DBNL

drebrin like, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 7:44044639-44069456

Links

ENSG00000136279 ∙ NCBI:28988 ∙ OMIM:610106 ∙ HGNC:2696 ∙ Uniprot:Q9UJU6 ∙ 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 DBNL gene.

• Glycogen storage disease type X (127 variants)
• Inborn genetic diseases (41 variants)
• not provided (36 variants)
• not specified (9 variants)
• PGAM2-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DBNL 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		1
missense			19	2		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding	4	3	83	40	7	137
Total	4	3	102	43	7

Highest pathogenic variant AF is 0.0000133

Variants in DBNL

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

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

Position	Type	Phenotype	Significance	ClinVar
7-44050261-C-G		not specified	Uncertain significance (Apr 25, 2022)
7-44050264-C-T			Likely benign (Jan 01, 2023)
7-44056886-G-C		not specified	Uncertain significance (Aug 30, 2021)
7-44056896-C-A		not specified	Uncertain significance (May 23, 2023)
7-44058145-G-A		not specified	Uncertain significance (Nov 10, 2022)
7-44058165-C-T		not specified	Uncertain significance (May 26, 2022)
7-44058171-G-A		not specified	Uncertain significance (Dec 02, 2022)
7-44058205-G-A		not specified	Uncertain significance (Apr 12, 2022)
7-44058210-C-T		not specified	Uncertain significance (Mar 01, 2023)
7-44058232-G-T		not specified	Likely benign (Oct 20, 2023)
7-44058234-C-T		not specified	Uncertain significance (Nov 15, 2021)
7-44058246-T-C		not specified	Uncertain significance (Oct 26, 2022)
7-44058278-G-C		not specified	Uncertain significance (Jun 28, 2023)
7-44058434-C-T			Likely benign (Jul 01, 2022)
7-44058470-G-A		not specified	Uncertain significance (Feb 07, 2023)
7-44058887-T-C		not specified	Uncertain significance (Apr 28, 2022)
7-44058891-C-T		not specified	Uncertain significance (Jan 30, 2024)
7-44059402-C-G		not specified	Uncertain significance (Sep 12, 2023)
7-44059419-C-G		not specified	Uncertain significance (Sep 26, 2023)
7-44059561-C-T		not specified	Likely benign (Oct 03, 2022)
7-44059564-C-T		not specified	Likely benign (Feb 17, 2024)
7-44059568-C-T			Likely benign (Feb 01, 2024)
7-44059587-G-A		not specified	Uncertain significance (Oct 12, 2022)
7-44059599-G-C		not specified	Uncertain significance (Jan 04, 2024)
7-44059633-A-C		not specified	Uncertain significance (Jul 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DBNL	protein_coding	protein_coding	ENST00000468694	13	24817

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0179	0.982	125693	0	50	125743	0.000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.11	217	268	0.809	0.0000165	2862
Missense in Polyphen		53	98.091	0.54032		1004
Synonymous	0.991	92	105	0.877	0.00000686	824
Loss of Function	3.29	8	26.1	0.306	0.00000120	291

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000210	0.000210
Ashkenazi Jewish	0.00298	0.00298
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000973	0.0000967
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Adapter protein that binds F-actin and DNM1, and thereby plays a role in receptor-mediated endocytosis. Plays a role in the reorganization of the actin cytoskeleton, formation of cell projections, such as neurites, in neuron morphogenesis and synapse formation via its interaction with WASL and COBL. Does not bind G- actin and promote actin polymerization by itself. Required for the formation of organized podosome rosettes (By similarity). May act as a common effector of antigen receptor-signaling pathways in leukocytes. Acts as a key component of the immunological synapse that regulates T-cell activation by bridging TCRs and the actin cytoskeleton to gene activation and endocytic processes. {ECO:0000250, ECO:0000269|PubMed:14729663}.
• Pathway: T-Cell antigen Receptor (TCR) Signaling Pathway;Neutrophil degranulation;TCR;Caspase-mediated cleavage of cytoskeletal proteins;Apoptotic cleavage of cellular proteins;Innate Immune System;Immune System;Apoptotic execution phase;Apoptosis;Programmed Cell Death;Neuronal System;Neurexins and neuroligins;Protein-protein interactions at synapses;JNK signaling in the CD4+ TCR pathway;TCR signaling in naïve CD4+ T cells (Consensus)

Recessive Scores

• pRec: 0.720

Intolerance Scores

• loftool: 0.531
• rvis_EVS: -0.02
• rvis_percentile_EVS: 52.09

Haploinsufficiency Scores

• pHI: 0.201
• hipred: N
• hipred_score: 0.414
• ghis: 0.545

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.870

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dbnl
• 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); immune system phenotype; respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); 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); 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); hematopoietic system phenotype; growth/size/body region phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: adaptive immune response;receptor-mediated endocytosis;activation of JUN kinase activity;synapse assembly;Rac protein signal transduction;neutrophil degranulation;neuron projection morphogenesis;podosome assembly;ruffle assembly
• Cellular component: Golgi membrane;ruffle;podosome;extracellular region;cytoplasm;early endosome;cytosol;plasma membrane;cell cortex;postsynaptic density;lamellipodium;cell junction;dendrite;clathrin-coated vesicle membrane;secretory granule lumen;extracellular exosome;tertiary granule lumen;ficolin-1-rich granule lumen
• Molecular function: actin binding;protein binding;protein C-terminus binding;enzyme activator activity;protein domain specific binding;cadherin binding;actin filament binding