SNTA1

syntrophin alpha 1, the group of PDZ domain containing

Basic information

Region (hg38): 20:33407956-33443763

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

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Long QT syndrome 12	AD	Cardiovascular	Surveillance (eg, with electrocardiography), preventive measures and medical management may be beneficial to decrease morbidity and mortality	Cardiovascular	10220144; 18591664

ClinVar

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

• Long QT syndrome (262 variants)
• Cardiovascular phenotype (212 variants)
• not provided (138 variants)
• Long QT syndrome 12 (103 variants)
• not specified (57 variants)
• Congenital long QT syndrome (26 variants)
• Inborn genetic diseases (7 variants)
• Long QT syndrome 1 (3 variants)
• Becker muscular dystrophy (1 variants)
• Long QT syndrome 2 (1 variants)
• Brugada syndrome (1 variants)
• Ventricular fibrillation, paroxysmal familial, type 1 (1 variants)
• SNTA1-related condition (1 variants)
• Ventricular tachycardia (1 variants)
• Primary dilated cardiomyopathy (1 variants)
• Sick sinus syndrome (1 variants)
• Duchenne muscular dystrophy (1 variants)
• Wolff-Parkinson-White pattern (1 variants)
• Atrial fibrillation;Long QT syndrome (1 variants)
• Dilated cardiomyopathy 3B (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.

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			3	118		121
missense		1	194	6	2	203
nonsense			5			5
start loss			1			1
frameshift			7			7
inframe indel						0
splice donor/acceptor (+/-2bp)			5			5
splice region			7	11	1	19
non coding			11	25	7	43
Total	0	1	226	149	9

Highest pathogenic variant AF is 0.0000131

Variants in SNTA1

This is a list of pathogenic ClinVar variants found in the SNTA1 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-33408095-C-G		Long QT syndrome 12	Uncertain significance (Aug 19, 2021)
20-33408164-C-T		Long QT syndrome 12 • Congenital long QT syndrome	Benign/Likely benign (Jan 12, 2018)
20-33408165-G-A		Congenital long QT syndrome • Long QT syndrome 12	Benign/Likely benign (Jan 12, 2018)
20-33408174-C-T		Long QT syndrome 12	Uncertain significance (Jan 13, 2018)
20-33408276-G-A		Long QT syndrome 12	Conflicting classifications of pathogenicity (Jan 12, 2018)
20-33408375-G-A		Long QT syndrome 12	Uncertain significance (Jan 13, 2018)
20-33408385-C-T		Congenital long QT syndrome • Long QT syndrome 12	Benign/Likely benign (Jan 12, 2018)
20-33408428-G-T		Long QT syndrome 12 • Congenital long QT syndrome	Conflicting classifications of pathogenicity (Jan 12, 2018)
20-33408493-G-A		not specified	Likely benign (Nov 20, 2015)
20-33408499-G-A		SNTA1-related disorder	Conflicting classifications of pathogenicity (May 06, 2019)
20-33408501-C-T		Congenital long QT syndrome • Long QT syndrome 12	Uncertain significance (Jan 12, 2018)
20-33408504-C-CTTCT		Cardiovascular phenotype	Likely benign (Jun 16, 2023)
20-33408507-C-A		Long QT syndrome	Uncertain significance (Mar 22, 2021)
20-33408519-C-A		Cardiovascular phenotype	Likely benign (Feb 24, 2024)
20-33408520-C-G		Long QT syndrome	Uncertain significance (Apr 22, 2019)
20-33408521-C-T		Long QT syndrome 12 • Long QT syndrome	Uncertain significance (Oct 03, 2023)
20-33408526-C-T		Cardiovascular phenotype	Uncertain significance (Mar 09, 2022)
20-33408526-CG-C		not specified	Uncertain significance (Feb 06, 2018)
20-33408527-G-A		Long QT syndrome • Long QT syndrome 12	Uncertain significance (Jun 28, 2022)
20-33408537-G-T		Long QT syndrome • Long QT syndrome 12 • Cardiovascular phenotype	Benign/Likely benign (Jan 31, 2024)
20-33408538-G-A		Long QT syndrome 12	Uncertain significance (Dec 06, 2021)
20-33408539-C-G		Long QT syndrome • Long QT syndrome 12 • Cardiovascular phenotype	Uncertain significance (Mar 13, 2023)
20-33408540-C-T		Long QT syndrome • Cardiovascular phenotype	Likely benign (Oct 05, 2022)
20-33408541-G-A		Long QT syndrome • Long QT syndrome 12 • Cardiovascular phenotype	Uncertain significance (Jan 30, 2023)
20-33408541-G-T		Long QT syndrome	Uncertain significance (Nov 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SNTA1	protein_coding	protein_coding	ENST00000217381	8	35938

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00564	0.990	125724	0	24	125748	0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.17	203	256	0.794	0.0000165	3151
Missense in Polyphen		64	90.114	0.71021		1105
Synonymous	-0.0190	116	116	1.00	0.00000798	1124
Loss of Function	2.49	7	18.6	0.376	9.90e-7	218

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000214	0.000213
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000124	0.000123
Middle Eastern	0.0000544	0.0000544
South Asian	0.000131	0.000131
Other	0.000163	0.000163

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

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

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