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Intellectual disability

Region: ISCA-37498-Loss

11q13.2q13.4 recurrent region (includes SHANK2, FGFs) Loss

Amber List (moderate evidence)
Chromosome: 11
GRCh38 Position: 67996175-71525885
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, 3:22 p.m. | Last Modified: 12 Nov 2025, 3:22 p.m.
Panel Version: 9.167
https://search.clinicalgenome.org/kb/gene-dosage/region/ISCA-37498

ClinGen review (Last Evaluated:06/25/2025): Reported in at least 2 individuals with developmental delay/intellectual disability, dysmorphic features, dental anomalies, long slender fingers with 5th finger clinodactyly, and additional clinical features. Another patient (PMID: 28018436) was reported to have an overlapping 11q13 deletion that involves most of the recurrent region with a similar clinical phenotype. All reported deletions of the recurrent 11q13.2q13.4 region with informative parental testing have been shown to be de novo. Case-control data are currently uninformative due to the rarity of this deletion. Additionally, this deletion encompasses two curated dosage sensitive genes, KMT5B and SHANK2.

Sources: ClinGen
Created: 12 Nov 2025, 3:21 p.m. | Last Modified: 12 Nov 2025, 3:59 p.m.
Panel Version: 9.174

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

Phenotypes
Developmental delay/intellectual disability, dysmorphic features, dental anomalies, long slender fingers with 5th finger clinodactyly, and additional clinical features

Publications

Created: 12 Nov 2025, 3:21 p.m.
Last Modified: 12 Nov 2025, 3:59 p.m.
Panel version: 9.166

Details

ISCA ID
ISCA-37498-Loss
ISCA Region Name
11q13.2q13.4 recurrent region (includes SHANK2, FGFs) Loss
Chromosome
11
GRCh38 Coordinates
67996175-71525885
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 delay/intellectual disability, dysmorphic features, dental anomalies, long slender fingers with 5th finger clinodactyly, and additional 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-37498-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-37498-Loss was added Region: ISCA-37498-Loss was added to Intellectual disability. Sources: ClinGen Q3_25_promote_green tags were added to Region: ISCA-37498-Loss. Mode of inheritance for Region: ISCA-37498-Loss was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for Region: ISCA-37498-Loss were set to 28211979; 21373257; 37152320 Phenotypes for Region: ISCA-37498-Loss were set to Developmental delay/intellectual disability, dysmorphic features, dental anomalies, long slender fingers with 5th finger clinodactyly, and additional clinical features Review for Region: ISCA-37498-Loss was set to GREEN