15q25.2q25.3 recurrent region (distal, LCR C-LCR D)

  • 1
    Haplo
    Score
  • 0
    Triplo
    Score

Region Facts

Region Name
15q25.2q25.3 recurrent region (distal, LCR C-LCR D)
Cytoband
15q25.2-q25.3
Genomic Coordinates
GRCh37/hg19 chr15:85139652-85713001 NCBI Ensembl UCSC
GRCh38/hg38 chr15:84596421-85169770 NCBI Ensembl UCSC

Dosage Sensitivity Summary (Region)

Dosage ID:
ISCA-37514
Curation Status:
Complete
Issue Type:
Dosage Curation - Region
Description:
The 15q25.2q25.3 region contains a cluster of low copy repeats (LCRs) that mediate recurrent copy number changes through non-allelic homologous recombination. This review refers to CNVs involving recurrent breakpoint regions LCR C and LCR D.
Haploinsufficiency:
Little Evidence for Haploinsufficiency (1)
Triplosensitivity:
No Evidence for Triplosensitivity (0)
Last Evaluated:
06/26/2020

Haploinsufficiency (HI) Score Details

HI Score:
1
HI Evidence Strength:
Little Evidence for Haploinsufficiency (Disclaimer)
HI Evidence:
  • PUBMED: 23239641
    Doelken, et al. (2013) described a male patient with three microdeletions, including a microdeletion of the 15q25.2q25.3 region (LCR C-D, distal). He had severely delayed psychomotor and language development, epileptiform signs by EEG, plagiocephaly, microcephaly, dysmorphic craniofacial features (which included strabismus, myopathic facies, hypoplastic nasal alae, bitemporal sparse hair), camptodactyly of the 5th fingers, left-sided retractile testis, and recurrent infections. The 15q25.2q25.3 deletion was inherited from a healthy father. Additionally, this patient had a 1q21.1 deletion (maternal inheritance) and a de novo hemizygous deletion of the Xq12 region (including OPHN1). Therefore, the authors acknowledge that the patient's clinical findings might be the result of the combination of the three microdeletions.
HI Evidence Comments:
Few published reports of 15q25.2q25.3 region (LCR C-D, distal) deletion exist in the literature; however, statistical enrichment has been observed from case-control comparison (reviewed below). Therefore, the current haploinsufficiency score is 1. Additional relevant literature is summarized below: Case-control studies PMID: 25217958 Coe, et al. (2014): In a large-scale case-control comparison study of the relative prevalence of copy number variants in children with ID/DD, MCA, and other developmental phenotypes compared to controls, deletions of the recurrent 15q25.2q25.3 region (LCR C-D, distal) we observed in 7/29,085 cases versus 0/19,584 controls (p=0.0272; LR=Inf, CI: 1.23 to Inf), demonstrating enrichment of this deletion in the clinical population. See also Cooper et al. (2014), PMID 21841781. PMID: 21841781 Cooper, et al. (2011): In a large-scale case-control comparison study of CNVs in 15,767 children with developmental and intellectual disability, five patients were described with microdeletions of 15q25.2q25.3. Three of these patients were described to have developmental delay (one also had a seizure disorder), one had autism, and one had muscle weakness. The inheritance is unknown for 4 of the patients and maternally inherited for one. PMID: 19166990 Itsara, et al. (2009) analyzed the combined data from three population studies composed of approximately 2500 individuals. Four affected patients (two with autism and two with schizophrenia) were identified with deletions in 15q25.2q25.3. Comparison between the case and control data did not reach statistical significance.

Triplosensitivity (TS) Score Details

TS Score:
0
TS Evidence Strength:
No Evidence for Triplosensitivity (Disclaimer)
TS Evidence Comments:
As yet, no published reports of 15q25.2q25.3 region (LCR C-D, distal) duplication exist in the literature and statistical enrichment has not been observed from case-control comparison (reviewed below). Therefore, the current triplosensitivity score is 0. Additional relevant literature is summarized below: Case-control studies PMID: 25217958 Coe, et al. (2014): In a large-scale case-control comparison study of the relative prevalence of copy number variants in children with ID/DD, MCA, and other developmental phenotypes compared to controls, deletions of the recurrent 15q25.2q25.3 region (LCR C-D, distal) we observed in 2/29,085 cases versus 0/19,584 controls (p= 0.3570; LR=Inf, CI: 0.175 to Inf), demonstrating a lack of enrichment of this duplication in the clinical population. See also Cooper et al. (2014), PMID 21841781.

Genomic View

Select assembly: (NC_000015.9) ()