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.

• not_specified (38 variants)

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. These statistics are base on transcript: NM_000001374.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			39			39
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1			1
Total	0	0	40	0	0

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
		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

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

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