DEF6 DEF6 guanine nucleotide exchange factor [Homo sapiens (human)] - Gene

Summary

Official Symbol: DEF6provided by HGNC
Official Full Name: DEF6 guanine nucleotide exchange factorprovided by HGNC
Primary source: HGNC:HGNC:2760
See related: Ensembl:ENSG00000023892 MIM:610094; AllianceGenome:HGNC:2760
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: IBP; SLAT; IMD87; SWAP70L
Summary: DEF6, or IBP, is a guanine nucleotide exchange factor (GEF) for RAC (MIM 602048) and CDC42 (MIM 116952) that is highly expressed in B and T cells (Gupta et al., 2003 [PubMed 12923183]).[supplied by OMIM, Mar 2008]
Expression: Broad expression in lymph node (RPKM 23.3), bone marrow (RPKM 22.5) and 21 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 6p21.31

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (35297818..35321771)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (35120899..35144853)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (35265595..35289548)

Chromosome 6 - NC_000006.12 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?

DEF6 deficiency, a mendelian susceptibility to EBV infection, lymphoma, and autoimmunity.
Title: DEF6 deficiency, a mendelian susceptibility to EBV infection, lymphoma, and autoimmunity.
High expression levels of DEF6 predicts a poor prognosis for patients with clear cell renal cell carcinoma.
Title: High expression levels of DEF6 predicts a poor prognosis for patients with clear cell renal cell carcinoma.
this study identifies Def6 as a novel inhibitor of osteoclastogenesis in physiological and inflammatory conditions
Title: Def6 Restrains Osteoclastogenesis and Inflammatory Bone Resorption.
DEF6 expression may serve as an independent prognostic factor, and interacted positively with p16 toward high tumor stage and shorter survival.
Title: DEF6 expression in ovarian carcinoma correlates with poor patient survival.
IBP was expressed ectopically in someoral squamous cell carcinoma samples and correlated significantly with tumor size, differentiation, clinical stage and distant metastases
Title: Ectopically expressed IBP promotes cell proliferation in oral squamous cell carcinoma.
DEF6, a novel substrate for the Tec kinase ITK, contains a glutamine-rich aggregation-prone region and forms cytoplasmic granules that co-localize with P-bodies.
Title: DEF6, a novel substrate for the Tec kinase ITK, contains a glutamine-rich aggregation-prone region and forms cytoplasmic granules that co-localize with P-bodies.
Observational study of gene-disease association and gene-gene interaction. (HuGE Navigator)
Title: Polymorphisms in innate immunity genes and risk of childhood leukemia.
Observational study of gene-disease association. (HuGE Navigator)
Title: The role of height-associated loci identified in genome wide association studies in the determination of pediatric stature.
level of expression correlates with the degree of malignancy in breast carcinoma tissues
Title: The ectopic expression of IFN regulatory factor 4-binding protein is correlated with the malignant behavior of human breast cancer cells.
Overexpression of the Interferon regulatory factor 4-binding protein is associated with Colorectal Carcinoma.
Title: Overexpression of the Interferon regulatory factor 4-binding protein in human colorectal cancer and its clinical significance.

Submit: New GeneRIF Correction See all GeneRIFs (14)

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

Associated conditions

Description	Tests
Immunodeficiency 87 and autoimmunity MedGen: C5562070 OMIM: 619573 GeneReviews: Not available	not available

EBI GWAS Catalog

Description
Many sequence variants affecting diversity of adult human height. 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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

MARC_2875-2876:991933604:3 (e-PCR)
- UniSTS:230968

RH91902 (e-PCR)
- UniSTS:92482

MARC_17107-17108:1020871549:3 (e-PCR)
- UniSTS:268221

AL035190 (e-PCR)
- UniSTS:94692

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables guanyl-nucleotide exchange factor activity	TAS Traceable Author Statement more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in regulation of small GTPase mediated signal transduction	TAS Traceable Author Statement more info
involved_in vesicle-mediated transport to the plasma membrane	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoskeleton	IEA Inferred from Electronic Annotation more info
located_in cytosol	IDA Inferred from Direct Assay more info
located_in cytosol	TAS Traceable Author Statement more info
located_in filopodium	IEA Inferred from Electronic Annotation more info
located_in membrane	HDA more info	PubMed
located_in nucleoplasm	IDA Inferred from Direct Assay more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in perinuclear region of cytoplasm	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: differentially expressed in FDCP 6 homolog

Names: DEF-6; IRF4-binding protein; SWAP-70-like adaptor protein of T cells

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_022047.4 → NP_071330.3 differentially expressed in FDCP 6 homolog

See identical proteins and their annotated locations for NP_071330.3

Status: VALIDATED

Source sequence(s)

AJ276095, AY241694, Z97832

Consensus CDS

CCDS4802.1

UniProtKB/Swiss-Prot

Q86VF4, Q9H4E7

UniProtKB/TrEMBL

B2RBP7

Related

ENSP00000319831.5, ENST00000316637.7

Conserved Domains (2) summary

cd13273
Location:210 → 319

PH_SWAP-70; Switch-associated protein-70 Pleckstrin homology (PH) domain

pfam00169
Location:217 → 312

PH; PH domain