SNF8 SNF8 subunit of ESCRT-II [Homo sapiens (human)] - Gene

Summary

Official Symbol: SNF8provided by HGNC
Official Full Name: SNF8 subunit of ESCRT-IIprovided by HGNC
Primary source: HGNC:HGNC:17028
See related: Ensembl:ENSG00000159210 MIM:610904; AllianceGenome:HGNC:17028
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: Dot3; EAP30; NEDOA; VPS22; DEE115
Summary: The protein encoded by this gene is a component of the endosomal sorting complex required for transport II (ESCRT-II), which regulates the movement of ubiquitinylated transmembrane proteins to the lysosome for degradation. This complex also interacts with the RNA polymerase II elongation factor (ELL) to overcome the repressive effects of ELL on RNA polymerase II activity. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2015]
Expression: Ubiquitous expression in kidney (RPKM 18.5), fat (RPKM 18.4) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 17q21.32

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	17	NC_000017.11 (48929316..48944842, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	17	NC_060941.1 (49793036..49808559, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	17	NC_000017.10 (47006678..47022204, complement)

Chromosome 17 - NC_000017.11 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 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?

Bi-allelic variants in SNF8 cause a disease spectrum ranging from severe developmental and epileptic encephalopathy to syndromic optic atrophy.
Title: Bi-allelic variants in SNF8 cause a disease spectrum ranging from severe developmental and epileptic encephalopathy to syndromic optic atrophy.
data describe an unappreciated role for EAP30 in IRF3-dependent innate antiviral response in the nucleus.
Title: Pivotal role for the ESCRT-II complex subunit EAP30/SNF8 in IRF3-dependent innate antiviral defense.
Taken together, these data suggest an active role for ESCRT-II and CHMP6 in ESCRT-mediated abscission
Title: Inhibition of ESCRT-II-CHMP6 interactions impedes cytokinetic abscission and leads to cell death.
Modulating SNF8 expression levels alters the TRPC6 channel current and can modulate activation of NFAT-mediated transcription downstream of gain-of-function mutant TRPC6.
Title: SNF8, a member of the ESCRT-II complex, interacts with TRPC6 and enhances its channel activity.
Vps22 has an important role in ligand-induced EGFR and CXCR4 turnover; termination of EGF signaling occurs prior to ESCRT-II engagement
Title: Vps22/EAP30 in ESCRT-II mediates endosomal sorting of growth factor and chemokine receptors destined for lysosomal degradation.
mammalian ESCRTII is made up of hVps25p, hVps22p, and hVps36p and may be redundant, cargo-specific, or not required for protein sorting at the multivesicular body
Title: Degradation of endocytosed epidermal growth factor and virally ubiquitinated major histocompatibility complex class I is independent of mammalian ESCRTII.
there are probably multiple pathways for protein sorting/multivesicular body vesicle formation in human cells and that human immunodeficiency virus type 1 does not utilize an ESCRT-II-dependent pathway to leave the cell
Title: Human ESCRT-II complex and its role in human immunodeficiency virus type 1 release.

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Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Developmental and epileptic encephalopathy 115 MedGen: CN377534 OMIM: 620783 GeneReviews: Not available	not available
Neurodevelopmental disorder plus optic atrophy MedGen: CN377627 OMIM: 620784 GeneReviews: Not available	not available

EBI GWAS Catalog

Description
Large-scale association analysis identifies 13 new susceptibility loci for coronary artery disease. 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)

HIV-1 interactions

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Replication interactions

Interaction	Pubs
shRNA knockdown of SNF8 (ESCRT-II component) impairs intracellular and extracellular (supernatant) HIV-1 CA-p24 production when using VSV-pseudotyped virus; replication is enhanced by SNF8	PubMed

Protein interactions

Protein	Gene	Interaction	Pubs
Pr55(Gag)	gag	Depletion of EAP30 by siRNA leads to a block to HIV-1 genomic RNA trafficking, resulting in the accumulation of genomic RNA in the nucleus and juxtanuclear domains and reduced viral structural protein Gag and virus production levels	PubMed
	gag	EAP30 interacts with HIV-1 Gag and Staufen1 in live cell tri-molecular fluorescence complementary assay	PubMed
capsid	gag	Knockdown of SNF8 (ESCRT-II component) decreases extracellular HIV-1 CA-p24 levels when using VSV-pseudotyped virus	PubMed
	gag	Knockdown of SNF8 (ESCRT-II component) impairs HIV-1 intracellular CA-p24 production when using VSV-pseudotyped virus	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D17S1827 (e-PCR), detects polymorphism
- UniSTS:57866

