PSD4 pleckstrin and Sec7 domain containing 4 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PSD4provided by HGNC
Official Full Name: pleckstrin and Sec7 domain containing 4provided by HGNC
Primary source: HGNC:HGNC:19096
See related: Ensembl:ENSG00000125637 MIM:614442; AllianceGenome:HGNC:19096
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: TIC; EFA6B
Summary: Predicted to enable guanyl-nucleotide exchange factor activity and phospholipid binding activity. Predicted to be involved in regulation of ARF protein signal transduction. Located in ruffle membrane. [provided by Alliance of Genome Resources, Nov 2024]
Expression: Ubiquitous expression in lymph node (RPKM 21.5), spleen (RPKM 20.1) and 22 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 2q14.1

Exon count:: 17

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (113173971..113209391)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (113600541..113635966)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (113931548..113966968)

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 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?

DDR1 promotes hepatocellular carcinoma metastasis through recruiting PSD4 to ARF6.
Title: DDR1 promotes hepatocellular carcinoma metastasis through recruiting PSD4 to ARF6.
TNF-alpha/NF-kappaB signaling epigenetically represses PSD4 transcription to promote alcohol-related hepatocellular carcinoma progression.
Title: TNF-α/NF-κB signaling epigenetically represses PSD4 transcription to promote alcohol-related hepatocellular carcinoma progression.
EFA6B regulates a stop signal for collective invasion in breast cancer.
Title: EFA6B regulates a stop signal for collective invasion in breast cancer.
results identify EFA6B as a novel antagonist in breast cancer and they point to its regulatory and signaling pathways as rational therapeutic targets in aggressive forms of this disease
Title: EFA6B antagonizes breast cancer.
One of the cytohesin family of guanine nucleotide exchange factors, Tic may act on the ARF family of GTP-binding proteins. A PH domain with similar sequence and relative position to those in other cytohesins may allow association with phosphoinositides.
Title: Cytohesins and centaurins: mediators of PI 3-kinase-regulated Arf signaling.

Submit: New GeneRIF Correction

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

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

D2S2911 (e-PCR)
- UniSTS:79481

RH92848 (e-PCR)
- UniSTS:91006

RH47027 (e-PCR)
- UniSTS:52889

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables guanyl-nucleotide exchange factor activity	IEA Inferred from Electronic Annotation more info
enables phospholipid binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in regulation of ARF protein signal transduction	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
NOT located_in cleavage furrow	IDA Inferred from Direct Assay more info	PubMed
located_in membrane	HDA more info	PubMed
is_active_in ruffle membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in ruffle membrane	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: PH and SEC7 domain-containing protein 4

Names: ADP-ribosylation factor guanine nucleotide-exchange factor 6; SEC7 homolog; exchange factor for ADP-ribosylation factor guanine nucleotide factor 6 B; exchange factor for ADP-ribosylation factor guanine nucleotide factor 6B; exchange factor for ARF6 B; pleckstrin homology and SEC7 domain-containing protein 4; telomeric of interleukin-1 cluster 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.

mRNA and Protein(s)

NM_012455.3 → NP_036587.2 PH and SEC7 domain-containing protein 4

See identical proteins and their annotated locations for NP_036587.2

Status: VALIDATED

Source sequence(s)

AC016683

Consensus CDS

CCDS33276.1

UniProtKB/Swiss-Prot

A6NEG7, A8K1Y0, O95621, Q4ZG34, Q6GPH8, Q8IYP4, Q8NDX1

Related

ENSP00000245796.6, ENST00000245796.11

Conserved Domains (3) summary

cd00171
Location:570 → 738

Sec7; Sec7 domain; Domain named after the S. cerevisiae SEC7 gene product. The Sec7 domain is the central domain of the guanine-nucleotide-exchange factors (GEFs) of the ADP-ribosylation factor family of small GTPases (ARFs) . It carries the exchange factor ...

cd13295
Location:772 → 900

PH_EFA6; Exchange Factor for ARF6 Pleckstrin homology (PH) domain

pfam00169
Location:794 → 892

PH; PH domain