SNTB2

syntrophin beta 2, the group of PDZ domain containing

Basic information

Region (hg38): 16:69187146-69309052

Previous symbols: [ "SNT2B2", "SNTL", "D16S2531E" ]

Links

ENSG00000168807 ∙ NCBI:6645 ∙ OMIM:600027 ∙ HGNC:11169 ∙ Uniprot:Q13425 ∙ 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 SNTB2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNTB2 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			28			28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	0	0

Variants in SNTB2

This is a list of pathogenic ClinVar variants found in the SNTB2 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-69187182-G-C		not specified	Uncertain significance (Apr 07, 2023)
16-69187186-C-T		not specified	Uncertain significance (Apr 06, 2024)
16-69187189-C-T		not specified	Uncertain significance (Dec 27, 2023)
16-69187223-G-C		not specified	Uncertain significance (Aug 22, 2023)
16-69187231-C-T		not specified	Uncertain significance (Jan 29, 2024)
16-69187387-C-T		not specified	Uncertain significance (Jan 23, 2024)
16-69187395-G-T		not specified	Uncertain significance (Jun 21, 2023)
16-69187438-T-G		not specified	Uncertain significance (Jul 09, 2021)
16-69187449-A-C		not specified	Uncertain significance (Feb 10, 2022)
16-69187452-C-T		not specified	Uncertain significance (Jan 29, 2024)
16-69187462-C-T		not specified	Uncertain significance (Dec 15, 2023)
16-69187479-G-A		not specified	Uncertain significance (Feb 27, 2024)
16-69187536-G-A		not specified	Uncertain significance (Sep 29, 2023)
16-69187723-C-T		not specified	Uncertain significance (Jan 17, 2024)
16-69245635-A-C		not specified	Uncertain significance (Apr 26, 2023)
16-69245638-A-G		not specified	Uncertain significance (Apr 23, 2024)
16-69245679-C-A		not specified	Uncertain significance (Sep 13, 2023)
16-69245719-C-T		not specified	Uncertain significance (Jan 24, 2023)
16-69245729-C-A		not specified	Uncertain significance (Oct 12, 2021)
16-69260097-G-A		not specified	Uncertain significance (Dec 19, 2022)
16-69260132-G-A		not specified	Uncertain significance (Apr 04, 2023)
16-69260144-A-G		not specified	Uncertain significance (Apr 23, 2024)
16-69260219-G-A		not specified	Uncertain significance (Apr 28, 2022)
16-69284092-C-G		not specified	Uncertain significance (Dec 05, 2022)
16-69284125-G-A		not specified	Uncertain significance (Mar 16, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SNTB2	protein_coding	protein_coding	ENST00000336278	7	121924

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000428	0.992	125737	0	11	125748	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.32	156	262	0.596	0.0000136	3420
Missense in Polyphen		23	60.744	0.37864		692
Synonymous	0.965	95	108	0.882	0.00000604	1163
Loss of Function	2.36	9	20.5	0.439	0.00000118	223

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.0000530	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

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. May play a role in the regulation of secretory granules via its interaction with PTPRN.
• 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: 0.140

Haploinsufficiency Scores

• pHI: 0.789
• hipred: Y
• hipred_score: 0.694
• ghis: 0.690

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.673

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sntb2
• 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); normal phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Cellular component: cytoplasm;microtubule;focal adhesion;dystrophin-associated glycoprotein complex;membrane;transport vesicle membrane;protein-containing complex;synapse
• Molecular function: RNA binding;actin binding;structural molecule activity;protein binding;calmodulin binding