SH3BP4 SH3 domain binding protein 4 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SH3BP4provided by HGNC
Official Full Name: SH3 domain binding protein 4provided by HGNC
Primary source: HGNC:HGNC:10826
See related: Ensembl:ENSG00000130147 MIM:605611; AllianceGenome:HGNC:10826
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: TTP; BOG25
Summary: This gene encodes a protein with 3 Asn-Pro-Phe (NPF) motifs, an SH3 domain, a PXXP motif, a bipartite nuclear targeting signal, and a tyrosine phosphorylation site. This protein is involved in cargo-specific control of clathrin-mediated endocytosis, specifically controlling the internalization of a specific protein receptor. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in salivary gland (RPKM 12.0), gall bladder (RPKM 8.4) and 24 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 2q37.2

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (234952017..235055714)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (235441072..235544683)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (235860661..235964358)

Chromosome 2 - NC_000002.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

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?

SH3BP4 promotes neuropilin-1 and alpha5-integrin endocytosis and is inhibited by Akt.
Title: SH3BP4 promotes neuropilin-1 and α5-integrin endocytosis and is inhibited by Akt.
The data uncover the tumor-suppressive role of SH3BP4 that functions as a negative feedback regulator of Wnt signaling through modulating beta-catenin's subcellular localization.
Title: SH3BP4 Regulates Intestinal Stem Cells and Tumorigenesis by Modulating β-Catenin Nuclear Localization.
A SNP in the 3'UTR of SH3BP4 (rs56161233) that overlaps predicted miR-100-binding sites and is predicted to disrupt several miRNA-mRNA interactions was associated with overall survival of laryngeal cancer.
Title: MicroRNA-Related Genetic Variants Associated with Survival of Head and Neck Squamous Cell Carcinoma.
SH3BP4 has been identified as a novel pigmentation gene. The SH3BP4 is a direct target of miR-125b. The SH3BP4 is transcriptionally regulated by MITF as its direct target.
Title: SH3BP4, a novel pigmentation gene, is inversely regulated by miR-125b and MITF.
SH3BP4 is a negative regulator of the Rag GTPase complex and amino acid-dependent mTORC1 signaling.
Title: SH3BP4 is a negative regulator of amino acid-Rag GTPase-mTORC1 signaling.
Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
Results show that TTP (SH3BP4), a SH3-containing protein, specifically regulates the internalization of the transferrin receptor (TfR).
Title: TTP specifically regulates the internalization of the transferrin receptor.

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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
Genome wide study of maternal and parent-of-origin effects on the etiology of orofacial clefts. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association scan for survival on dialysis in African-Americans with type 2 diabetes. 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	Genome-wide shRNA screening identifies SH3BP4, which is required for HIV-1 Nef-induced downregulation of CD4 in HeLa CD4+ cells	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

Cda19e02 (e-PCR)
- UniSTS:54901

SHGC-33127 (e-PCR)
- UniSTS:15993

WI-14192 (e-PCR)
- UniSTS:22462

A004W19 (e-PCR)
- UniSTS:24043

RH93190 (e-PCR)
- UniSTS:85758

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables GDP-dissociation inhibitor activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables small GTPase binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
NOT involved_in amino acid import	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cellular response to amino acid stimulus	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in endocytosis	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of GTPase activity	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of TOR signaling	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of cell growth	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of cell population proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of autophagy	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein localization to lysosome	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of catalytic activity	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in clathrin-coated pit	IEA Inferred from Electronic Annotation more info
located_in clathrin-coated vesicle	IEA Inferred from Electronic Annotation more info
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in extracellular exosome	HDA more info	PubMed
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: SH3 domain-binding protein 4

Names: EH-binding protein 10; transferrin receptor-trafficking protein

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.

