SNX17 sorting nexin 17 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SNX17provided by HGNC
Official Full Name: sorting nexin 17provided by HGNC
Primary source: HGNC:HGNC:14979
See related: Ensembl:ENSG00000115234 MIM:605963; AllianceGenome:HGNC:14979
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
Summary: This gene encodes a member of the sorting nexin family. Members of this family contain a phox (PX) domain, which is a phosphoinositide binding domain, and are involved in intracellular trafficking. This protein does not contain a coiled coil region, like some family members, but contains a B41 domain. This protein interacts with the cytoplasmic domain of P-selectin, and may function in the intracellular trafficking of P-selectin. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, May 2012]
Expression: Ubiquitous expression in spleen (RPKM 29.0), lymph node (RPKM 26.3) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 2p23.3

Exon count:: 16

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (27370616..27377535)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (27413013..27419930)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (27593483..27600402)

Chromosome 2 - NC_000002.12 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
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?

Promotion of esophageal adenocarcinoma metastasis via Wnt/ss-catenin signal pathway by sorting nexins 3.
Title: Promotion of esophageal adenocarcinoma metastasis via Wnt/ß-catenin signal pathway by sorting nexins 3.
SNX17 Recruits USP9X to Antagonize MIB1-Mediated Ubiquitination and Degradation of PCM1 during Serum-Starvation-Induced Ciliogenesis.
Title: SNX17 Recruits USP9X to Antagonize MIB1-Mediated Ubiquitination and Degradation of PCM1 during Serum-Starvation-Induced Ciliogenesis.
HPV-16 L2 recruitment of SNX17 occurs prior to capsid disassembly.
Title: Characterizing the spatio-temporal role of sorting nexin 17 in human papillomavirus trafficking.
The double knockdown of SNX17 and SNX27 results in a striking reduction of papillomavirus 16 infection due to interruption of their binding to the L2 viral protein.
Title: A Novel PDZ Domain Interaction Mediates the Binding between Human Papillomavirus 16 L2 and Sorting Nexin 27 and Modulates Virion Trafficking.
SNX17 plays a role in the maintenance of normal surface levels of activating receptors and integrins to permit optimum T cell activation at the immune synapse.
Title: SNX17 affects T cell activation by regulating TCR and integrin recycling.
Data indicate that the major binding site for binding of sorting nexin 17 (SNX17) is confined to the NPXF2 motif in cytoplasmic adaptor protein Krev interaction trapped 1 (KRIT1).
Title: Structural determinants for binding of sorting nexin 17 (SNX17) to the cytoplasmic adaptor protein Krev interaction trapped 1 (KRIT1).
Sorting nexin 17 regulates ApoER2 recycling and reelin signaling.
Title: Sorting nexin 17 regulates ApoER2 recycling and reelin signaling.
The authors demonstrate that SNX17 is essential for infection with all papillomavirus types analyzed, indicating an evolutionarily highly conserved virus entry mechanism.
Title: SNX17 facilitates infection with diverse papillomavirus types.
depletion of SNX17 in HeLa cells resulted in lysosomal degradation of multiple members of the integrin family of extracellular matrix recep-tors.
Title: SNX17 protects integrins from degradation by sorting between lysosomal and recycling pathways.
SNX17 regulates amyloid precursor protein trafficking and processing in the early endosomes
Title: Adaptor protein sorting nexin 17 regulates amyloid precursor protein trafficking and processing in the early endosomes.

Submit: New GeneRIF Correction See all GeneRIFs (13)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genetic variants associated with breast size also influence breast cancer risk. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide characterization of shared and distinct genetic components that influence blood lipid levels in ethnically diverse human populations. 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

RH75415 (e-PCR)
- UniSTS:85566

WI-19785 (e-PCR)
- UniSTS:44874

RH25297 (e-PCR)
- UniSTS:91723

D2S2598 (e-PCR)
- UniSTS:76624

WIAF-1573 (e-PCR)
- UniSTS:52419

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables low-density lipoprotein particle receptor binding	IDA Inferred from Direct Assay more info	PubMed
enables phosphatidylinositol binding	IBA Inferred from Biological aspect of Ancestor more info
enables phosphatidylinositol binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables signaling receptor binding	NAS Non-traceable Author Statement more info	PubMed

Process	Evidence Code	Pubs
involved_in aorta development	IEA Inferred from Electronic Annotation more info
involved_in cardiac septum development	IEA Inferred from Electronic Annotation more info
involved_in cholesterol catabolic process	IC Inferred by Curator more info	PubMed
involved_in coronary vasculature development	IEA Inferred from Electronic Annotation more info
involved_in endocytic recycling	IBA Inferred from Biological aspect of Ancestor more info
involved_in endocytic recycling	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in endosomal transport	NAS Non-traceable Author Statement more info	PubMed
involved_in intracellular protein transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in intracellular protein transport	NAS Non-traceable Author Statement more info	PubMed
involved_in kidney development	IEA Inferred from Electronic Annotation more info
involved_in receptor-mediated endocytosis	IEA Inferred from Electronic Annotation more info
involved_in regulation of endocytosis	NAS Non-traceable Author Statement more info	PubMed
involved_in signal transduction	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in Golgi apparatus	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasmic vesicle	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	IDA Inferred from Direct Assay more info	PubMed
is_active_in early endosome	IBA Inferred from Biological aspect of Ancestor more info
located_in early endosome	IDA Inferred from Direct Assay more info	PubMed
located_in endosome	IDA Inferred from Direct Assay more info	PubMed
located_in endosome membrane	IDA Inferred from Direct Assay more info	PubMed
located_in intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info
located_in membrane	NAS Non-traceable Author Statement more info	PubMed
part_of protein-containing complex	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: sorting nexin-17

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_001267059.2 → NP_001253988.1 sorting nexin-17 isoform 2

See identical proteins and their annotated locations for NP_001253988.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region compared to variant 1. The resulting protein (isoform 2) is shorter compared to isoform 1.

