ASTN2

astrotactin 2, the group of Fibronectin type III domain containing|Small nucleolar RNA protein coding host genes

Basic information

Region (hg38): 9:116423112-117415070

Links

ENSG00000148219NCBI:23245OMIM:612856HGNC:17021Uniprot:O75129AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • autism spectrum disorder (Limited), mode of inheritance: AD
  • intellectual disability (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ASTN2 gene.

  • Bardet-Biedl_syndrome (555 variants)
  • not_provided (228 variants)
  • Sarcotubular_myopathy (215 variants)
  • Bardet-Biedl_syndrome_11 (208 variants)
  • not_specified (189 variants)
  • TRIM32-related_disorder (166 variants)
  • Inborn_genetic_diseases (71 variants)
  • ASTN2-related_disorder (30 variants)
  • Retinal_dystrophy (5 variants)
  • Autosomal_recessive_limb-girdle_muscular_dystrophy (4 variants)
  • Limb-girdle_muscular_dystrophy,_recessive (2 variants)
  • Elevated_circulating_creatine_kinase_concentration (1 variants)
  • See_cases (1 variants)
  • Limb-girdle_muscular_dystrophy (1 variants)
  • Myopathy (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ASTN2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001365068.1. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
19
clinvar
10
clinvar
29
missense
169
clinvar
9
clinvar
3
clinvar
181
nonsense
1
clinvar
1
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
1
clinvar
1
Total 0 0 171 28 13

Highest pathogenic variant AF is 0.00007620639

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
ASTN2protein_codingprotein_codingENST00000361209 22989845
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.000.0002941257340141257480.0000557
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.166036890.8760.00004178290
Missense in Polyphen21.19621.671916
Synonymous-1.393262961.100.00001792627
Loss of Function6.12858.60.1370.00000291671

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0002390.000239
Ashkenazi Jewish0.00009920.0000992
East Asian0.00005660.0000544
Finnish0.000.00
European (Non-Finnish)0.00003530.0000352
Middle Eastern0.00005660.0000544
South Asian0.00003270.0000327
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Mediates recycling of the neuronal cell adhesion molecule ASTN1 to the anterior pole of the cell membrane in migrating neurons. Promotes ASTN1 internalization and intracellular transport of endocytosed ASTN1 (By similarity). Selectively binds inositol-4,5-bisphosphate, inositol-3,4,5- trisphosphate and inositol-1,3,4,5-tetrakisphosphate, suggesting it is recruited to membranes that contain lipids with a phosphoinositide headgroup (Ref.6). {ECO:0000250|UniProtKB:Q80Z10, ECO:0000269|Ref.6}.;

Recessive Scores

pRec
0.110

Intolerance Scores

loftool
0.363
rvis_EVS
-2.27
rvis_percentile_EVS
1.26

Haploinsufficiency Scores

pHI
0.286
hipred
Y
hipred_score
0.563
ghis
0.571

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.366

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Astn2
Phenotype
integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan);

Gene ontology

Biological process
protein transport;establishment of body hair planar orientation;negative regulation of protein localization to cell surface
Cellular component
early endosome;late endosome;cell cortex;integral component of membrane;clathrin-coated vesicle;perikaryon;cell pole
Molecular function
calcium ion binding;inositol 1,3,4,5 tetrakisphosphate binding