DNASE2B

deoxyribonuclease 2 beta

Basic information

Region (hg38): 1:84398484-84415018

Links

ENSG00000137976 ∙ NCBI:58511 ∙ OMIM:608057 ∙ HGNC:28875 ∙ Uniprot:Q8WZ79 ∙ 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 DNASE2B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DNASE2B 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			13			13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			3			3
Total	0	0	16	0	0

Variants in DNASE2B

This is a list of pathogenic ClinVar variants found in the DNASE2B region.

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

Position	Type	Phenotype	Significance	ClinVar
1-84401911-T-C		not specified	Uncertain significance (Jul 09, 2021)
1-84408444-A-C		not specified	Uncertain significance (Oct 20, 2021)
1-84408453-A-G		not specified	Uncertain significance (Jan 30, 2024)
1-84408465-A-C		not specified	Uncertain significance (Dec 19, 2023)
1-84408501-A-C		not specified	Uncertain significance (Nov 11, 2024)
1-84410877-T-G		not specified	Uncertain significance (Dec 21, 2023)
1-84410968-A-G		not specified	Uncertain significance (Dec 14, 2023)
1-84412424-A-C		not specified	Uncertain significance (Oct 25, 2022)
1-84412513-C-T		not specified	Uncertain significance (Jul 26, 2024)
1-84412532-A-T		not specified	Uncertain significance (Jun 06, 2022)
1-84414591-G-A		not specified	Uncertain significance (Oct 19, 2021)
1-84414615-A-T		not specified	Uncertain significance (Sep 08, 2024)
1-84414634-T-G		not specified	Uncertain significance (Oct 20, 2021)
1-84414642-A-G		not specified	Uncertain significance (Dec 03, 2021)
1-84414694-T-A		not specified	Uncertain significance (Jun 12, 2023)
1-84414722-G-A		not specified	Uncertain significance (Dec 28, 2022)
1-84414746-A-G		not specified	Uncertain significance (Apr 19, 2024)
1-84414762-G-A		not specified	Uncertain significance (Jan 26, 2022)
1-84414815-C-A		not specified	Uncertain significance (Sep 26, 2024)
1-84414819-T-C		not specified	Uncertain significance (Dec 09, 2023)
1-84414861-G-A		not specified	Uncertain significance (Jan 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DNASE2B	protein_coding	protein_coding	ENST00000370665	6	16487

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.66e-16	0.00290	125308	1	438	125747	0.00175

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.155	172	178	0.967	0.00000858	2344
Missense in Polyphen		66	64.538	1.0227		879
Synonymous	-0.420	70	65.7	1.07	0.00000308	665
Loss of Function	-0.606	22	19.1	1.15	0.00000109	223

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00155	0.00149
Ashkenazi Jewish	0.00	0.00
East Asian	0.00557	0.00551
Finnish	0.00652	0.00649
European (Non-Finnish)	0.00125	0.00123
Middle Eastern	0.00557	0.00551
South Asian	0.000600	0.000588
Other	0.00151	0.00147

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Hydrolyzes DNA under acidic conditions. Does not require divalent cations for activity. Participates in the degradation of nuclear DNA during lens cell differentiation. {ECO:0000269|PubMed:11700027, ECO:0000269|PubMed:12944971}.
• Pathway: Lysosome - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.888
• rvis_EVS: 0.88
• rvis_percentile_EVS: 89.07

Haploinsufficiency Scores

• pHI: 0.209
• hipred: N
• hipred_score: 0.310

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.199

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dnase2b
• Phenotype: vision/eye phenotype; skeleton phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: apoptotic DNA fragmentation
• Cellular component: extracellular region;lysosome
• Molecular function: deoxyribonuclease II activity