ZFYVE16 zinc finger FYVE-type containing 16 [Homo sapiens (human)] - Gene

Summary

Official Symbol: ZFYVE16provided by HGNC
Official Full Name: zinc finger FYVE-type containing 16provided by HGNC
Primary source: HGNC:HGNC:20756
See related: Ensembl:ENSG00000039319 MIM:608880
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: PPP1R69
Summary: This gene encodes an endosomal protein that belongs to the FYVE zinc finger family of proteins. The encoded protein is thought to regulate membrane trafficking in the endosome. This protein functions as a scaffold protein in the transforming growth factor-beta signaling pathway and is involved in positive and negative feedback regulation of the bone morphogenetic protein signaling pathway. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Sep 2013]
Expression: Ubiquitous expression in brain (RPKM 10.1), endometrium (RPKM 9.9) and 25 other tissues See more
Orthologs: mouse all

Genomic context

Location:: 5q14.1

Exon count:: 24

Annotation release	Status	Assembly	Chr	Location
109	current	GRCh38.p12 (GCF_000001405.38)	5	NC_000005.10 (80407615..80483379)
105	previous assembly	GRCh37.p13 (GCF_000001405.25)	5	NC_000005.9 (79703386..79775498)

Chromosome 5 - NC_000005.10 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 FunctionsWhat's a GeneRIF?

Two SNPs located near the ZFYVE16 gene on chromosome 5 may have played a role in the early, multicompartment sacrocolpopexy failure.
Title: Genetic Mutation that May Contribute to Failure of Prolapse Surgery in White Women: A Case-Control Study.
Disruption of proper localization to the endosomes and the Y515 phosphorylation of Endofin enhanced MAPK activation suggesting that Endofin negatively modulates EGFR signaling following receptor endocytosis.
Title: EGF-induced tyrosine phosphorylation of Endofin is dependent on PI3K activity and proper localization to endosomes.
our study is the first to identify and validate Endofin, DCBLD2, and KIAA0582 as part of a complex EGF phosphotyrosine signaling network
Title: Phosphoproteomics identified Endofin, DCBLD2, and KIAA0582 as novel tyrosine phosphorylation targets of EGF signaling and Iressa in human cancer cells.
marked recruitment of TOM1 to endosomes was observed in cells overexpressing endofin or its carboxyl-terminal fragment
Title: Endofin recruits TOM1 to endosomes.
Facilitates TGF-beta signaling as a scaffold protein to promote the R-Smad-Smad4 complex formation by bringing Smad4 to the proximity of the receptor complex.
Title: Endofin, a FYVE domain protein, interacts with Smad4 and facilitates transforming growth factor-beta signaling.
The key mode of action of Trx-SARA was to reduce the level of Smad2 and Smad3 in complex with Smad4 after TGF-beta1 stimulation.
Title: Inhibition of transforming growth factor-beta1-induced signaling and epithelial-to-mesenchymal transition by the Smad-binding peptide aptamer Trx-SARA.

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)

Pathways from BioSystems

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BMP receptor signaling, organism-specific biosystem (from Pathway Interaction Database)
BMP receptor signaling, organism-specific biosystem
BMP receptor signaling
Endocytosis, organism-specific biosystem (from KEGG)
Endocytosis, organism-specific biosystemEndocytosis is a mechanism for cells to remove ligands, nutrients, and plasma membrane (PM) proteins, and lipids from the cell surface, bringing them into the cell interior. Transmembrane proteins en...
Endocytosis, conserved biosystem (from KEGG)
Endocytosis, conserved biosystemEndocytosis is a mechanism for cells to remove ligands, nutrients, and plasma membrane (PM) proteins, and lipids from the cell surface, bringing them into the cell interior. Transmembrane proteins en...
Signal Transduction, organism-specific biosystem (from REACTOME)
Signal Transduction, organism-specific biosystemSignal transduction is a process in which extracellular signals elicit changes in cell state and activity. Transmembrane receptors sense changes in the cellular environment by binding ligands, such a...
Signaling by BMP, organism-specific biosystem (from REACTOME)
Signaling by BMP, organism-specific biosystemBone morphogenetic proteins (BMPs) have many biological activities in various tissues, including bone, cartilage, blood vessels, heart, kidney, neurons, liver and lung. They are members of the Transf...
TGF-beta Signaling Pathway, organism-specific biosystem (from WikiPathways)
TGF-beta Signaling Pathway, organism-specific biosystemThe signal transduction mechanisms underlying the pathophysiological activities of transforming growth factor-? (TGF-?) have been extensively studied since its discovery nearly 30 years ago. TGF-? li...
TGF-beta receptor signaling, organism-specific biosystem (from Pathway Interaction Database)
TGF-beta receptor signaling, organism-specific biosystem
TGF-beta receptor signaling
TGF-beta signaling pathway, organism-specific biosystem (from KEGG)
TGF-beta signaling pathway, organism-specific biosystemThe transforming growth factor-beta (TGF-beta) family members, which include TGF-betas, activins and bone morphogenetic proteins (BMPs), are structurally related secreted cytokines found in species r...
TGF-beta signaling pathway, conserved biosystem (from KEGG)
TGF-beta signaling pathway, conserved biosystemThe transforming growth factor-beta (TGF-beta) family members, which include TGF-betas, activins and bone morphogenetic proteins (BMPs), are structurally related secreted cytokines found in species r...

