ASTN2 astrotactin 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: ASTN2provided by HGNC
Official Full Name: astrotactin 2provided by HGNC
Primary source: HGNC:HGNC:17021
See related: Ensembl:ENSG00000148219 MIM:612856; AllianceGenome:HGNC:17021
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: bA67K19.1
Summary: This gene encodes a protein that is expressed in the brain and may function in neuronal migration, based on functional studies of the related astrotactin 1 gene in human and mouse. A deletion at this locus has been associated with schizophrenia. Multiple transcript variants encoding different proteins have been found for this locus. [provided by RefSeq, May 2010]
Expression: Biased expression in prostate (RPKM 6.8), brain (RPKM 6.4) and 13 other tissues See more
Orthologs: mouse all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 9q33.1

Exon count:: 25

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	9	NC_000009.12 (116423112..117415057, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	9	NC_060933.1 (128616101..129608884, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	9	NC_000009.11 (119185391..120177335, complement)

Chromosome 9 - NC_000009.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

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

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Genetic Variation in the ASTN2 Locus in Cardiovascular, Metabolic and Psychiatric Traits: Evidence for Pleiotropy Rather Than Shared Biology.
Title: Genetic Variation in the ASTN2 Locus in Cardiovascular, Metabolic and Psychiatric Traits: Evidence for Pleiotropy Rather Than Shared Biology.
Rare copy number variants in ASTN2 gene in patients with neurodevelopmental disorders.
Title: Rare copy number variants in ASTN2 gene in patients with neurodevelopmental disorders.
Effects of rs958804 and rs7858836 single-nucleotide polymorphisms of the ASTN2 gene on pain-related phenotypes in patients who underwent laparoscopic colectomy and mandibular sagittal split ramus osteotomy.
Title: Effects of rs958804 and rs7858836 single-nucleotide polymorphisms of the ASTN2 gene on pain-related phenotypes in patients who underwent laparoscopic colectomy and mandibular sagittal split ramus osteotomy.
Chimeric RNA ASTN2-PAPPAas aggravates tumor progression and metastasis in human esophageal cancer.
Title: Chimeric RNA ASTN2-PAPPA(as) aggravates tumor progression and metastasis in human esophageal cancer.
ASTN2 localizes primarily to endocytic and autophagocytic vesicles in the cell soma and in subsets of dendritic spines
Title: ASTN2 modulates synaptic strength by trafficking and degradation of surface proteins.
Our study suggests that the MEF2D, PRDM16 and ASTN2 genes from GWAS are associated with migraine susceptibility, especially migraine without aura , among Chinese patients. It appears that there is no association with serotonin receptor related genes.
Title: Multilocus analysis reveals three candidate genes for Chinese migraine susceptibility.
The findings of this study do not support a major role of ASTN2 variants in ADHD or its comorbid disorders respective aADHD associated personality traits.
Title: The role of ASTN2 variants in childhood and adult ADHD, comorbid disorders and associated personality traits.
Results present the structure of ASTN-2 consisting of a combination of polypeptide folds: a perforin-like domain, a minimal epidermal growth factor-like module, a unique form of fibronectin type III domain and an annexin-like domain. Structural and biophysical data show that ASTN-2 binds inositol triphosphates, suggesting a mechanism for membrane recognition or secondary messenger regulation of its activity.
Title: Structure of astrotactin-2: a conserved vertebrate-specific and perforin-like membrane protein involved in neuronal development.
The expression of coding and non-coding genes with SAFB1 cross-link sites was altered by SAFB1 knockdown. The isoform-specific expression of neural cell adhesion molecule (NCAM1) and ASTN2 was influenced by SAFB1.
Title: iCLIP identifies novel roles for SAFB1 in regulating RNA processing and neuronal function.
Study found a significant association of ASTN2 genetic variants with age at onset in Alzheimer's disease in two independent samples together with in silico analysis that demonstrated potential role of ASTN2 in the pathogenesis of the disease
Title: Polymorphisms within ASTN2 gene are associated with age at onset of Alzheimer's disease.

Submit: New GeneRIF Correction See all GeneRIFs (18)

Phenotypes

Go to the top of the page Help

Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Copy number response

Description
Copy number response Haploinsufficency Little evidence for dosage pathogenicity (Last evaluated 2021-03-09) ClinGen Genome Curation PagePubMed Triplosensitivity No evidence available (Last evaluated 2021-03-09) ClinGen Genome Curation Page

