SNTB1 syntrophin beta 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SNTB1provided by HGNC
Official Full Name: syntrophin beta 1provided by HGNC
Primary source: HGNC:HGNC:11168
See related: Ensembl:ENSG00000172164 MIM:600026; AllianceGenome:HGNC:11168
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: A1B; SNT2; BSYN2; 59-DAP; DAPA1B; SNT2B1; TIP-43
Summary: Dystrophin is a large, rod-like cytoskeletal protein found at the inner surface of muscle fibers. Dystrophin is missing in Duchenne Muscular Dystrophy patients and is present in reduced amounts in Becker Muscular Dystrophy patients. The protein encoded by this gene is a peripheral membrane protein found associated with dystrophin and dystrophin-related proteins. This gene is a member of the syntrophin gene family, which contains at least two other structurally-related genes. [provided by RefSeq, Jul 2008]
Expression: Broad expression in thyroid (RPKM 41.8), adrenal (RPKM 32.7) and 22 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 8q24.12

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	8	NC_000008.11 (120535756..120812046, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	8	NC_060932.1 (121664208..121941521, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	8	NC_000008.10 (121547996..121824286, complement)

Chromosome 8 - NC_000008.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The SNTB1 and ZFHX1B gene have susceptibility in northern Han Chinese populations with high myopia.
Title: The SNTB1 and ZFHX1B gene have susceptibility in northern Han Chinese populations with high myopia.
SNTB1 regulates colorectal cancer cell proliferation and metastasis through YAP1 and the WNT/beta-catenin pathway.
Title: SNTB1 regulates colorectal cancer cell proliferation and metastasis through YAP1 and the WNT/β-catenin pathway.
Association of SNTB1 with High Myopia.
Title: Association of SNTB1 with High Myopia.
Association of the ZC3H11B, ZFHX1B and SNTB1 genes with myopia of different severities.
Title: Association of the ZC3H11B, ZFHX1B and SNTB1 genes with myopia of different severities.
Our study confirms that the two susceptibility loci ZFHX1B and SNTB1 are associated with moderate to high myopia in a Han Chinese population, as well as in a European population, when both SNPs are combined.
Title: Association and interaction of myopia with SNP markers rs13382811 and rs6469937 at ZFHX1B and SNTB1 in Han Chinese and European populations.
SNPs within the SNTB1 gene are associated with increased risk of oral cancer.
Title: Single nucleotide polymorphisms in an Indian cohort and association of CNTN4, MMP2 and SNTB1 variants with oral cancer.
SNTB1 and MCPH1 are located on chromosome 8, which may be involved in neuroticism, avoidant personality and depression.
Title: Association of microcephalin 1, syntrophin-beta 1, and other genes with automatic thoughts in the Japanese population.
beta1-syntrophin acts through a class-I PDZ interaction with the C terminus of ABCA1 to regulate the cellular distribution and activity of the transporter
Title: Purification of ATP-binding cassette transporter A1 and associated binding proteins reveals the importance of beta1-syntrophin in cholesterol efflux.

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
A genome-wide meta-analysis identifies novel loci associated with schizophrenia and bipolar disorder. EBI GWAS Catalog EBI GWAS CatalogPubMed
A genome-wide meta-analysis identifies two novel loci associated with high myopia in the Han Chinese population. EBI GWAS Catalog EBI GWAS CatalogPubMed
Common variants at 5q22 associate with pediatric eosinophilic esophagitis. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study identifies ZFHX1B as a susceptibility locus for severe myopia. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of chronic periodontitis in a general German population. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Nef	nef	Yeast two hybrid assay identifies the HIV-1 Nef-interacting protein syntrophin	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

WI-17825 (e-PCR)
- UniSTS:38656

WI-17164 (e-PCR)
- UniSTS:52225

RH92195 (e-PCR)
- UniSTS:91704

D8S1112 (e-PCR), detects polymorphism
- UniSTS:52306

SHGC-142320 (e-PCR)
- UniSTS:171388

RH45192 (e-PCR)
- UniSTS:30599

WIAF-2216 (e-PCR)
- UniSTS:41632

G59991 (e-PCR)
- UniSTS:137126

RH119080 (e-PCR)
- UniSTS:138413

STS-N30895 (e-PCR)
- UniSTS:31968

D8S1999 (e-PCR)
- UniSTS:5603

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables PDZ domain binding	IEA Inferred from Electronic Annotation more info
enables actin binding	IEA Inferred from Electronic Annotation more info
enables calmodulin binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables structural molecule activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in muscle contraction	TAS Traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in cytoskeleton	IEA Inferred from Electronic Annotation more info
part_of dystrophin-associated glycoprotein complex	IBA Inferred from Biological aspect of Ancestor more info
located_in focal adhesion	HDA more info	PubMed
is_active_in intracellular anatomical structure	IBA Inferred from Biological aspect of Ancestor more info
part_of protein-containing complex	IDA Inferred from Direct Assay more info	PubMed
located_in sarcolemma	IEA Inferred from Electronic Annotation more info
is_active_in synapse	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: beta-1-syntrophin

Names: 59 kDa dystrophin-associated protein A1 basic component 1; dystrophin-associated protein A1, 59kD, basic component 1; syntrophin, beta 1 (dystrophin-associated protein A1, 59kDa, basic component 1); syntrophin-2; tax interaction protein 43

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_021021.4 → NP_066301.1 beta-1-syntrophin

See identical proteins and their annotated locations for NP_066301.1

Status: REVIEWED

Source sequence(s)

AC105142, AK292655, BC098573

Consensus CDS

CCDS6334.1

UniProtKB/Swiss-Prot

A8K9E0, O14912, Q13884, Q4KMG8

Related

ENSP00000431124.1, ENST00000517992.2

Conserved Domains (4) summary

smart00233
Location:323 → 433

PH; Pleckstrin homology domain

cd00992
Location:111 → 192

PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

cd01258
Location:242 → 299

PHsplit_syntrophin; Syntrophin Split Pleckstrin homology (PH) domain

pfam00169
Location:323 → 433

PH; PH domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000008.11 Reference GRCh38.p14 Primary Assembly

Range

120535756..120812046 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047422126.1 → XP_047278082.1 beta-1-syntrophin isoform X2
XM_047422127.1 → XP_047278083.1 beta-1-syntrophin isoform X2
XM_011517239.3 → XP_011515541.1 beta-1-syntrophin isoform X1

UniProtKB/TrEMBL

A0A3B3ITC2

Related

ENSP00000497707.1, ENST00000648490.1

Conserved Domains (4) summary

smart00233
Location:323 → 375

PH; Pleckstrin homology domain

cd00992
Location:111 → 192

PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

cd01258
Location:242 → 299

PHsplit_syntrophin; Syntrophin Split Pleckstrin homology (PH) domain

pfam00169
Location:323 → 375

PH; PH domain