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

STS-R68242 (e-PCR)
- UniSTS:64512

WI-17790 (e-PCR)
- UniSTS:41229

PMC156606P1 (e-PCR)
- UniSTS:271408

PMC156606P4 (e-PCR)
- UniSTS:271411

D8S2279 (e-PCR)
- UniSTS:473907

WI-15051 (e-PCR)
- UniSTS:5708

D15S1477 (e-PCR)
- UniSTS:474482

ZFYVE16 (e-PCR)
- UniSTS:504955

SHGC-84992 (e-PCR)
- UniSTS:104913

RH70374 (e-PCR)
- UniSTS:72408

Homology

Homologs of the ZFYVE16 gene: The ZFYVE16 gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, chicken, zebrafish, and frog.
Orthologs from Annotation Pipeline: 213 organisms have orthologs with human gene ZFYVE16
Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
1-phosphatidylinositol binding	IDA Inferred from Direct Assay more info	PubMed
metal ion binding	IEA Inferred from Electronic Annotation more info
phosphatidylinositol-3,4,5-trisphosphate binding	IDA Inferred from Direct Assay more info	PubMed
protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
BMP signaling pathway	TAS Traceable Author Statement more info
endosomal transport	IBA Inferred from Biological aspect of Ancestor more info	PubMed
endosomal transport	IMP Inferred from Mutant Phenotype more info	PubMed
protein targeting to lysosome	IBA Inferred from Biological aspect of Ancestor more info	PubMed
protein targeting to lysosome	IMP Inferred from Mutant Phenotype more info	PubMed
regulation of endocytosis	TAS Traceable Author Statement more info	PubMed
signal transduction	NAS Non-traceable Author Statement more info	PubMed
vesicle organization	NAS Non-traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
cytosol	IDA Inferred from Direct Assay more info
early endosome	IBA Inferred from Biological aspect of Ancestor more info	PubMed
early endosome	IDA Inferred from Direct Assay more info	PubMed
early endosome membrane	IBA Inferred from Biological aspect of Ancestor more info	PubMed
early endosome membrane	TAS Traceable Author Statement more info
intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info

General protein information

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Preferred Names: zinc finger FYVE domain-containing protein 16

Names: endosome-associated FYVE-domain protein; protein phosphatase 1, regulatory subunit 69; zinc finger, FYVE domain containing 16

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_001105251.4 → NP_001098721.2 zinc finger FYVE domain-containing protein 16 isoform a

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3 and 5 encode the same protein (isoform a).

Source sequence(s)

AC008771

Consensus CDS

CCDS4050.1

Related

ENSP00000423663.1, ENST00000510158.5
NM_001284236.3 → NP_001271165.2 zinc finger FYVE domain-containing protein 16 isoform a

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2 ,3 and 5 encode the same protein (isoform a).

