GeneBe

SNTA1

syntrophin alpha 1, the group of PDZ domain containing

Basic information

Region (hg38): 20:33407957-33443763

Previous symbols: [ "SNT1" ]

Links

ENSG00000101400 ∙ NCBI:6640 ∙ OMIM:601017 ∙ HGNC:11167 ∙ Uniprot:Q13424 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • long QT syndrome 12 (Limited), mode of inheritance: AD
  • long QT syndrome 12 (Limited), mode of inheritance: AD
  • long QT syndrome (Disputed Evidence), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Long QT syndrome 12ADCardiovascularSurveillance (eg, with electrocardiography), preventive measures and medical management may be beneficial to decrease morbidity and mortalityCardiovascular10220144; 18591664

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SNTA1 gene.

  • Cardiovascular_phenotype (378 variants)
  • Long_QT_syndrome (357 variants)
  • not_provided (143 variants)
  • Long_QT_syndrome_12 (92 variants)
  • not_specified (62 variants)
  • Congenital_long_QT_syndrome (18 variants)
  • SNTA1-related_disorder (10 variants)
  • Long_QT_syndrome_1 (2 variants)
  • Wolff-Parkinson-White_pattern (1 variants)
  • Dilated_cardiomyopathy_3B (1 variants)
  • Atrial_fibrillation (1 variants)
  • Long_QT_syndrome_2 (1 variants)
  • Becker_muscular_dystrophy (1 variants)
  • Ventricular_fibrillation (1 variants)
  • Sick_sinus_syndrome (1 variants)
  • Ventricular_tachycardia (1 variants)
  • Primary_dilated_cardiomyopathy (1 variants)
  • Duchenne_muscular_dystrophy (1 variants)
  • Ventricular_fibrillation,_paroxysmal_familial,_type_1 (1 variants)
  • Brugada_syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNTA1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003098.3. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
4
clinvar
184
clinvar
1
clinvar
 189
missense
2
clinvar
275
clinvar
48
clinvar
3
clinvar
 328
nonsense
7
clinvar
 7
start loss
2
 2
frameshift
11
clinvar
 11
splice donor/acceptor (+/-2bp)
6
clinvar
 6
Total 0 2 305 232 4

Highest pathogenic variant AF is 0.0000254037

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SNTA1protein_codingprotein_codingENST00000217381 835938
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.005640.9901257240241257480.0000954
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.172032560.7940.00001653151
Missense in Polyphen6490.1140.710211105
Synonymous-0.01901161161.000.000007981124
Loss of Function2.49718.60.3769.90e-7218

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0002140.000213
Ashkenazi Jewish0.000.00
East Asian0.00005440.0000544
Finnish0.000.00
European (Non-Finnish)0.0001240.000123
Middle Eastern0.00005440.0000544
South Asian0.0001310.000131
Other0.0001630.000163

dbNSFP

Source: dbNSFP

Function
FUNCTION: Adapter protein that binds to and probably organizes the subcellular localization of a variety of membrane proteins. May link various receptors to the actin cytoskeleton and the extracellular matrix via the dystrophin glycoprotein complex. Plays an important role in synapse formation and in the organization of UTRN and acetylcholine receptors at the neuromuscular synapse. Binds to phosphatidylinositol 4,5- bisphosphate (By similarity). {ECO:0000250}.;
Disease
DISEASE: Long QT syndrome 12 (LQT12) [MIM:612955]: A heart disorder characterized by a prolonged QT interval on the ECG and polymorphic ventricular arrhythmias. They cause syncope and sudden death in response to exercise or emotional stress, and can present with a sentinel event of sudden cardiac death in infancy. {ECO:0000269|PubMed:18591664, ECO:0000269|PubMed:19684871}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway
Disopyramide Action Pathway;Procainamide (Antiarrhythmic) Action Pathway;Phenytoin (Antiarrhythmic) Action Pathway;Fosphenytoin (Antiarrhythmic) Action Pathway;Bopindolol Action Pathway;Timolol Action Pathway;Carteolol Action Pathway;Bevantolol Action Pathway;Practolol Action Pathway;Dobutamine Action Pathway;Isoprenaline Action Pathway;Arbutamine Action Pathway;Amiodarone Action Pathway;Levobunolol Action Pathway;Metipranolol Action Pathway;Mexiletine Action Pathway;Lidocaine (Antiarrhythmic) Action Pathway;Quinidine Action Pathway;Sotalol Action Pathway;Epinephrine Action Pathway;Betaxolol Action Pathway;Atenolol Action Pathway;Alprenolol Action Pathway;Acebutolol Action Pathway;Muscle/Heart Contraction;Diltiazem Action Pathway;Propranolol Action Pathway;Pindolol Action Pathway;Penbutolol Action Pathway;Oxprenolol Action Pathway;Metoprolol Action Pathway;Esmolol Action Pathway;Bisoprolol Action Pathway;Bupranolol Action Pathway;Nebivolol Action Pathway;Amlodipine Action Pathway;Verapamil Action Pathway;Nitrendipine Action Pathway;Nisoldipine Action Pathway;Nimodipine Action Pathway;Ibutilide Action Pathway;Tocainide Action Pathway;Flecainide Action Pathway;Isradipine Action Pathway;Fosphenytoin (Antiarrhythmic) Metabolism Pathway;Nifedipine Action Pathway;Felodipine Action Pathway;Nadolol Action Pathway;Carvedilol Action Pathway;Labetalol Action Pathway;Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways;Signaling mediated by p38-gamma and p38-delta (Consensus)

Recessive Scores

pRec
0.133

Intolerance Scores

loftool
0.386
rvis_EVS
-0.36
rvis_percentile_EVS
29.16

Haploinsufficiency Scores

pHI
0.134
hipred
Y
hipred_score
0.853
ghis
0.539

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.717

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Snta1
Phenotype
homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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);

Gene ontology

Biological process
regulation of heart rate;muscle contraction;regulation of ventricular cardiac muscle cell membrane repolarization;ventricular cardiac muscle cell action potential;negative regulation of peptidyl-cysteine S-nitrosylation;regulation of sodium ion transmembrane transport
Cellular component
cytoplasm;cytoskeleton;dystrophin-associated glycoprotein complex;syntrophin complex;lateral plasma membrane;cell junction;neuromuscular junction;protein-containing complex;sarcolemma;synapse
Molecular function
actin binding;structural molecule activity;protein binding;calmodulin binding;sodium channel regulator activity;PDZ domain binding;ion channel binding;nitric-oxide synthase binding;ATPase binding