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Intellectual disability
Region: ISCA-46296-Loss
15q24 recurrent region (LCR A-LCR C) Loss

Chromosome: 15
GRCh38 Position: 72671374-75215971
Haploinsufficiency Score: Sufficient evidence suggesting dosage sensitivity is associated with clinical phenotype
Triplosensitivity Score:
Required percent of overlap: 60%
Variant types: CNV Loss

1 review

Arina Puzriakova (Genomics England Curator)

Green List (high evidence)

Comment on list classification: This region has Sufficient Evidence for Haploinsufficiency in ClinGen and should be promoted to Green at the next GMS panel update.

Panel inclusion has been reviewed and approved by the Genomics England Clinical team.
Created: 12 Nov 2025, 3:50 p.m. | Last Modified: 12 Nov 2025, 3:50 p.m.

Panel Version: 9.171

https://search.clinicalgenome.org/kb/gene-dosage/region/ISCA-46296

ClinGen review (Last Evaluated:10/24/2025): Deletion of the 15q24 LCR A-C recurrent region has been reported in at least 5 patients. The reported clinical findings include developmental delays (speech and motor), intellectual disability, brain anomalies, non-specific craniofacial abnormalities, hypotonia, ocular abnormalities, hearing loss, and other variable clinical features. In all cases where parental studies have been performed, deletions were found to be de novo. Case-control comparison studies have provided evidence for enrichment of this deletion in the clinical population, although overall numbers are somewhat limited.
Sources: ClinGen
Created: 12 Nov 2025, 3:49 p.m.

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

Phenotypes
Developmental delays, intellectual disability, brain anomalies, non-specific craniofacial abnormalities, hypotonia, ocular abnormalities, hearing loss, and other variable clinical features

Publications

Created: 12 Nov 2025, 3:49 p.m.

Panel version: 9.170

Details

ISCA ID

ISCA-46296-Loss

ISCA Region Name

15q24 recurrent region (LCR A-LCR C) Loss

Chromosome

GRCh38 Coordinates

72671374-75215971

Haploinsufficiency Score

Sufficient evidence suggesting dosage sensitivity is associated with clinical phenotype

Triplosensitivity Score

Required percent of overlap

60%

Mode of Inheritance

MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

Sources

Expert Review Amber
ClinGen

Phenotypes

Developmental delays, intellectual disability, brain anomalies, non-specific craniofacial abnormalities, hypotonia, ocular abnormalities, hearing loss, and other variable clinical features

Tags

Q3_25_promote_green

Clinvar variants

Variants in

Penetrance

None

Variant types

CNV Loss

Publications

History Filter Activity

12 Nov 2025, Gel status: 2

Entity classified by Genomics England curator

Arina Puzriakova (Genomics England Curator)

Region: isca-46296-loss has been classified as Amber List (Moderate Evidence).

12 Nov 2025, Gel status: 1

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

Arina Puzriakova (Genomics England Curator)

Region: ISCA-46296-Loss was added Region: ISCA-46296-Loss was added to Intellectual disability. Sources: ClinGen Q3_25_promote_green tags were added to Region: ISCA-46296-Loss. Mode of inheritance for Region: ISCA-46296-Loss was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for Region: ISCA-46296-Loss were set to 22180641; 19921647 Phenotypes for Region: ISCA-46296-Loss were set to Developmental delays, intellectual disability, brain anomalies, non-specific craniofacial abnormalities, hypotonia, ocular abnormalities, hearing loss, and other variable clinical features Review for Region: ISCA-46296-Loss was set to GREEN

Intellectual disability Region: ISCA-46296-Loss 15q24 recurrent region (LCR A-LCR C) Loss