DBNL
Basic information
Region (hg38): 7:44044640-44069456
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- Glycogen storage disease type X (5 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 | 2 | |||||
missense | 22 | 26 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 87 | 49 | 151 | |||
Total | 5 | 3 | 109 | 55 | 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) | |||
7-44056874-T-C | not specified | Uncertain significance (Apr 12, 2024) | ||
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) |
GnomAD
Source:
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:
- 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