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

ENSG00000148219

∙ NCBI:23245 ∙ OMIM:612856 ∙ HGNC:17021 ∙ Uniprot:O75129 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
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

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ASTN2	protein_coding	protein_coding	ENST00000361209	22	989845

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000294	125734	0	14	125748	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.16	603	689	0.876	0.0000417	8290
Missense in Polyphen		2	1.1962	1.6719		16
Synonymous	-1.39	326	296	1.10	0.0000179	2627
Loss of Function	6.12	8	58.6	0.137	0.00000291	671

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000239	0.000239
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.0000566	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000353	0.0000352
Middle Eastern	0.0000566	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

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

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

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