Source sequence(s)

AC074117, AK300144

UniProtKB/TrEMBL

B4DE48, B4DTB8

Conserved Domains (3) summary

cd06885
Location:2 → 94

PX_SNX17_31; The phosphoinositide binding Phox Homology domain of Sorting Nexins 17 and 31

cd13337
Location:257 → 376

FERM-like_C_SNX17; Atypical FERM-like domain C-lobe of Sorting nexin 17

cl00155
Location:104 → 174

UBQ; Ubiquitin-like proteins
NM_001267060.2 → NP_001253989.1 sorting nexin-17 isoform 3

See identical proteins and their annotated locations for NP_001253989.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) lacks an alternate in-frame exon in the 5' coding region compared to variant 1. The resulting protein (isoform 3) is shorter compared to isoform 1.

Source sequence(s)

AC074117, AK298869

Consensus CDS

CCDS58704.1

UniProtKB/TrEMBL

B4DE48

Related

ENSP00000439208.1, ENST00000537606.5

Conserved Domains (3) summary

cd13337
Location:244 → 363

FERM-like_C_SNX17; Atypical FERM-like domain C-lobe of Sorting nexin 17

cl02563
Location:2 → 81

PX_domain; The Phox Homology domain, a phosphoinositide binding module

cl09511
Location:94 → 226

FERM_B-lobe; FERM domain B-lobe
NM_001267061.2 → NP_001253990.1 sorting nexin-17 isoform 4

See identical proteins and their annotated locations for NP_001253990.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) contains an alternate 5' exon contains an alternate exon, lacks a portion of the 5' coding region, and initiates translation at an alternate upstream start codon, compared to variant 1. The encoded protein (isoform 4) has a distinct N-terminus and is shorter than isoform 1.

Source sequence(s)

AC074117, AK298620

UniProtKB/TrEMBL

B4DE48, B4DQ37

Conserved Domains (3) summary

cd06885
Location:2 → 86

PX_SNX17_31; The phosphoinositide binding Phox Homology domain of Sorting Nexins 17 and 31

cd13337
Location:249 → 368

FERM-like_C_SNX17; Atypical FERM-like domain C-lobe of Sorting nexin 17

cl00155
Location:96 → 166

UBQ; Ubiquitin-like proteins
NM_014748.4 → NP_055563.1 sorting nexin-17 isoform 1

See identical proteins and their annotated locations for NP_055563.1

Status: REVIEWED

Description

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

Source sequence(s)

AC074117, D31764

Consensus CDS

CCDS1750.1

UniProtKB/Swiss-Prot

B4DQM7, Q15036, Q53HN7, Q6IAS3

UniProtKB/TrEMBL

B4DE48

Related

ENSP00000233575.2, ENST00000233575.7

Conserved Domains (3) summary

cd06885
Location:2 → 106

PX_SNX17_31; The phosphoinositide binding Phox Homology domain of Sorting Nexins 17 and 31

cd13337
Location:269 → 388

FERM-like_C_SNX17; Atypical FERM-like domain C-lobe of Sorting nexin 17

cl09511
Location:119 → 251

FERM_B-lobe; FERM domain B-lobe

RNA

NR_049782.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (5) uses an alternate splice site in an internal exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AC074117, AK297054
NR_049783.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (6) uses an alternate splice site in an internal exon and lacks an alternate exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AC074117, AK293252
NR_049784.2 RNA Sequence

Status: REVIEWED

Description

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

Source sequence(s)

AC074117, BC021108

Related

ENST00000427123.5
NR_049785.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (8) uses an alternate splice site in an internal exon and lacks an alternate exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AC074117, AK308487

Related

ENST00000440760.5
NR_049786.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (9) lacks an alternate exon and contains an alternate exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AC074117, AK298856
NR_049787.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (10) lacks two alternate 5' exons compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AC074117, AK295278
NR_049788.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (11) lacks three exons compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AC074117, BC032320

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_000002.12 Reference GRCh38.p14 Primary Assembly

Range

27370616..27377535

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011533203.3 → XP_011531505.1 sorting nexin-17 isoform X1

See identical proteins and their annotated locations for XP_011531505.1

UniProtKB/TrEMBL

B4DDM3, B7ZAQ8

Conserved Domains (2) summary

cd13337
Location:55 → 174

FERM-like_C_SNX17; Atypical FERM-like domain C-lobe of Sorting nexin 17

cl09511
Location:27 → 60

FERM_B-lobe; FERM domain B-lobe