ASTN1

astrotactin 1, the group of Fibronectin type III domain containing|MicroRNA protein coding host genes

Basic information

Region (hg38): 1:176857301-177164973

Previous symbols: [ "ASTN" ]

Links

ENSG00000152092 ∙ NCBI:460 ∙ OMIM:600904 ∙ HGNC:773 ∙ Uniprot:O14525 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ASTN1 gene.

• Inborn genetic diseases (53 variants)
• not provided (9 variants)
• Abnormal corpus callosum morphology (2 variants)
• Abnormal brain morphology (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ASTN1 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				4		4
missense		1	51	3		55
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	1	51	7	0

Variants in ASTN1

This is a list of pathogenic ClinVar variants found in the ASTN1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-176864291-T-C		ASTN1-related disorder	Likely benign (Aug 01, 2022)
1-176864318-G-A		not specified	Uncertain significance (Feb 15, 2023)
1-176864344-C-T			Likely benign (Sep 01, 2023)
1-176864360-C-T		not specified	Uncertain significance (Aug 12, 2021)
1-176864400-C-T		not specified	Uncertain significance (Jun 22, 2023)
1-176864435-C-T		ASTN1-related disorder	Likely benign (Apr 08, 2023)
1-176864438-C-T		not specified	Uncertain significance (Oct 06, 2022)
1-176868976-T-A			not provided (-)
1-176876558-C-T		not specified	Uncertain significance (Mar 07, 2024)
1-176876585-C-T		not specified	Uncertain significance (Jun 18, 2021)
1-176876588-C-T		not specified	Uncertain significance (Oct 22, 2021)
1-176876616-G-T		not specified	Uncertain significance (Feb 27, 2024)
1-176882887-G-A		not specified	Likely pathogenic (Mar 14, 2024)
1-176882938-T-G		Abnormal corpus callosum morphology	Conflicting classifications of pathogenicity (Sep 01, 2023)
1-176884351-T-G		not specified	Uncertain significance (Jun 05, 2023)
1-176884386-C-T		not specified	Uncertain significance (Jun 02, 2023)
1-176884476-G-A		not specified	Conflicting classifications of pathogenicity (Nov 01, 2023)
1-176888072-C-G		not specified	Uncertain significance (Apr 07, 2022)
1-176888153-C-T		not specified	Uncertain significance (Dec 27, 2023)
1-176894617-T-A		not specified	Uncertain significance (Dec 28, 2022)
1-176894639-G-C		not specified	Uncertain significance (Feb 28, 2023)
1-176894678-A-T		not specified	Uncertain significance (Oct 26, 2022)
1-176894732-G-A		Abnormal corpus callosum morphology	Uncertain significance (Sep 01, 2017)
1-176894801-G-A		not specified	Uncertain significance (Mar 20, 2023)
1-176894824-G-A		not specified	Uncertain significance (Mar 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ASTN1	protein_coding	protein_coding	ENST00000361833	23	307672

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000155	125736	0	12	125748	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.65	644	773	0.833	0.0000452	8482
Missense in Polyphen		287	374.81	0.76573		4098
Synonymous	0.168	309	313	0.988	0.0000189	2538
Loss of Function	6.47	7	62.0	0.113	0.00000317	691

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000905	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000452	0.0000439
Middle Eastern	0.000109	0.000109
South Asian	0.0000983	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Neuronal adhesion molecule that is required for normal migration of young postmitotic neuroblasts along glial fibers, especially in the cerebellum. Required for normal rate of migration of granule cells during brain development and for normal cerebellum development. {ECO:0000250|UniProtKB:Q61137}.
• Pathway: Ectoderm Differentiation (Consensus)

Recessive Scores

• pRec: 0.117

Intolerance Scores

• loftool: 0.162
• rvis_EVS: -1.1
• rvis_percentile_EVS: 6.98

Haploinsufficiency Scores

• pHI: 0.125
• hipred: Y
• hipred_score: 0.605
• ghis: 0.586

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.166

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Astn1
• Phenotype: cellular phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: neuron migration;neuron cell-cell adhesion;locomotory behavior
• Cellular component: cellular_component;endosome;external side of plasma membrane;integral component of membrane;clathrin-coated vesicle;perikaryon