SNX20 sorting nexin 20 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SNX20provided by HGNC
Official Full Name: sorting nexin 20provided by HGNC
Primary source: HGNC:HGNC:30390
See related: Ensembl:ENSG00000167208 MIM:613281; AllianceGenome:HGNC:30390
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: SLIC1
Summary: SNX20 interacts with the cytoplasmic domain of PSGL1 (SELPLG; MIM 600738) and cycles PSGL1 into endosomes.[supplied by OMIM, Feb 2010]
Expression: Biased expression in lymph node (RPKM 7.6), appendix (RPKM 6.3) and 12 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 16q12.1

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	16	NC_000016.10 (50666300..50681312, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	16	NC_060940.1 (56463916..56478923, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	16	NC_000016.9 (50700211..50715223, complement)

Chromosome 16 - NC_000016.10 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 Functions

What's a GeneRIF?

DNA methylation-regulated SNX20 overexpression correlates with poor prognosis, immune cell infiltration, and low-grade glioma progression.
Title: DNA methylation-regulated SNX20 overexpression correlates with poor prognosis, immune cell infiltration, and low-grade glioma progression.
Identification of molecular subtyping system and four-gene prognostic signature with immune-related genes for uveal melanoma.
Title: Identification of molecular subtyping system and four-gene prognostic signature with immune-related genes for uveal melanoma.
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.
Serves as a sorting molecule that cycles P-selectin ligand protein into endosomes with no impact on leukocyte recruitment.
Title: SLIC-1/sorting nexin 20: a novel sorting nexin that directs subcellular distribution of PSGL-1.

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 scan of Ashkenazi Jewish Crohn's disease suggests novel susceptibility loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
Discovery of six new susceptibility loci and analysis of pleiotropic effects in leprosy. 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

RH102218 (e-PCR)
- UniSTS:96552

RH77862 (e-PCR)
- UniSTS:36908

RH98498 (e-PCR)
- UniSTS:89135

SHGC-31023 (e-PCR)
- UniSTS:77661

RH68075 (e-PCR)
- UniSTS:5239

G67945 (e-PCR)
- UniSTS:225687

G67944 (e-PCR)
- UniSTS:225688

D16S3136 (e-PCR), detects polymorphism
- UniSTS:21156

SHGC-17274 (e-PCR)
- UniSTS:43175

SGC34205 (e-PCR)
- UniSTS:45553

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables phosphatidylinositol phosphate binding	IBA Inferred from Biological aspect of Ancestor more info
enables phosphatidylinositol-3-phosphate binding	ISS Inferred from Sequence or Structural Similarity more info
enables phosphatidylinositol-4,5-bisphosphate binding	ISS Inferred from Sequence or Structural Similarity more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in protein transport	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
is_active_in early endosome membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in early endosome membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in plasma membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: sorting nexin-20

Names: selectin ligand-interactor cytoplasmic 1

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_001144972.2 → NP_001138444.1 sorting nexin-20 isoform 3

See identical proteins and their annotated locations for NP_001138444.1

Status: VALIDATED

Description

Transcript Variant: This variant (3) uses an alternative 3' exon, compared to variant 1. The resulting isoform (3) has a distinct C-terminus and is shorter than isoform 1.

Source sequence(s)

AK055837, AK292650, BC063423, D20065

Consensus CDS

CCDS45481.1

UniProtKB/Swiss-Prot

Q7Z614

Related

ENSP00000388875.2, ENST00000423026.6

Conserved Domains (1) summary

cl02563
Location:76 → 94

PX_domain; The Phox Homology domain, a phosphoinositide binding module
NM_153337.3 → NP_699168.1 sorting nexin-20 isoform 2

See identical proteins and their annotated locations for NP_699168.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) uses an alternative 3' exon, compared to variant 1. The resulting isoform (2) has a distinct C-terminus and is shorter than isoform 1.

Source sequence(s)

AA278249, AK055837, BC063423, D20065

Consensus CDS

CCDS10744.1

UniProtKB/Swiss-Prot

Q7Z614

Related

ENSP00000300590.3, ENST00000300590.7

Conserved Domains (1) summary

cl02563
Location:76 → 95

PX_domain; The Phox Homology domain, a phosphoinositide binding module
NM_182854.4 → NP_878274.1 sorting nexin-20 isoform 1

See identical proteins and their annotated locations for NP_878274.1

Status: VALIDATED

Description

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

Source sequence(s)

AA278249, AC007608, AY302441, BF446287

Consensus CDS

CCDS10745.1

UniProtKB/Swiss-Prot

A8K9D5, Q08E98, Q6P4H2, Q7Z614, Q8IV59

Related

ENSP00000332062.4, ENST00000330943.9

Conserved Domains (1) summary

cd07300
Location:76 → 189

PX_SNX20; The phosphoinositide binding Phox Homology domain of Sorting Nexin 20