ZFYVE28 zinc finger FYVE-type containing 28 [Homo sapiens (human)] - Gene

Summary

Official Symbol: ZFYVE28provided by HGNC
Official Full Name: zinc finger FYVE-type containing 28provided by HGNC
Primary source: HGNC:HGNC:29334
See related: Ensembl:ENSG00000159733 MIM:614176; AllianceGenome:HGNC:29334
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: LST2; LYST2; lst-2
Summary: Enables phosphatidylinositol-3-phosphate binding activity. Involved in negative regulation of epidermal growth factor-activated receptor activity. Located in cytosol and early endosome membrane. [provided by Alliance of Genome Resources, Nov 2024]
Expression: Ubiquitous expression in testis (RPKM 1.1), brain (RPKM 1.1) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 4p16.3

Exon count:: 16

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	4	NC_000004.12 (2269597..2418645, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	4	NC_060928.1 (2268369..2417399, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	4	NC_000004.11 (2271324..2420372, complement)

Chromosome 4 - NC_000004.12 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?

ZFYVE28 mediates insulin resistance by promoting phosphorylated insulin receptor degradation via increasing late endosomes production.
Title: ZFYVE28 mediates insulin resistance by promoting phosphorylated insulin receptor degradation via increasing late endosomes production.
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.
Study concludes that endosomal localization of Lst2 (ZFYVE28), along with an ability to divert incoming EGFR molecules to degradation in lysosomes, is regulated by ubiquitinylation/deubiquitinylation cycles.
Title: Monoubiquitinylation regulates endosomal localization of Lst2, a negative regulator of EGF receptor signaling.

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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 association study (GWAS) of Chagas cardiomyopathy in Trypanosoma cruzi seropositive subjects. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of clinical dimensions of schizophrenia: polygenic effect on disorganized symptoms. 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

D4S43 (e-PCR)
- UniSTS:147240

G34099 (e-PCR)
- UniSTS:61494

D4S43 (e-PCR)
- UniSTS:147270

D4S43 (e-PCR)
- UniSTS:147301

SHGC-31255 (e-PCR)
- UniSTS:4792

D4S522 (e-PCR)
- UniSTS:26558

D4S1193 (e-PCR)
- UniSTS:35015

D4S43 (e-PCR)
- UniSTS:146890

D4S43 (e-PCR)
- UniSTS:148221

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables phosphatidylinositol-3-phosphate binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in negative regulation of epidermal growth factor receptor signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of epidermal growth factor receptor signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of epidermal growth factor-activated receptor activity	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in cytosol	IDA Inferred from Direct Assay more info	PubMed
is_active_in early endosome membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in early endosome membrane	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: lateral signaling target protein 2 homolog

Names: hLst2; lateral signaling target-2 homolog; zinc finger FYVE domain-containing protein 28; zinc finger, FYVE domain containing 28

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_001172656.2 → NP_001166127.1 lateral signaling target protein 2 homolog isoform 3

Status: VALIDATED

Description

Transcript Variant: This variant (3) represents use of an alternate promoter and 5' UTR, uses an upstream start codon, and lacks an alternate in-frame exon, compared to variant 1. The resulting isoform (3) has a longer N-terminus and lacks an internal segment, compared to isoform 1.

Source sequence(s)

AB046863, AK293775, AK294710, AL645924, BC032605, BC137309, BM128958

Consensus CDS

CCDS54711.1

UniProtKB/Swiss-Prot

Q9HCC9

Related

ENSP00000425706.1, ENST00000511071.5

Conserved Domains (1) summary

cd15731
Location:780 → 844

FYVE_LST2; FYVE domain found in lateral signaling target protein 2 homolog (Lst2) and similar proteins
NM_001172657.2 → NP_001166128.1 lateral signaling target protein 2 homolog isoform 4

Status: VALIDATED

Description

Transcript Variant: This variant (4) represents use of an alternate promoter and 5' UTR, uses an upstream start codon, and uses an alternate 3' coding region and 3' UTR, compared to variant 1. The resulting isoform (4) has a longer N-terminus and a shorter and distinct C-terminus, compared to isoform 1.

Source sequence(s)

AL158068, AL645924, BC032605, BC053664

Consensus CDS

CCDS54712.1

UniProtKB/Swiss-Prot

Q9HCC9

Related

ENSP00000423694.1, ENST00000503000.1
NM_001172658.3 → NP_001166129.1 lateral signaling target protein 2 homolog isoform 5

Status: VALIDATED

Description

Transcript Variant: This variant (5) represents use of an alternate promoter and 5' UTR, uses an upstream start codon, and uses an alternate 3' coding region and 3' UTR, compared to variant 1. The resulting isoform (5) has a longer N-terminus and a shorter and distinct C-terminus, compared to isoform 1.

Source sequence(s)

AL645924, BC032605, BC035793, BC137310

Consensus CDS

CCDS54710.1

UniProtKB/Swiss-Prot

Q9HCC9

Related

ENSP00000422638.1, ENST00000509171.5
NM_001172659.2 → NP_001166130.1 lateral signaling target protein 2 homolog isoform 1

Status: VALIDATED

Description

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

Source sequence(s)

AB046863, AK294874, AK316484, BC035793, BC137310, BM128958

Consensus CDS

CCDS54708.1

UniProtKB/Swiss-Prot

Q9HCC9

Related

ENSP00000426299.1, ENST00000515312.5

Conserved Domains (1) summary

cd15731
Location:740 → 804

FYVE_LST2; FYVE domain found in lateral signaling target protein 2 homolog (Lst2) and similar proteins
NM_001172660.3 → NP_001166131.1 lateral signaling target protein 2 homolog isoform 6

Status: VALIDATED

Description

Transcript Variant: This variant (6) uses an alternate 3' coding region and 3' UTR, compared to variant 1. The resulting isoform (6) has a shorter and distinct C-terminus, compared to isoform 1.

Source sequence(s)

AK316484, BC035793, BC137310

Consensus CDS

CCDS54709.1

UniProtKB/Swiss-Prot

Q9HCC9

Related

ENSP00000425766.1, ENST00000515169.5
NM_020972.3 → NP_066023.2 lateral signaling target protein 2 homolog isoform 2

See identical proteins and their annotated locations for NP_066023.2

Status: VALIDATED

Description

Transcript Variant: This variant (2) represents use of an alternate promoter and 5' UTR and uses an upstream start codon, compared to variant 1. The resulting isoform (2) has a longer N-terminus, compared to isoform 1.

Source sequence(s)

AB046863, AK294874, AL645924, BC032605, BC137310, BM128958

Consensus CDS

CCDS33942.1

UniProtKB/Swiss-Prot

B2RP83, B3KX50, B7Z1Q7, B7Z2G9, B7Z2M2, B7ZB19, E9PB54, E9PB64, E9PG77, Q7Z6J3, Q9HCC9

Related

ENSP00000290974.3, ENST00000290974.7

Conserved Domains (1) summary

cd15731
Location:810 → 874

FYVE_LST2; FYVE domain found in lateral signaling target protein 2 homolog (Lst2) and similar proteins