DTNA

dystrobrevin alpha, the group of Zinc fingers ZZ-type

Basic information

Region (hg38): 18:34493290-34891844

Links

ENSG00000134769 ∙ NCBI:1837 ∙ OMIM:601239 ∙ HGNC:3057 ∙ Uniprot:Q9Y4J8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• left ventricular noncompaction 1 (Limited), mode of inheritance: AD
• Meniere disease (Limited), mode of inheritance: AD
• left ventricular noncompaction 1 (Limited), mode of inheritance: AD
• dilated cardiomyopathy (Limited), mode of inheritance: AD
• congenital heart disease (Disputed Evidence), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Left ventricular noncompaction 1	AD	Cardiovascular	The condition may affect cardiac function and may include arrhythmias, and surveillance (eg, with echocardiography and EKG), preventive measures, and medical management may be beneficial to decrease morbidity	Cardiovascular	11238270; 16427346

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DTNA gene.

• Left ventricular noncompaction 1 (367 variants)
• not provided (189 variants)
• not specified (105 variants)
• Inborn genetic diseases (13 variants)
• DTNA-related condition (5 variants)
• Left ventricular noncompaction cardiomyopathy (5 variants)
• Primary dilated cardiomyopathy (4 variants)
• Cardiomyopathy (3 variants)
• Primary familial hypertrophic cardiomyopathy (2 variants)
• See cases (1 variants)
• Noncompaction cardiomyopathy;Cardiac arrhythmia (1 variants)
• Hypertrophic cardiomyopathy (1 variants)
• Meniere disease (1 variants)
• Ventricular tachycardia;Primary dilated cardiomyopathy;Left ventricular noncompaction cardiomyopathy (1 variants)
• Primary dilated cardiomyopathy;Systolic heart failure (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DTNA 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				98	5	103
missense			182	7	3	192
nonsense			4			4
start loss						0
frameshift		1	4			5
inframe indel						0
splice donor/acceptor (+/-2bp)			5			5
splice region			12	21	3	36
non coding			10	87	80	177
Total	0	1	205	192	88

Highest pathogenic variant AF is 0.00000657

Variants in DTNA

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

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

Position	Type	Phenotype	Significance	ClinVar
18-34493498-C-A		not specified	Likely benign (Feb 12, 2016)
18-34493526-G-C		not specified	Likely benign (Dec 03, 2015)
18-34493576-G-A			Benign (May 06, 2019)
18-34593487-G-C			Likely benign (Mar 10, 2022)
18-34593534-C-T			Benign (Apr 22, 2015)
18-34593745-C-T			Likely benign (Sep 21, 2020)
18-34679369-A-T			Benign (Jun 23, 2018)
18-34679573-G-A		not specified	Likely benign (Jul 06, 2016)
18-34710406-G-C		not specified	Benign (Apr 17, 2014)
18-34710451-G-T		not specified	Likely benign (Sep 02, 2016)
18-34710457-T-C			Benign (Feb 10, 2016)
18-34710675-AGT-A			Benign (Nov 12, 2019)
18-34710675-AGTGT-A			Benign (Nov 04, 2020)
18-34710675-A-AGT			Benign (Feb 03, 2020)
18-34710675-A-AGTGT			Benign (Feb 03, 2020)
18-34755689-A-T			Benign (Jun 28, 2018)
18-34755697-A-G			Likely benign (Jun 14, 2018)
18-34755951-A-G		not specified	Benign (Jan 08, 2014)
18-34755980-A-G		Left ventricular noncompaction 1	Uncertain significance (Dec 25, 2021)
18-34755980-A-T		Left ventricular noncompaction 1	Uncertain significance (Sep 01, 2021)
18-34755985-A-T		Left ventricular noncompaction 1	Uncertain significance (Jan 20, 2023)
18-34755991-T-A		Left ventricular noncompaction 1	Uncertain significance (Jun 15, 2022)
18-34755991-T-C		Left ventricular noncompaction 1	Likely benign (Jul 26, 2019)
18-34755992-G-C		Left ventricular noncompaction 1	Uncertain significance (Jan 18, 2024)
18-34755993-G-C		not specified	Uncertain significance (May 22, 2014)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DTNA	protein_coding	protein_coding	ENST00000598334	18	398555

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.635	0.365	125729	0	19	125748	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.42	327	408	0.802	0.0000237	4758
Missense in Polyphen		86	140.92	0.61029		1749
Synonymous	0.0106	152	152	0.999	0.00000880	1395
Loss of Function	4.78	9	42.7	0.211	0.00000235	472

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000271	0.000271
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000704	0.0000703
Middle Eastern	0.000163	0.000163
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in the formation and stability of synapses as well as being involved in the clustering of nicotinic acetylcholine receptors.
• Disease: DISEASE: Left ventricular non-compaction 1 (LVNC1) [MIM:604169]: A form of left ventricular non-compaction, a cardiomyopathy due to myocardial morphogenesis arrest and characterized by a hypertrophic left ventricle, a severely thickened 2-layered myocardium, numerous prominent trabeculations, deep intertrabecular recesses, and poor systolic function. Clinical manifestations are variable. Some affected individuals experience no symptoms at all, others develop heart failure. In some cases, left ventricular non-compaction is associated with other congenital heart anomalies. LVNC1 is an autosomal dominant condition. {ECO:0000269|PubMed:11238270}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Recessive Scores

• pRec: 0.204

Intolerance Scores

• loftool: 0.180
• rvis_EVS: -0.51
• rvis_percentile_EVS: 21.65

Haploinsufficiency Scores

• pHI: 0.923
• hipred: Y
• hipred_score: 0.716
• ghis: 0.566

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.842

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dtna
• Phenotype: 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); 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton phenotype; muscle phenotype; limbs/digits/tail 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); growth/size/body region phenotype

Gene ontology

• Biological process: striated muscle contraction;signal transduction;chemical synaptic transmission;neuromuscular synaptic transmission
• Cellular component: cytoplasm;cell junction;axon;extrinsic component of cytoplasmic side of plasma membrane;protein-containing complex;sarcolemma;synapse
• Molecular function: protein binding;zinc ion binding;PDZ domain binding