1. Panels
  2. Intellectual disability
  3. LINC01578
Genes in panel
Prev Next
Regions in panel
Prev Next

Intellectual disability

Gene: LINC01578

Green List (high evidence)
LINC01578 (long intergenic non-protein coding RNA 1578)
EnsemblGeneIds (GRCh38): ENSG00000272888
EnsemblGeneIds (GRCh37): ENSG00000272888
LINC01578 is in 1 panel

3 reviews

Achchuthan Shanmugasundram (Genomics England Curator)

Comment on phenotypes: This gene has now been associated with relevant phenotype in OMIM (MIM #621012), but not yet in Gene2Phenotype.
Created: 5 Mar 2025, 10:54 a.m. | Last Modified: 5 Mar 2025, 10:54 a.m.
Panel Version: 8.119
Created: 5 Mar 2025, 10:54 a.m.
Last Modified: 5 Mar 2025, 10:54 a.m.
Panel version: 8.119

Sarah Leigh (Genomics England Curator)

Green List (high evidence)

The rating of this gene has been updated to green and the mode of inheritance set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted following NHS Genomic Medicine Service approval.
Created: 24 Feb 2025, 6:15 p.m. | Last Modified: 24 Feb 2025, 6:15 p.m.
Panel Version: 8.97
CHASERR / LINC01578 variants have not been associated with a condition in OMIM, G2P or MONDO. Ganesh et al (PMID: 39442041) report three unrelated children with heterozygous de novo deletions (25kb, 22kb, 8.4kb), which encompass the 5' section of the CHASERR gene. The author were also able to demonstrate that two of these deletions resulted in an increased expression of the cis allele of the neighboring gene - CHD2, resulting in overexpression of the CHD2 protein.
Created: 12 Nov 2024, 11:50 a.m. | Last Modified: 12 Nov 2024, 11:50 a.m.
Panel Version: 8.20

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Created: 12 Nov 2024, 11:50 a.m.
Last Modified: 12 Nov 2024, 11:50 a.m.
Panel version: 8.97

Zornitza Stark (Australian Genomics)

Green List (high evidence)

CHASERR (aka LINC01578) encodes a human long noncoding RNA (lncRNA) adjacent to CHD2, a coding gene in which de novo loss-of-function variants cause developmental and epileptic encephalopathy. Three unrelated children reported with a syndromic, early-onset neurodevelopmental disorder, each of whom had a de novo deletion in the CHASERR locus. The children had severe encephalopathy, shared facial dysmorphisms, cortical atrophy, and cerebral hypomyelination - a phenotype that is distinct from the phenotypes of patients with CHD2 haploinsufficiency. CHASERR deletion results in increased CHD2 protein abundance in patient-derived cell lines and increased expression of the CHD2 transcript in cis, indicating bidirectional dosage sensitivity in human disease.
Sources: Literature
Created: 11 Nov 2024, 6:12 a.m.

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Phenotypes
Neurodevelopmental disorder, MONDO:0700092, CHASERR-related

Publications

Created: 11 Nov 2024, 6:12 a.m.

Panel version: 8.16

Details

Mode of Inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Sources
  • Expert Review Green
  • NHS GMS
Phenotypes
  • Neurodevelopmental disorder with dysmorphic facies, absent speech and ambulation, and brain abnormalities, OMIM:621012
Tags
new-gene-name locus-type-rna-long-non-coding gene-checked
Clinvar variants
Variants in LINC01578
Penetrance
None
Publications
Panels with this gene

History Filter Activity

12 Mar 2025, Gel status: 3

Added Tag

Achchuthan Shanmugasundram (Genomics England Curator)

Tag gene-checked tag was added to gene: LINC01578.

5 Mar 2025, Gel status: 3

Set Phenotypes

Achchuthan Shanmugasundram (Genomics England Curator)

Phenotypes for gene: LINC01578 were changed from Neurodevelopmental disorder, MONDO:0700092, CHASERR-related to Neurodevelopmental disorder with dysmorphic facies, absent speech and ambulation, and brain abnormalities, OMIM:621012

5 Mar 2025, Gel status: 3

Added Tag

Achchuthan Shanmugasundram (Genomics England Curator)

Tag locus-type-rna-long-non-coding tag was added to gene: LINC01578.

25 Feb 2025, Gel status: 3

Removed Tag, Removed Tag

Sarah Leigh (Genomics England Curator)

Tag Q3_24_promote_green was removed from gene: LINC01578. Tag Q3_24_NHS_review was removed from gene: LINC01578.

24 Feb 2025, Gel status: 3

Added New Source, Added New Source, Status Update

Sarah Leigh (Genomics England Curator)

Source NHS GMS was added to LINC01578. Source Expert Review Green was added to LINC01578. Rating Changed from Amber List (moderate evidence) to Green List (high evidence)

12 Nov 2024, Gel status: 2

Added Tag, Added Tag, Added Tag

Sarah Leigh (Genomics England Curator)

Tag new-gene-name tag was added to gene: LINC01578. Tag Q3_24_promote_green tag was added to gene: LINC01578. Tag Q3_24_NHS_review tag was added to gene: LINC01578.

12 Nov 2024, Gel status: 2

Entity classified by Genomics England curator

Sarah Leigh (Genomics England Curator)

Gene: linc01578 has been classified as Amber List (Moderate Evidence).

11 Nov 2024, Gel status: 0

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

Zornitza Stark (Australian Genomics)

gene: LINC01578 was added gene: LINC01578 was added to Intellectual disability. Sources: Literature Mode of inheritance for gene: LINC01578 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: LINC01578 were set to 39442041 Phenotypes for gene: LINC01578 were set to Neurodevelopmental disorder, MONDO:0700092, CHASERR-related Review for gene: LINC01578 was set to GREEN