DBN1

drebrin 1

Basic information

Region (hg38): 5:177456608-177474401

Previous symbols: [ "D0S117E" ]

Links

ENSG00000113758 ∙ NCBI:1627 ∙ OMIM:126660 ∙ HGNC:2695 ∙ Uniprot:Q16643 ∙ 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 DBN1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DBN1 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	4	5
missense			45	2	1	48
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					2	2
non coding						0
Total	0	0	45	3	5

Variants in DBN1

This is a list of pathogenic ClinVar variants found in the DBN1 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-177457446-T-C		not specified	Uncertain significance (Feb 25, 2025)
5-177457676-C-G		not specified	Uncertain significance (Nov 27, 2023)
5-177457681-G-A		not specified	Uncertain significance (Dec 16, 2023)
5-177457714-G-A		not specified	Uncertain significance (Feb 28, 2024)
5-177458054-G-A			Benign (Apr 06, 2018)
5-177458156-G-A		not specified	Uncertain significance (Mar 01, 2025)
5-177458234-C-G		not specified	Uncertain significance (Oct 25, 2024)
5-177458254-C-A		not specified	Uncertain significance (Apr 22, 2022)
5-177458278-G-A		not specified	Uncertain significance (Sep 12, 2023)
5-177458284-G-A			Likely benign (Aug 20, 2018)
5-177458324-C-T		not specified	Uncertain significance (Mar 16, 2022)
5-177458335-G-A		not specified	Uncertain significance (Jan 29, 2024)
5-177458401-A-G		not specified	Uncertain significance (May 10, 2022)
5-177458432-C-T		not specified	Uncertain significance (Dec 22, 2023)
5-177458507-C-T		not specified	Likely benign (Dec 22, 2023)
5-177458519-C-T		not specified	Uncertain significance (Feb 05, 2024)
5-177458528-C-T		not specified	Uncertain significance (Aug 08, 2023)
5-177458543-C-T		not specified	Uncertain significance (Feb 05, 2024)
5-177458584-G-A		not specified	Uncertain significance (Dec 20, 2023)
5-177458587-C-T		not specified	Uncertain significance (Jan 27, 2025)
5-177458675-C-T		not specified	Uncertain significance (Jan 19, 2024)
5-177459118-G-T		not specified	Uncertain significance (Mar 08, 2024)
5-177459146-T-A		not specified	Uncertain significance (Feb 13, 2025)
5-177459155-C-G		not specified	Uncertain significance (Jul 20, 2021)
5-177459163-C-T		not specified	Uncertain significance (Nov 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DBN1	protein_coding	protein_coding	ENST00000292385	14	17794

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.997	0.00295	125738	0	10	125748	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.670	358	396	0.905	0.0000251	4197
Missense in Polyphen		106	164.53	0.64427		1793
Synonymous	-0.211	178	174	1.02	0.0000125	1314
Loss of Function	4.83	4	34.8	0.115	0.00000190	373

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000904	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000448	0.0000439
Middle Eastern	0.000109	0.0000544
South Asian	0.0000671	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Drebrins might play some role in cell migration, extension of neuronal processes and plasticity of dendrites. Required for actin polymerization at immunological synapses (IS) and for CXCR4 recruitment to IS. {ECO:0000269|PubMed:20215400}.

Recessive Scores

• pRec: 0.195

Intolerance Scores

• loftool: 0.546
• rvis_EVS: -0.09
• rvis_percentile_EVS: 47.12

Haploinsufficiency Scores

• pHI: 0.241
• hipred: Y
• hipred_score: 0.580
• ghis: 0.484

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.587

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dbn1
• Phenotype: 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; homeostasis/metabolism phenotype; skeleton phenotype; embryo phenotype; liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms 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; 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); 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); vision/eye phenotype

Gene ontology

• Biological process: actin filament organization;cell communication by chemical coupling;cell communication by electrical coupling;positive regulation of synaptic plasticity;maintenance of protein location in cell;regulation of neuronal synaptic plasticity;regulation of dendrite development;cytoplasmic sequestering of protein;positive regulation of dendritic spine morphogenesis;neural precursor cell proliferation;positive regulation of receptor localization to synapse
• Cellular component: cytoplasm;cytoskeleton;gap junction;postsynaptic density;actin cytoskeleton;dendrite;growth cone;cortical cytoskeleton;actomyosin;postsynaptic membrane;glutamatergic synapse;postsynaptic cytosol
• Molecular function: actin binding;protein binding;profilin binding;cadherin binding