FGD5 FYVE, RhoGEF and PH domain containing 5 [Homo sapiens (human)] - Gene

Summary

Official Symbol: FGD5provided by HGNC
Official Full Name: FYVE, RhoGEF and PH domain containing 5provided by HGNC
Primary source: HGNC:HGNC:19117
See related: Ensembl:ENSG00000154783 MIM:614788; AllianceGenome:HGNC:19117
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: ZFYVE23
Summary: Predicted to enable guanyl-nucleotide exchange factor activity and small GTPase binding activity. Predicted to be involved in actin cytoskeleton organization; filopodium assembly; and regulation of cell shape. Located in plasma membrane. [provided by Alliance of Genome Resources, Nov 2024]
Expression: Broad expression in spleen (RPKM 15.9), lung (RPKM 13.8) and 22 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 3p25.1

Exon count:: 21

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (14810688..14934571)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (14813154..14937021)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (14860469..14976078)

Chromosome 3 - NC_000003.12 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?

Common Variants on FGD5 Increase Hazard of Mortality or Rehospitalization in Patients With Heart Failure From the ASCEND-HF Trial.
Title: Common Variants on FGD5 Increase Hazard of Mortality or Rehospitalization in Patients With Heart Failure From the ASCEND-HF Trial.
FGD5 regulates endothelial cell PI3 kinase-beta to promote neo-angiogenesis.
Title: FGD5 regulates endothelial cell PI3 kinase-β to promote neo-angiogenesis.
Faciogenital dysplasia 5 confers the cancer stem cell-like traits of gastric cancer cells through enhancing Sox2 protein stability.
Title: Faciogenital dysplasia 5 confers the cancer stem cell-like traits of gastric cancer cells through enhancing Sox2 protein stability.
Long non-coding RNA FGD5-AS1 enhances osteosarcoma cell proliferation and migration by targeting miR-506-3p/RAB3D axis.
Title: Long non-coding RNA FGD5-AS1 enhances osteosarcoma cell proliferation and migration by targeting miR-506-3p/RAB3D axis.
lncRNA FGD5AS1 promotes breast cancer progression by regulating the hsamiR1955p/NUAK2 axis.
Title: lncRNA FGD5‑AS1 promotes breast cancer progression by regulating the hsa‑miR‑195‑5p/NUAK2 axis.
FGD5 facilitates tumor growth by regulating EGFR ubiquitination in gastric cancer.
Title: FGD5 facilitates tumor growth by regulating EGFR ubiquitination in gastric cancer.
A high level of lncFGD5-AS1 inhibits epithelial-to-Mesenchymal transition by regulating the miR-196a-5p/SMAD6/BMP axis in gastric Cancer.
Title: A high level of lncFGD5-AS1 inhibits epithelial-to-Mesenchymal transition by regulating the miR-196a-5p/SMAD6/BMP axis in gastric Cancer.
Faciogenital Dysplasia 5 supports cancer stem cell traits in basal-like breast cancer by enhancing EGFR stability.
Title: Faciogenital Dysplasia 5 supports cancer stem cell traits in basal-like breast cancer by enhancing EGFR stability.
*FGD5 tyrosine phosphorylation is essential for endothelial junction stabilization.
Title: VE-PTP inhibition stabilizes endothelial junctions by activating FGD5.
Human FYVE domain containing proteins, those within the faciogenital dysplasia (Fgd) subfamily are particularly divergent and couple with GTPases to exert unique cellular functions.
Title: Structure and function of the Fgd family of divergent FYVE domain proteins (1).

Submit: New GeneRIF Correction See all GeneRIFs (18)

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

D3S3380 (e-PCR)
- UniSTS:72209

G19158 (e-PCR)
- UniSTS:53575

RH24948 (e-PCR)
- UniSTS:88469

SHGC-83942 (e-PCR)
- UniSTS:103619

RH119842 (e-PCR)
- UniSTS:133587

D3S2881E (e-PCR)
- UniSTS:59612

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables guanyl-nucleotide exchange factor activity	IBA Inferred from Biological aspect of Ancestor more info
enables guanyl-nucleotide exchange factor activity	ISS Inferred from Sequence or Structural Similarity more info
enables guanyl-nucleotide exchange factor activity	TAS Traceable Author Statement more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables small GTPase binding	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in actin cytoskeleton organization	ISS Inferred from Sequence or Structural Similarity more info
involved_in cytoskeleton organization	ISS Inferred from Sequence or Structural Similarity more info
involved_in filopodium assembly	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of GTPase activity	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of cell shape	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of small GTPase mediated signal transduction	TAS Traceable Author Statement more info

