ASTN1

protein-coding

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

Gene summary

Astrotactin is a neuronal adhesion molecule required for glial-guided migration of young postmitotic neuroblasts in cortical regions of developing brain, including cerebrum, hippocampus, cerebellum, and olfactory bulb (Fink et al., 1995).[supplied by OMIM, Jun 2009]

Previous symbols:

ASTN

MANE transcript

NM_004319.3

Inheritance

ClinVar variants

P:2U:170B:15

Top phenotype

cerebral malformation

gnomAD constraint

pLI —, LoF o/e 0.11

Max pathogenic AF

—

Genomic locus

chr1:176,857,302-177,164,973

External References & Databases

Ensembl (ENSG00000152092)

Transcript & Mutation Effects

hg38 • Region Span ~307.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

cerebral malformationSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0016054

Submitter: PanelApp Australia

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ASTN1 variants in ClinVar

6 Conditions Cataloged

not specifiedTotal: 157

not providedTotal: 22

ASTN1-related disorderTotal: 3

Abnormal corpus callosum morphologyTotal: 2

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

Abnormal brain morphologyTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_004319.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	8 clinvar		9
missense		1 clinvar	164 clinvar	7 clinvar		172
nonsense		1 clinvar	2 clinvar			3
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	2	170	15	0	187

Highest pathogenic variant AF is 0.0000018586877

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 20 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_004319.3	RefSeq	NP_004310.1	23	MANE Select
ENST00000361833.7	Ensembl	ENSP00000354536.2	23	MANE Select
NM_001286164.2	RefSeq	NP_001273093.1	23	Standard
NM_001364856.2	RefSeq	NP_001351785.1	23	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Ectoderm Differentiation

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

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000361833
Coding exons: 23
Length: 307672
Individuals with no LoFs: 125736
Homozygous LoFs: 0
Heterozygous LoFs: 12
Defined: 125748
p: 0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.65	644	773	0.833	0.0000452	8482
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000045	0.000044	rare
South Asian	0.000098	0.000098	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.117

Intolerance Scores

LoFtool: 0.162
RVIS EVS: -1.1
RVIS percentile EVS: 6.98

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.166

Gene Damage Prediction

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