EBI GWAS Catalog

Description
A genome-wide association study of host genetic determinants of the antibody response to Anthrax Vaccine Adsorbed. EBI GWAS Catalog EBI GWAS CatalogPubMed
A genome-wide meta-analysis identifies novel loci associated with schizophrenia and bipolar disorder. EBI GWAS Catalog EBI GWAS CatalogPubMed
Common variants at 12q14 and 12q24 are associated with hippocampal volume. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association analysis identifies susceptibility loci for migraine without aura. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of smoking behaviours in patients with COPD. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide joint meta-analysis of SNP and SNP-by-smoking interaction identifies novel loci for pulmonary function. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide meta-analysis identifies new susceptibility loci for migraine. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genomewide pharmacogenomic study of metabolic side effects to antipsychotic drugs. EBI GWAS Catalog EBI GWAS CatalogPubMed
Molecular genetics of adult ADHD: converging evidence from genome-wide association and extended pedigree linkage studies. EBI GWAS Catalog EBI GWAS CatalogPubMed
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. EBI GWAS Catalog EBI GWAS CatalogPubMed
The genetic architecture of economic and political preferences. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

Markers

RH118771 (e-PCR)
- UniSTS:138760

SHGC-111190 (e-PCR)
- UniSTS:168206

D9S1078 (e-PCR)
- UniSTS:11800

SHGC-147166 (e-PCR)
- UniSTS:175651

D8S2278 (e-PCR)
- UniSTS:473906

D8S2279 (e-PCR)
- UniSTS:473907

RH122151 (e-PCR)
- UniSTS:134711

SHGC-31358 (e-PCR)
- UniSTS:14919

G10349 (e-PCR)
- UniSTS:80213

D9S754 (e-PCR), detects polymorphism
- UniSTS:149078

D9S2151 (e-PCR)
- UniSTS:18022

D9S1802 (e-PCR), detects polymorphism
- UniSTS:22888

SHGC-111330 (e-PCR)
- UniSTS:168306

G31091 (e-PCR)
- UniSTS:73590

SHGC-112252 (e-PCR)
- UniSTS:168566

RH18010 (e-PCR)
- UniSTS:3960

SHGC-145228 (e-PCR)
- UniSTS:174457

G19227 (e-PCR)
- UniSTS:16766

SHGC-13641 (e-PCR)
- UniSTS:72071

SHGC-83580 (e-PCR)
- UniSTS:95887

AU047468 (e-PCR)
- UniSTS:110479

RH18537 (e-PCR)
- UniSTS:35731

D3S3184 (e-PCR)
- UniSTS:153509

NoName (e-PCR)
- UniSTS:483753

REN46569 (e-PCR)
- UniSTS:371369

SHGC-156050 (e-PCR)
- UniSTS:185003

WI-14828 (e-PCR)
- UniSTS:81077

SHGC-14316 (e-PCR)
- UniSTS:18621

SHGC-147438 (e-PCR)
- UniSTS:175809

SHGC-86299 (e-PCR)
- UniSTS:185025

G63257 (e-PCR)
- UniSTS:140226

D9S154 (e-PCR), detects polymorphism
- UniSTS:17112

D11S3553 (e-PCR)
- UniSTS:152792

D9S154 (e-PCR), detects polymorphism
- UniSTS:17113

SHGC-143647 (e-PCR)
- UniSTS:171998

SHGC-8898 (e-PCR)
- UniSTS:18657

RH119226 (e-PCR)
- UniSTS:138735

SHGC-150831 (e-PCR)
- UniSTS:173557

SHGC-35384 (e-PCR)
- UniSTS:47102

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables calcium ion binding	IDA Inferred from Direct Assay more info
enables inositol 1,3,4,5 tetrakisphosphate binding	IBA Inferred from Biological aspect of Ancestor more info
enables inositol 1,3,4,5 tetrakisphosphate binding	IDA Inferred from Direct Assay more info

Process	Evidence Code	Pubs
involved_in establishment of body hair planar orientation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of protein localization to cell surface	IEA Inferred from Electronic Annotation more info
involved_in neuron cell-cell adhesion	IBA Inferred from Biological aspect of Ancestor more info
involved_in neuron migration	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein localization to cell surface	IEA Inferred from Electronic Annotation more info
involved_in protein transport	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in cell cortex	IEA Inferred from Electronic Annotation more info
located_in cell pole	IEA Inferred from Electronic Annotation more info
located_in clathrin-coated vesicle	IEA Inferred from Electronic Annotation more info
located_in early endosome	IEA Inferred from Electronic Annotation more info
is_active_in endosome	IBA Inferred from Biological aspect of Ancestor more info
located_in late endosome	IEA Inferred from Electronic Annotation more info
is_active_in membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in membrane	IEA Inferred from Electronic Annotation more info
located_in perikaryon	IEA Inferred from Electronic Annotation more info

General protein information

Go to the top of the page Help

Preferred Names: astrotactin-2

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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.

Genomic

NG_021409.2 RefSeqGene

Range

5001..996946

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001184734.1 → NP_001171663.1 astrotactin-2 isoform e

See identical proteins and their annotated locations for NP_001171663.1

Status: REVIEWED

Description

Transcript Variant: This variant (5) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. This variant also lacks a segment in the 3' coding region compared to variant 1. The encoded isoform (e) has distinct N- and C-termini and is shorter than isoform a.

