ASTN2

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

Basic information

Region (hg38): 9:116423111-117415070

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 (461 variants)
• not provided (218 variants)
• Sarcotubular myopathy (78 variants)
• Bardet-Biedl syndrome 11 (73 variants)
• Inborn genetic diseases (67 variants)
• Bardet-Biedl syndrome 11;Sarcotubular myopathy (44 variants)
• Sarcotubular myopathy;Bardet-Biedl syndrome 11 (41 variants)
• TRIM32-related condition (29 variants)
• not specified (25 variants)
• ASTN2-related condition (3 variants)
• Autosomal recessive limb-girdle muscular dystrophy (2 variants)
• Limb-Girdle Muscular Dystrophy, Recessive (2 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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				9	10	19
missense			49	4	3	56
nonsense			1			1
start loss						0
frameshift						0
inframe indel			1		1	2
splice donor/acceptor (+/-2bp)			1			1
splice region					1	1
non coding	24	18	340	146	11	539
Total	24	18	392	159	25

Highest pathogenic variant AF is 0.0000131

Variants in ASTN2

This is a list of pathogenic ClinVar variants found in the ASTN2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
9-116425855-C-T		not specified	Uncertain significance (Aug 13, 2021)
9-116425856-G-A		not specified	Uncertain significance (Jun 22, 2021)
9-116425872-G-A		ASTN2-related disorder	Likely benign (Aug 08, 2019)
9-116425875-C-T		ASTN2-related disorder	Likely benign (Sep 26, 2019)
9-116425912-G-A		not specified	Uncertain significance (Nov 07, 2023)
9-116425970-C-T		not specified	Uncertain significance (Aug 16, 2022)
9-116425987-T-C		not specified	Uncertain significance (Dec 12, 2023)
9-116425996-G-A		not specified	Uncertain significance (Dec 26, 2023)
9-116426008-C-A		ASTN2-related disorder	Likely benign (Sep 25, 2023)
9-116426021-C-T		not specified	Uncertain significance (May 03, 2023)
9-116426026-C-T		not specified	Uncertain significance (Dec 07, 2022)
9-116426027-G-T			Benign (Dec 31, 2019)
9-116426050-C-T		not specified	Uncertain significance (Sep 16, 2021)
9-116426068-C-T		not specified	Uncertain significance (Dec 27, 2022)
9-116440600-C-A		ASTN2-related disorder	Benign (Oct 21, 2019)
9-116440713-C-T		not specified	Uncertain significance (May 31, 2023)
9-116440777-A-G		not specified	Uncertain significance (Oct 17, 2023)
9-116440792-T-C		not specified	Uncertain significance (Aug 13, 2021)
9-116442452-C-T		See cases	Uncertain significance (Aug 24, 2022)
9-116487408-T-A		not specified	Uncertain significance (Sep 22, 2023)
9-116487408-T-C		not specified	Uncertain significance (Dec 18, 2023)
9-116487411-C-T			Benign (Dec 31, 2019)
9-116487434-C-T		not specified	Uncertain significance (May 17, 2023)
9-116487455-G-A		ASTN2-related disorder	Benign (Dec 31, 2019)
9-116487461-A-C		not specified	Uncertain significance (Nov 14, 2023)

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