Genomic

NG_033930.1 RefSeqGene

Range

5034..108731

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001371302.1 → NP_001358231.1 SH3 domain-binding protein 4

Status: REVIEWED

Source sequence(s)

AC010148, AC114814

Consensus CDS

CCDS2513.1

UniProtKB/Swiss-Prot

O95082, Q309A3, Q53QD0, Q53TD1, Q9P0V3

UniProtKB/TrEMBL

A8K594

Conserved Domains (3) summary

cd11757
Location:59 → 110

SH3_SH3BP4; Src Homology 3 domain of SH3 domain-binding protein 4

pfam07653
Location:658 → 722

SH3_2; Variant SH3 domain

cl02517
Location:324 → 404

ZU5; ZU5 domain
NM_001371303.1 → NP_001358232.1 SH3 domain-binding protein 4

Status: REVIEWED

Source sequence(s)

AC010148, AC114814

Consensus CDS

CCDS2513.1

UniProtKB/Swiss-Prot

O95082, Q309A3, Q53QD0, Q53TD1, Q9P0V3

UniProtKB/TrEMBL

A8K594

Conserved Domains (3) summary

cd11757
Location:59 → 110

SH3_SH3BP4; Src Homology 3 domain of SH3 domain-binding protein 4

pfam07653
Location:658 → 722

SH3_2; Variant SH3 domain

cl02517
Location:324 → 404

ZU5; ZU5 domain
NM_001371304.1 → NP_001358233.1 SH3 domain-binding protein 4

Status: REVIEWED

Source sequence(s)

AC010148, AC114814

Consensus CDS

CCDS2513.1

UniProtKB/Swiss-Prot

O95082, Q309A3, Q53QD0, Q53TD1, Q9P0V3

UniProtKB/TrEMBL

A8K594

Related

ENSP00000340237.4, ENST00000344528.8

Conserved Domains (3) summary

cd11757
Location:59 → 110

SH3_SH3BP4; Src Homology 3 domain of SH3 domain-binding protein 4

pfam07653
Location:658 → 722

SH3_2; Variant SH3 domain

cl02517
Location:324 → 404

ZU5; ZU5 domain
NM_001371305.1 → NP_001358234.1 SH3 domain-binding protein 4

Status: REVIEWED

Source sequence(s)

AC010148, AC114814

Consensus CDS

CCDS2513.1

UniProtKB/Swiss-Prot

O95082, Q309A3, Q53QD0, Q53TD1, Q9P0V3

UniProtKB/TrEMBL

A8K594

Conserved Domains (3) summary

cd11757
Location:59 → 110

SH3_SH3BP4; Src Homology 3 domain of SH3 domain-binding protein 4

pfam07653
Location:658 → 722

SH3_2; Variant SH3 domain

cl02517
Location:324 → 404

ZU5; ZU5 domain
NM_001371306.1 → NP_001358235.1 SH3 domain-binding protein 4

Status: REVIEWED

Source sequence(s)

AC010148, AC114814

Consensus CDS

CCDS2513.1

UniProtKB/Swiss-Prot

O95082, Q309A3, Q53QD0, Q53TD1, Q9P0V3

UniProtKB/TrEMBL

A8K594

Conserved Domains (3) summary

cd11757
Location:59 → 110

SH3_SH3BP4; Src Homology 3 domain of SH3 domain-binding protein 4

pfam07653
Location:658 → 722

SH3_2; Variant SH3 domain

cl02517
Location:324 → 404

ZU5; ZU5 domain
NM_014521.3 → NP_055336.1 SH3 domain-binding protein 4

See identical proteins and their annotated locations for NP_055336.1

Status: REVIEWED

Source sequence(s)

AF147747, BC057396

Consensus CDS

CCDS2513.1

UniProtKB/Swiss-Prot

O95082, Q309A3, Q53QD0, Q53TD1, Q9P0V3

UniProtKB/TrEMBL

A8K594

Related

ENSP00000375867.2, ENST00000392011.7

Conserved Domains (3) summary

cd11757
Location:59 → 110

SH3_SH3BP4; Src Homology 3 domain of SH3 domain-binding protein 4

pfam07653
Location:658 → 722

SH3_2; Variant SH3 domain

cl02517
Location:324 → 404

ZU5; ZU5 domain