Component	Evidence Code	Pubs
located_in Golgi apparatus	ISS Inferred from Sequence or Structural Similarity more info
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
located_in cytoskeleton	IEA Inferred from Electronic Annotation more info
located_in cytosol	TAS Traceable Author Statement more info
located_in early endosome	IEA Inferred from Electronic Annotation more info
located_in endoplasmic reticulum	IEA Inferred from Electronic Annotation more info
located_in lamellipodium	ISS Inferred from Sequence or Structural Similarity more info
located_in plasma membrane	IDA Inferred from Direct Assay more info
located_in ruffle	ISS Inferred from Sequence or Structural Similarity more info
located_in ruffle membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: FYVE, RhoGEF and PH domain-containing protein 5

Names: zinc finger FYVE domain-containing protein 23

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_001320276.2 → NP_001307205.1 FYVE, RhoGEF and PH domain-containing protein 5 isoform 2

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks an in-frame exon in the 3' coding region, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.

Source sequence(s)

AC090937, AW589887, BC144300, DB293373

UniProtKB/TrEMBL

B7ZM68

Related

ENSP00000445949.1, ENST00000543601.5

Conserved Domains (5) summary

cd15792
Location:1101 → 1223

PH1_FGD5; FYVE, RhoGEF and PH domain containing/faciogenital dysplasia protein 5, N-terminal Pleckstrin Homology (PH) domain

cd15742
Location:1237 → 1303

FYVE_FGD5; FYVE-like domain found in FYVE, RhoGEF and PH domain-containing protein 5 (FGD5) and similar proteins

pfam00169
Location:1116 → 1207

PH; PH domain

pfam00621
Location:896 → 1083

RhoGEF; RhoGEF domain

cl17171
Location:1356 → 1413

PH-like; Pleckstrin homology-like domain
NM_152536.4 → NP_689749.3 FYVE, RhoGEF and PH domain-containing protein 5 isoform 1

See identical proteins and their annotated locations for NP_689749.3

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AC087591, AC090937

Consensus CDS

CCDS46767.1

UniProtKB/Swiss-Prot

B3KVQ3, Q6MZY1, Q6ZNL6, Q7Z303, Q8IYP3, Q8N861, Q8N8G4

UniProtKB/TrEMBL

A0A2X0SFF2, A3KMQ0

Related

ENSP00000285046.5, ENST00000285046.10

Conserved Domains (5) summary

PHA03169
Location:132 → 323

PHA03169; hypothetical protein; Provisional

cd13237
Location:1366 → 1456

PH2_FGD5_FGD6; FYVE, RhoGEF and PH domain containing/faciogenital dysplasia proteins 5 and 6 pleckstrin homology (PH) domain, C-terminus

cd15792
Location:1101 → 1223

PH1_FGD5; FYVE, RhoGEF and PH domain containing/faciogenital dysplasia protein 5, N-terminal Pleckstrin Homology (PH) domain

cd15742
Location:1237 → 1303

FYVE_FGD5; FYVE-like domain found in FYVE, RhoGEF and PH domain-containing protein 5 (FGD5) and similar proteins

pfam00621
Location:896 → 1082

RhoGEF; RhoGEF domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000003.12 Reference GRCh38.p14 Primary Assembly

Range

14810688..14934571

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011533422.2 → XP_011531724.2 FYVE, RhoGEF and PH domain-containing protein 5 isoform X1
XM_011533423.2 → XP_011531725.2 FYVE, RhoGEF and PH domain-containing protein 5 isoform X3
XM_047447514.1 → XP_047303470.1 FYVE, RhoGEF and PH domain-containing protein 5 isoform X2
XM_047447515.1 → XP_047303471.1 FYVE, RhoGEF and PH domain-containing protein 5 isoform X4

Alternate T2T-CHM13v2.0

Genomic

NC_060927.1 Alternate T2T-CHM13v2.0

Range

14813154..14937021

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054345395.1 → XP_054201370.1 FYVE, RhoGEF and PH domain-containing protein 5 isoform X1
XM_054345396.1 → XP_054201371.1 FYVE, RhoGEF and PH domain-containing protein 5 isoform X2
XM_054345397.1 → XP_054201372.1 FYVE, RhoGEF and PH domain-containing protein 5 isoform X3
XM_054345398.1 → XP_054201373.1 FYVE, RhoGEF and PH domain-containing protein 5 isoform X4