Source sequence(s)

AI341147, BC143292, DA015423

UniProtKB/TrEMBL

B7ZKP3, B7ZKP4

Conserved Domains (2) summary

cd00063
Location:131 → 240

FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...

cl02616
Location:1 → 87

MACPF; MAC/Perforin domain
NM_001184735.1 → NP_001171664.1 astrotactin-2 isoform f

Status: REVIEWED

Description

Transcript Variant: This variant (6) has multiple differences compared to variant 1. These differences result in a distinct 5' UTR and lead to translation initiation at an alternate start codon, compared to variant 1. The encoded isoform (f) has distinct N- and C-termini and is shorter than isoform a.

Source sequence(s)

AK024064, AL133284, BC010680, DA015423

Consensus CDS

CCDS55334.1

UniProtKB/TrEMBL

X6R5P2

Related

ENSP00000351460.4, ENST00000358637.4

Conserved Domains (1) summary

cl02616
Location:1 → 87

MACPF; MAC/Perforin domain
NM_001365068.1 → NP_001351997.1 astrotactin-2 isoform g precursor

Status: REVIEWED

Source sequence(s)

AL133282, AL133284, AL137024, AL157829, AL354981, AL355608, AL358792, AL392085

Consensus CDS

CCDS6816.1

UniProtKB/Swiss-Prot

A2A2T7, A2A2T9, O75129, Q52LQ2, Q5JVX8, Q5JVX9, Q5JVY1, Q5VXG8, Q5VZX6, Q8N6P8, Q8WV47, Q96FL4, Q9UHW6

UniProtKB/TrEMBL

A0A0A0MRH9

Related

ENSP00000314038.4, ENST00000313400.9

Conserved Domains (2) summary

smart00457
Location:852 → 1035

MACPF; membrane-attack complex / perforin

pfam14670
Location:703 → 750

FXa_inhibition; Coagulation Factor Xa inhibitory site
NM_001365069.1 → NP_001351998.1 astrotactin-2 isoform h precursor

Status: REVIEWED

Source sequence(s)

AL133282, AL133284, AL137024, AL157829, AL354981, AL355608, AL358792, AL392085

UniProtKB/TrEMBL

A0A0A0MRH9

Conserved Domains (2) summary

smart00457
Location:848 → 1031

MACPF; membrane-attack complex / perforin

pfam14670
Location:699 → 746

FXa_inhibition; Coagulation Factor Xa inhibitory site
NM_014010.5 → NP_054729.3 astrotactin-2 isoform a precursor

See identical proteins and their annotated locations for NP_054729.3

Status: REVIEWED

Description

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

Source sequence(s)

AL133282, AL133284, AL137024, AL157829, AL354981, AL355608, AL358792, AL392085

Consensus CDS

CCDS6815.1

UniProtKB/TrEMBL

A0A0A0MRH9

Related

ENSP00000354504.2, ENST00000361209.6

Conserved Domains (2) summary

smart00457
Location:801 → 984

MACPF; membrane-attack complex / perforin

pfam14670
Location:652 → 699

FXa_inhibition; Coagulation Factor Xa inhibitory site
NM_198186.3 → NP_937829.3 astrotactin-2 isoform b

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (b) has a distinct N-terminus and is shorter than isoform a.

Source sequence(s)

AI341147, BC029272, BX649176

Consensus CDS

CCDS48009.2

UniProtKB/TrEMBL

B7ZKP3

Related

ENSP00000288520.5, ENST00000288520.9

Conserved Domains (2) summary

cd00063
Location:169 → 289

FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...

cl02616
Location:42 → 136

MACPF; MAC/Perforin domain
NM_198187.3 → NP_937830.3 astrotactin-2 isoform c

See identical proteins and their annotated locations for NP_937830.3

Status: REVIEWED

Source sequence(s)

AI341147, BC143293, DA015423

UniProtKB/TrEMBL

B3KN99, B7ZKP5

Conserved Domains (2) summary

cd00063
Location:131 → 240

FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...

cl02616
Location:1 → 87

MACPF; MAC/Perforin domain
NM_198188.2 → NP_937831.1 astrotactin-2 isoform d

See identical proteins and their annotated locations for NP_937831.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. This variant also lacks a segment in the 3' coding region compared to variant 1. The encoded isoform (d) has distinct N- and C-termini and is shorter than isoform a.

Source sequence(s)

AI341147, AK024064, BC093835, DA015423

Consensus CDS

CCDS6814.1

UniProtKB/TrEMBL

B3KN99

Related

ENSP00000339925.4, ENST00000341734.8

Conserved Domains (2) summary

cd00063
Location:131 → 240

FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...

cl02616
Location:1 → 87

MACPF; MAC/Perforin domain