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Intellectual disability

Gene: ASTN1

Amber List (moderate evidence)
ASTN1 (astrotactin 1)
EnsemblGeneIds (GRCh38): ENSG00000152092
EnsemblGeneIds (GRCh37): ENSG00000152092
OMIM: 600904, Gene2Phenotype
ASTN1 is in 3 panels

3 reviews

Ida Ertmanska (Genomics England Curator)

Green List (high evidence)

Comment on list classification: There are more than 3 unrelated individuals reported with biallelic ASTN1 variants and a neurodevelopmental disorder. All reported individuals presented with developmental delay and/or intellectual disability, with variable severity. Based on available evidence, this gene should be promoted to Green for Intellectual disability.
Created: 10 Feb 2026, 3:24 p.m. | Last Modified: 10 Feb 2026, 3:24 p.m.
Panel Version: 9.250
PMID: 41544630 Levine et al., 2026
Report of 18 individuals from 12 unrelated families with biallelic ASTN1 variants and a neurodevelopmental disorder, plus one individual with digenic inheritance with heterozygous variants in ASTN1 and ASTN2. Of these, 6 families are previously unreported (F1-6). Method: exome seq. Phenotypic spectrum: ID/DD (18/18 - mild to severe), seizures and/or epileptiform activity on EEG (10/18), subtle dysmorphic features (11/18), hypotonia (10/18), ataxia (4/18), hyperreflexia (5/18), and other less common findings.
Brain MRI was abnormal in 11/15 tested individuals, with callosal dysgenesis (7/15) and dysgenesis of the cerebellum (5/15) being most common findings.
Variants included missense, nonsense, and splice type. 2 patients had other candidate variants reported:
P1 - KDM3A:c.1639C>T, (p.Arg547Ter) de novo, heterozygous
P4 - TRAK2:c.1675C>T, (p.Gln559Ter) homozygous
Neither of these genes is linked to disease in OMIM.

ASTN1 is not yet associated with disease in OMIM, ClinGen, or Gene2Phenotype (resources accessed 10th Feb 2026).
Created: 10 Feb 2026, 3:15 p.m. | Last Modified: 10 Feb 2026, 3:15 p.m.
Panel Version: 9.248

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
neurodevelopmental disorder, MONDO:0700092

Publications

Created: 10 Feb 2026, 3:15 p.m.
Last Modified: 10 Feb 2026, 3:15 p.m.
Panel version: 9.250

Arina Puzriakova (Genomics England Curator)

I don't know

Comment on list classification: As limited segregation and case-specific details for the individual identified in the second study (PMID:27431290), rating Amber until further cases reported.
Created: 24 Jul 2020, 10:34 a.m. | Last Modified: 24 Jul 2020, 10:34 a.m.
Panel Version: 3.182
Not associated with any phenotype in OMIM or G2P. Homozygous ASTN1 variants identified in three families, all as part of large screening studies of ID and related disorders.

PMID: 26539891 (2015) - Two affected sibs with ID and partial corpus callosum agenesis, born to consanguineous Turkish parents (second-degree cousins). The ASTN1 variant (c.G2224C; p.G742R) segregated with the phenotype (but testing in a third, unaffected sib was not performed).

PMID - 27431290 (2016) - Large screening study of patients with ID/DD. Authors state that likely causal variants were identified in ASTN1, supporting candidacy on the basis of the previous report. However, it was not possible to map this finding to a specific case/variant based on the published data.

PMID - 29706646 (2018) - Compound heterozygous variants ([c.3283A>C, p.Met1095Leu];[c.2770C>T, p.His924Tyr]) identified in a Polish patient with diffuse polymicrogyria, spastic tetraplegia, epilepsy and DD.
Created: 24 Jul 2020, 10:26 a.m. | Last Modified: 24 Jul 2020, 10:26 a.m.
Panel Version: 3.181

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Intellectual disability

Publications

Created: 24 Jul 2020, 10:26 a.m.
Last Modified: 24 Jul 2020, 10:26 a.m.
Panel version: 3.181

Zornitza Stark (Australian Genomics)

Green List (high evidence)

Three families reported as part of large cohorts albeit proposing multiple novel candidate genes with minimal detail and no functional validation.
Sources: Expert list
Created: 29 Jan 2020, 1:57 a.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Intellectual disability

Publications

Variants in this GENE are reported as part of current diagnostic practice

Created: 29 Jan 2020, 1:57 a.m.

Panel version: 3.0

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Amber
Phenotypes
  • neurodevelopmental disorder, MONDO:0700092
Tags
Q1_26_promote_green
OMIM
600904
Clinvar variants
Variants in ASTN1
Penetrance
None
Publications
Panels with this gene

History Filter Activity

10 Feb 2026, Gel status: 2

Set Phenotypes

Ida Ertmanska (Genomics England Curator)

Phenotypes for gene: ASTN1 were changed from neurodevelopmental disorder, MONDO:0700092 to neurodevelopmental disorder, MONDO:0700092

10 Feb 2026, Gel status: 2

Set Phenotypes

Ida Ertmanska (Genomics England Curator)

Phenotypes for gene: ASTN1 were changed from Intellectual disability to neurodevelopmental disorder, MONDO:0700092

10 Feb 2026, Gel status: 2

Set publications

Ida Ertmanska (Genomics England Curator)

Publications for gene: ASTN1 were set to 29706646; 27431290; 26539891

10 Feb 2026, Gel status: 2

Removed Tag, Added Tag

Ida Ertmanska (Genomics England Curator)

Tag watchlist was removed from gene: ASTN1. Tag Q1_26_promote_green tag was added to gene: ASTN1.

24 Jul 2020, Gel status: 2

Added Tag

Arina Puzriakova (Genomics England Curator)

Tag watchlist tag was added to gene: ASTN1.

24 Jul 2020, Gel status: 2

Entity classified by Genomics England curator

Arina Puzriakova (Genomics England Curator)

Gene: astn1 has been classified as Amber List (Moderate Evidence).

29 Jan 2020, Gel status: 0

Created, Added New Source, Set mode of inheritance, Set publications, Set Phenotypes

Zornitza Stark (Australian Genomics)

gene: ASTN1 was added gene: ASTN1 was added to Intellectual disability. Sources: Expert list Mode of inheritance for gene: ASTN1 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: ASTN1 were set to 29706646; 27431290; 26539891 Phenotypes for gene: ASTN1 were set to Intellectual disability Review for gene: ASTN1 was set to GREEN gene: ASTN1 was marked as current diagnostic