SNTB1

syntrophin beta 1, the group of PDZ domain containing|Pleckstrin homology domain containing

Basic information

Region (hg38): 8:120535744-120813273

Previous symbols: [ "SNT2B1" ]

Links

ENSG00000172164 ∙ NCBI:6641 ∙ OMIM:600026 ∙ HGNC:11168 ∙ Uniprot:Q13884 ∙ 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 SNTB1 gene.

• Inborn genetic diseases (32 variants)
• Lip and oral cavity carcinoma (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNTB1 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						0
missense			32			32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	32	0	0

Variants in SNTB1

This is a list of pathogenic ClinVar variants found in the SNTB1 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-120538902-A-G		not specified	Uncertain significance (Mar 11, 2022)
8-120538968-T-C		not specified	Uncertain significance (Mar 07, 2024)
8-120541827-C-T		not specified	Uncertain significance (Dec 20, 2021)
8-120541845-G-C		not specified	Uncertain significance (Apr 21, 2022)
8-120541897-T-C		not specified	Uncertain significance (Nov 10, 2022)
8-120541904-G-A		not specified	Uncertain significance (Jun 27, 2023)
8-120541974-G-A		not specified	Uncertain significance (Dec 02, 2022)
8-120548896-G-A		not specified	Uncertain significance (Mar 17, 2023)
8-120575140-C-T		not specified	Uncertain significance (Jan 23, 2023)
8-120575207-T-G		not specified	Uncertain significance (Mar 06, 2023)
8-120632452-C-T		not specified	Uncertain significance (Jan 19, 2022)
8-120632488-C-A		not specified	Uncertain significance (Feb 09, 2023)
8-120632491-T-C		not specified	Uncertain significance (Jan 03, 2024)
8-120632532-C-G		not specified	Uncertain significance (Feb 17, 2023)
8-120632557-A-C		not specified	Uncertain significance (Dec 13, 2023)
8-120632601-C-T		not specified	Uncertain significance (May 18, 2023)
8-120632614-C-T		not specified	Uncertain significance (Jan 02, 2024)
8-120632616-G-A		not specified	Uncertain significance (Dec 21, 2023)
8-120632616-G-C		not specified	Uncertain significance (Oct 26, 2022)
8-120632620-G-A		not specified	Uncertain significance (Jul 12, 2023)
8-120693708-C-T		not specified	Uncertain significance (Jan 17, 2024)
8-120693715-C-T		not specified	Uncertain significance (Aug 19, 2023)
8-120693716-A-T		not specified	Uncertain significance (Nov 10, 2022)
8-120693729-C-T		not specified	Uncertain significance (Dec 20, 2023)
8-120693795-G-A		not specified	Uncertain significance (Nov 18, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SNTB1	protein_coding	protein_coding	ENST00000395601	7	277529

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00103	0.997	125691	0	57	125748	0.000227

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.919	345	300	1.15	0.0000150	3439
Missense in Polyphen		76	82.666	0.91936		970
Synonymous	1.72	102	127	0.806	0.00000668	1124
Loss of Function	2.68	9	22.8	0.394	0.00000131	242

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000211	0.000210
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.000647	0.000647
European (Non-Finnish)	0.000248	0.000246
Middle Eastern	0.000272	0.000272
South Asian	0.000103	0.0000980
Other	0.000326	0.000326

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 dystrophin glycoprotein complex.
• 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 (Consensus)

Recessive Scores

• pRec: 0.148

Intolerance Scores

• loftool: 0.482
• rvis_EVS: -0.47
• rvis_percentile_EVS: 23.51

Haploinsufficiency Scores

• pHI: 0.607
• hipred: Y
• hipred_score: 0.775
• ghis: 0.478

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.882

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sntb1

Gene ontology

• Biological process: muscle contraction
• Cellular component: cytoplasm;cytoskeleton;focal adhesion;dystrophin-associated glycoprotein complex;protein-containing complex;sarcolemma;synapse
• Molecular function: actin binding;structural molecule activity;protein binding;calmodulin binding;PDZ domain binding