EAP30_9250 (e-PCR)
- UniSTS:467663

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables channel regulator activity	IDA Inferred from Direct Assay more info	PubMed
enables lipid binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein homodimerization activity	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in early endosome to late endosome transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in endocytic recycling	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in macroautophagy	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in macroautophagy	TAS Traceable Author Statement more info	PubMed
involved_in membrane fission	NAS Non-traceable Author Statement more info	PubMed
involved_in multivesicular body assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in multivesicular body assembly	NAS Non-traceable Author Statement more info	PubMed
involved_in multivesicular body assembly	TAS Traceable Author Statement more info	PubMed
involved_in multivesicular body sorting pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in multivesicular body sorting pathway	TAS Traceable Author Statement more info	PubMed
involved_in positive regulation of exosomal secretion	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of protein catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway	NAS Non-traceable Author Statement more info	PubMed
NOT involved_in regulation of MAP kinase activity	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of protein catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of protein complex stability	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
part_of ESCRT II complex	IBA Inferred from Biological aspect of Ancestor more info
part_of ESCRT II complex	IDA Inferred from Direct Assay more info	PubMed
part_of ESCRT II complex	IPI Inferred from Physical Interaction more info	PubMed
part_of ESCRT II complex	TAS Traceable Author Statement more info	PubMed
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	TAS Traceable Author Statement more info
located_in endosome membrane	IDA Inferred from Direct Assay more info	PubMed
located_in extracellular exosome	HDA more info	PubMed
located_in late endosome membrane	IDA Inferred from Direct Assay more info	PubMed
located_in membrane	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in perinuclear region of cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in recycling endosome	IDA Inferred from Direct Assay more info	PubMed
part_of transcription regulator complex	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: vacuolar-sorting protein SNF8

Names: EAP30 subunit of ELL complex; ELL-associated protein of 30 kDa; ESCRT-II complex subunit VPS22; SNF8, ESCRT-II complex subunit, homolog

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_001317192.2 → NP_001304121.1 vacuolar-sorting protein SNF8 isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate in-frame splice junction in the 3' end compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is 1 aa shorter compared to isoform 1.

Source sequence(s)

AC091133, BC008976, BC038830, BP342490

Consensus CDS

CCDS82156.1

UniProtKB/Swiss-Prot

Q96H20

Related

ENSP00000290330.3, ENST00000290330.7

Conserved Domains (1) summary

pfam04157
Location:6 → 224

EAP30; EAP30/Vps36 family
NM_001317193.2 → NP_001304122.1 vacuolar-sorting protein SNF8 isoform 3

Status: REVIEWED

Description

Transcript Variant: This variant (3) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (3) has the same N- and C-termini but is shorter compared to isoform 1.

Source sequence(s)

AC091133, BC008976, BE818533, BP342490

UniProtKB/Swiss-Prot

Q96H20

Conserved Domains (1) summary

pfam04157
Location:16 → 208

EAP30; EAP30/Vps36 family
NM_001317194.2 → NP_001304123.1 vacuolar-sorting protein SNF8 isoform 4

Status: REVIEWED

Description

Transcript Variant: This variant (4) contains two additional alternate exons compared to variant 1. The resulting isoform (4) has a shorter and distinct N-terminus compared to isoform 1.

Source sequence(s)

AC091133, BC008976, BE394098, BP342490

UniProtKB/Swiss-Prot

Q96H20

Conserved Domains (1) summary

pfam04157
Location:13 → 121

EAP30; EAP30/Vps36 family
NM_007241.4 → NP_009172.2 vacuolar-sorting protein SNF8 isoform 1

See identical proteins and their annotated locations for NP_009172.2

Status: REVIEWED

Description

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

Source sequence(s)

AC091133, BC008976, BP342490

Consensus CDS

CCDS11541.1

UniProtKB/Swiss-Prot

Q8IXY3, Q96H20, Q9UN50

Related

ENSP00000421380.1, ENST00000502492.6

Conserved Domains (1) summary

pfam04157
Location:6 → 225

EAP30; EAP30/Vps36 family

RNA

NR_133679.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (5) uses an alternate splice junction 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)

AC091133, BC008976, BG248541, BP342490