Source sequence(s)

AC008771

Consensus CDS

CCDS4050.1

Related

ENSP00000426848.1, ENST00000505560.5

Conserved Domains (2) summary

cd15729
Location:738 → 804

FYVE_endofin; FYVE domain found in endofin and similar proteins

pfam11979
Location:1167 → 1515

DUF3480; Domain of unknown function (DUF3480)
NM_001284237.2 → NP_001271166.2 zinc finger FYVE domain-containing protein 16 isoform b

Status: REVIEWED

Description

Transcript Variant: This variant (4) lacks several exons in the 3' coding region and contains a 3' terminal exon that extends past a splice site that is used in variant 1 resulting in an early stop codon, and a different 3' UTR, compared to variant 1. The encoded protein (isoform b) has a distinct C-terminus and is shorter than isoform a.

Source sequence(s)

AC008771
NM_001349434.2 → NP_001336363.2 zinc finger FYVE domain-containing protein 16 isoform a

Status: REVIEWED

Description

Transcript Variant: This variant (5) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3 and 5 encode the same protein (isoform a).

Source sequence(s)

AC008771

Consensus CDS

CCDS4050.1
NM_014733.6 → NP_055548.4 zinc finger FYVE domain-containing protein 16 isoform a

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longer isoform (a). Variants 1, 2, 3 and 5 encode the same protein (isoform a).

Source sequence(s)

AC008771

Consensus CDS

CCDS4050.1

Related

ENSP00000337159.5, ENST00000338008.9

RNA

NR_146172.1 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (6) contains three alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AB002303, AC008771, AL833087, BC063868, CB854699, DA216169
NR_146173.1 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (7) contains two alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AB002303, AC008771, AL833087, BC063868, CB854699, DA216169, DA216340
NR_146174.1 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (8) contains two alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AB002303, AC008771, AL833087, BC063868, CB854699, DA216169

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p13 Primary Assembly

Genomic

NC_000005.10 Reference GRCh38.p13 Primary Assembly

Range

80407615..80483379

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005248632.4 → XP_005248689.1 zinc finger FYVE domain-containing protein 16 isoform X1

See identical proteins and their annotated locations for XP_005248689.1

UniProtKB/Swiss-Prot

Q7Z3T8

Conserved Domains (2) summary

cd15729
Location:738 → 804

FYVE_endofin; FYVE domain found in endofin and similar proteins

pfam11979
Location:1167 → 1515

DUF3480; Domain of unknown function (DUF3480)
XM_017010092.2 → XP_016865581.1 zinc finger FYVE domain-containing protein 16 isoform X1

UniProtKB/Swiss-Prot

Q7Z3T8

Conserved Domains (2) summary

cd15729
Location:738 → 804

FYVE_endofin; FYVE domain found in endofin and similar proteins

pfam11979
Location:1167 → 1515

DUF3480; Domain of unknown function (DUF3480)
XM_017010091.1 → XP_016865580.1 zinc finger FYVE domain-containing protein 16 isoform X1

UniProtKB/Swiss-Prot

Q7Z3T8

Conserved Domains (2) summary

cd15729
Location:738 → 804

FYVE_endofin; FYVE domain found in endofin and similar proteins

pfam11979
Location:1167 → 1515

DUF3480; Domain of unknown function (DUF3480)
XM_024446270.1 → XP_024302038.1 zinc finger FYVE domain-containing protein 16 isoform X1

Conserved Domains (2) summary

cd15729
Location:738 → 804

FYVE_endofin; FYVE domain found in endofin and similar proteins

pfam11979
Location:1167 → 1515

DUF3480; Domain of unknown function (DUF3480)
XM_024446273.1 → XP_024302041.1 zinc finger FYVE domain-containing protein 16 isoform X2

Conserved Domains (1) summary

pfam11979
Location:355 → 703

DUF3480; Domain of unknown function (DUF3480)
XM_024446271.1 → XP_024302039.1 zinc finger FYVE domain-containing protein 16 isoform X2

Conserved Domains (1) summary

pfam11979
Location:355 → 703

DUF3480; Domain of unknown function (DUF3480)
XM_024446272.1 → XP_024302040.1 zinc finger FYVE domain-containing protein 16 isoform X2

Conserved Domains (1) summary

pfam11979
Location:355 → 703

DUF3480; Domain of unknown function (DUF3480)
XM_017010096.1 → XP_016865585.1 zinc finger FYVE domain-containing protein 16 isoform X3