SNX16 sorting nexin 16 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SNX16provided by HGNC
Official Full Name: sorting nexin 16provided by HGNC
Primary source: HGNC:HGNC:14980
See related: Ensembl:ENSG00000104497 MIM:614903; AllianceGenome:HGNC:14980
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. The protein encoded by this gene associates with late endosome membranes as is involved in tubule formation, cholesterol transport, and transport of tetraspanin CD81. The encoded protein also inhibits cell migration and tumorigenesis. [provided by RefSeq, Jan 2017]
Expression: Ubiquitous expression in testis (RPKM 6.1), esophagus (RPKM 5.5) and 24 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 8q21.13

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	8	NC_000008.11 (81799583..81842185, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	8	NC_060932.1 (82231264..82273872, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	8	NC_000008.10 (82711818..82754420, complement)

Chromosome 8 - NC_000008.11 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
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?

[Sorting Nexin 16:Structure,Function,and Role in Diseases].
Title: [Sorting Nexin 16:Structure,Function,and Role in Diseases].
BHLHE40 plays a pathological role in pre-eclampsia through upregulating SNX16 by transcriptional inhibition of miR-196a-5p.
Title: BHLHE40 plays a pathological role in pre-eclampsia through upregulating SNX16 by transcriptional inhibition of miR-196a-5p.
SNX16 activates c-Myc signaling by inhibiting ubiquitin-mediated proteasomal degradation of eEF1A2 in colorectal cancer development.
Title: SNX16 activates c-Myc signaling by inhibiting ubiquitin-mediated proteasomal degradation of eEF1A2 in colorectal cancer development.
SNX16 regulates the recycling trafficking of E-cadherin . SNX16 associates with the cytoplasmic domain of E-cadherin via PPII/alpha2 loop.
Title: SNX16 Regulates the Recycling of E-Cadherin through a Unique Mechanism of Coordinated Membrane and Cargo Binding.
Observational study of gene-disease association. (HuGE Navigator)
Title: Evaluation of nine candidate genes in patients with normal tension glaucoma: a case control study.
SNX16 is a sorting nexin that may function in the trafficking of proteins between the early and late endosomal compartments
Title: Evidence for a role of SNX16 in regulating traffic between the early and later endosomal compartments.

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

EBI GWAS Catalog

Description
A genome-wide search for loci interacting with known prostate cancer risk-associated genetic variants. EBI GWAS Catalog EBI GWAS CatalogPubMed
Association of genome-wide variation with the risk of incident heart failure in adults of European and African ancestry: a prospective meta-analysis from the cohorts for heart and aging research in genomic epidemiology (CHARGE) consortium. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide data reveal novel genes for methotrexate response in a large cohort of juvenile idiopathic arthritis cases. EBI GWAS Catalog EBI GWAS CatalogPubMed
GWAS meta-analysis and replication identifies three new susceptibility loci for ovarian cancer. 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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Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables identical protein binding	IPI Inferred from Physical Interaction 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

Process	Evidence Code	Pubs
involved_in early endosome to late endosome transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in early endosome to late endosome transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in endosome to lysosome transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in endosome to lysosome transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein targeting to lysosome	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein targeting to lysosome	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
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 early endosome membrane	IEA Inferred from Electronic Annotation more info
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
is_active_in late endosome	IBA Inferred from Biological aspect of Ancestor more info
located_in late endosome	IDA Inferred from Direct Assay more info	PubMed
located_in late endosome membrane	IEA Inferred from Electronic Annotation more info
located_in lysosome	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: sorting nexin-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_001348189.2 → NP_001335118.1 sorting nexin-16 isoform c

Status: REVIEWED

Description

Transcript Variant: This variant (4) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (c) has the same N- and C-termini but is shorter compared to isoform a.

Source sequence(s)

AC087349, AC132219

Conserved Domains (2) summary

cd07276
Location:76 → 185

PX_SNX16; The phosphoinositide binding Phox Homology domain of Sorting Nexin 16

cl25732
Location:202 → 307

SMC_N; RecF/RecN/SMC N terminal domain
NM_022133.4 → NP_071416.2 sorting nexin-16 isoform a

See identical proteins and their annotated locations for NP_071416.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (a). Variants 1 and 2 both encode the same isoform (a).

Source sequence(s)

AL833763, BC033630, CB962009, DA307370

Consensus CDS

CCDS6234.1

UniProtKB/Swiss-Prot

A8K4D8, P57768, Q658L0, Q8N4U3

Related

ENSP00000379621.2, ENST00000396330.6

Conserved Domains (2) summary

cd07276
Location:105 → 214

PX_SNX16; The phosphoinositide binding Phox Homology domain of Sorting Nexin 16

cl25732
Location:231 → 336

SMC_N; RecF/RecN/SMC N terminal domain
NM_152836.3 → NP_690049.1 sorting nexin-16 isoform a

See identical proteins and their annotated locations for NP_690049.1

Status: REVIEWED

Description

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

Source sequence(s)

AL833763, BC033630, CB962009

Consensus CDS

CCDS6234.1

UniProtKB/Swiss-Prot

A8K4D8, P57768, Q658L0, Q8N4U3

Related

ENSP00000322652.4, ENST00000345957.9

Conserved Domains (2) summary

cd07276
Location:105 → 214

PX_SNX16; The phosphoinositide binding Phox Homology domain of Sorting Nexin 16

cl25732
Location:231 → 336

SMC_N; RecF/RecN/SMC N terminal domain
NM_152837.3 → NP_690050.1 sorting nexin-16 isoform b

See identical proteins and their annotated locations for NP_690050.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in the 5' UTR and lacks an alternate in-frame exon compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a.

Source sequence(s)

AL833763, BC033630, CB962009

Consensus CDS

CCDS6235.1

UniProtKB/Swiss-Prot

P57768

Related

ENSP00000322631.4, ENST00000353788.8

Conserved Domains (2) summary

cl02563
Location:105 → 185

PX_domain; The Phox Homology domain, a phosphoinositide binding module

cl23720
Location:193 → 246

RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)

RNA

NR_145472.2 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC087349, AC132219
NR_145473.2 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC087349, AC132219
NR_145474.2 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC087349, AC132219
NR_145475.2 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC087349, AC132219

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000008.11 Reference GRCh38.p14 Primary Assembly

Range

81799583..81842185 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005251282.5 → XP_005251339.1 sorting nexin-16 isoform X2

See identical proteins and their annotated locations for XP_005251339.1

Conserved Domains (2) summary

cd07276
Location:76 → 185

PX_SNX16; The phosphoinositide binding Phox Homology domain of Sorting Nexin 16

cl25732
Location:202 → 307

SMC_N; RecF/RecN/SMC N terminal domain
XM_047422087.1 → XP_047278043.1 sorting nexin-16 isoform X3
XM_047422086.1 → XP_047278042.1 sorting nexin-16 isoform X2
XM_047422085.1 → XP_047278041.1 sorting nexin-16 isoform X1

UniProtKB/Swiss-Prot

A8K4D8, P57768, Q658L0, Q8N4U3
XM_011517574.3 → XP_011515876.1 sorting nexin-16 isoform X4

Conserved Domains (2) summary

pfam12269
Location:75 → 130

zf-CpG_bind_C; CpG binding protein zinc finger C terminal domain

cl02563
Location:1 → 57

PX_domain; The Phox Homology domain, a phosphoinositide binding module