Sep 15, 2021)
16-2237378-A-G		not specified	Uncertain significance (Jan 22, 2024)
16-2237524-C-T		not specified	Uncertain significance (Nov 14, 2024)
16-2237540-C-T		not specified	Uncertain significance (May 28, 2024)
16-2237569-G-C		not specified	Uncertain significance (Apr 20, 2024)
16-2237572-G-C		not specified	Uncertain significance (Jun 18, 2021)
16-2237587-G-T		not specified	Uncertain significance (Sep 02, 2024)
16-2237645-C-T		not specified	Uncertain significance (Nov 24, 2024)
16-2237771-T-C		not specified	Uncertain significance (Oct 01, 2024)
16-2237884-G-A		not specified	Uncertain significance (May 31, 2023)
16-2237938-G-A		not specified	Uncertain significance (Oct 20, 2023)
16-2237972-C-G		not specified	Uncertain significance (Sep 17, 2021)
16-2237984-A-C		not specified	Uncertain significance (Jul 14, 2021)
16-2238369-C-T		not specified	Uncertain significance (Sep 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DNASE1L2	protein_coding	protein_coding	ENST00000564065	6	2896

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.32e-7	0.343	123828	0	176	124004	0.000710

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.341	200	187	1.07	0.00000959	1890
Missense in Polyphen		79	79.569	0.99285		845
Synonymous	0.113	84	85.3	0.985	0.00000481	604
Loss of Function	0.520	11	13.0	0.844	6.29e-7	124

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00308	0.00276
Ashkenazi Jewish	0.000329	0.000300
East Asian	0.00103	0.00100
Finnish	0.000291	0.000279
European (Non-Finnish)	0.000549	0.000508
Middle Eastern	0.00103	0.00100
South Asian	0.00108	0.00105
Other	0.000533	0.000498

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Divalent cation-dependent acid DNA endonuclease involved in the breakdown of the nucleus during corneocyte formation of epidermal keratinocytes. May play an immune role by eliminating harmful DNA released into the extracellular environment by damaged epidermal cells. {ECO:0000269|PubMed:16902420}.

Recessive Scores

• pRec: 0.181

Intolerance Scores

• loftool: 0.532
• rvis_EVS: -0.09
• rvis_percentile_EVS: 46.74

Haploinsufficiency Scores

• pHI: 0.0300
• hipred: N
• hipred_score: 0.303
• ghis: 0.578

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.161

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dnase1l2
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); craniofacial phenotype; cellular phenotype; homeostasis/metabolism phenotype; skeleton phenotype; renal/urinary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); limbs/digits/tail phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); hearing/vestibular/ear phenotype; digestive/alimentary phenotype; vision/eye phenotype; immune system phenotype

Gene ontology

• Biological process: DNA catabolic process, endonucleolytic;hair follicle development;corneocyte development;DNA metabolic process;DNA catabolic process
• Cellular component: extracellular region;nucleus;cytoplasm
• Molecular function: DNA binding;deoxyribonuclease I activity;deoxyribonuclease activity;calcium ion binding