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Early onset or syndromic epilepsy

Region: ISCA-46297-Loss

16p12.2 recurrent region (distal)(includes OTOA) Loss

Green List (high evidence)
Chromosome: 16
GRCh38 Position: 21558792-21729102
Haploinsufficiency Score: Gene associated with autosomal recessive phenotype
Triplosensitivity Score:
Required percent of overlap: 60%
Variant types: CNV Loss

1 review

Arina Puzriakova (Genomics England Curator)

Red List (low evidence)

This region should be demoted from green to red at the next GMS panel update. ClinGen summary states that heterozygous deletions of this region are not dosage sensitive (https://search.clinicalgenome.org/kb/gene-dosage/region/ISCA-46297)

Homozygous distal 16p12.2 deletions, encompassing the OTOA gene, are associated with autosomal recessive deafness-22 (PMID: 19888295; 31204719; 39916398)

16p12.2 proximal deletions (distinct genomic coordinates) have been linked to neurodevelopmental phenotypes (PMID: 20154674; 25719193; 30836598; 30190612), however the evidence is classified as 'emerging' in ClinGen and is insufficient to add to diagnostic GMS panels at this time (https://search.clinicalgenome.org/kb/gene-dosage/region/ISCA-37409)
Created: 22 Apr 2026, 4:24 p.m. | Last Modified: 22 Apr 2026, 4:24 p.m.
Panel Version: 8.189
New green region added based on ClinGen Region Curation Results (version on 05 Aug 2022) following NHS Genomic Medicine Service approval.
Created: 2 Feb 2023, 3:19 p.m. | Last Modified: 2 Feb 2023, 3:19 p.m.
Panel Version: 3.31
Created: 2 Feb 2023, 3:19 p.m.
Last Modified: 2 Feb 2023, 3:19 p.m.
Panel version: 8.189

Details

ISCA ID
ISCA-46297-Loss
ISCA Region Name
16p12.2 recurrent region (distal)(includes OTOA) Loss
Chromosome
16
GRCh38 Coordinates
21558792-21729102
Haploinsufficiency Score
Gene associated with autosomal recessive phenotype
Triplosensitivity Score
Required percent of overlap
60%
Mode of Inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Sources
  • ClinGen
  • Expert Review Green
Tags
Q2_26_demote_red
Clinvar variants
Variants in
Penetrance
None
Variant types
CNV Loss
Publications

History Filter Activity

22 Apr 2026, Gel status: 3

Added Tag

Arina Puzriakova (Genomics England Curator)

Tag Q2_26_demote_red tag was added to Region: ISCA-46297-Loss.

2 Feb 2023, Gel status: 3

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

Arina Puzriakova (Genomics England Curator)

Region: ISCA-46297-Loss was added Region: ISCA-46297-Loss was added to Genetic epilepsy syndromes. Sources: Expert Review Green,ClinGen Mode of inheritance for Region: ISCA-46297-Loss was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for Region: ISCA-46297-Loss were set to 31204719; 19888295; 20301607; 25719193; 30836598