MCID: CHR391
MIFTS: 33

Chromosome 15q24 Deletion Syndrome

Categories: Genetic diseases, Rare diseases

Aliases & Classifications for Chromosome 15q24 Deletion Syndrome

Summaries for Chromosome 15q24 Deletion Syndrome

GARD : 20 The following summary is from Orphanet, a European reference portal for information on rare diseases and orphan drugs. Orpha Number: 94065 Definition 15q24 microdeletion syndrome is a rare chromosomal anomaly characterized cytogenetically by a 1.7-6.1 Mb deletion in chromosome 15q24 and clinically by pre- and post-natal growth retardation, intellectual disability, distinct facial features, and genital, skeletal, and digital anomalies. Epidemiology The prevalence of 15q24 deletion syndrome is unknown. To date, 19 cases with clinical data and detailed mapping of genomic breakpoints have been reported. Clinical description At birth, approximately 1/3 of patients have low birth weight consistent with intrauterine growth retardation. Feeding difficulties and failure to thrive are reported in about 20%. In later childhood, 30% show growth retardation and short stature and 17% obesity. Growth hormone (GH) deficiency may be present. Growth delay, feeding difficulties, and distinct facial features (long face with high anterior hairline, epicanthal folds, hypertelorism, downslanting palpebral fissures, sparse and broad medial eyebrows, broad and/or depressed nasal bridge, long smooth philtrum, and small mouth with full lower lip) are the most common early presenting symptoms. Most patients (90%) have digital deformities (proximally implanted and/or hypoplastic thumbs, clinodactyly, brachydactyly, overriding toes, toe syndactyly, small hands). Approximately 60% have skeletal complications (joint laxity and scoliosis ). Hernias are found as well as hypotonia (60%). Eye abnormalities are common ( nystagmus and strabismus ). Ear abnormalities are variable but common (large ears, ear lobe pits, anteverted ear lobes, and protuberant ears). Genital abnormalities are common in males (60%). Mild to moderate developmental delay is found in all patients. Behavior abnormalities, such as autism, hyperactivity, aggression, and attention deficit are reported in 37%. Approximately 50% of patients have abnormal brain imaging on magnetic resonance imaging (MRI). Nearly 40% have a history of recurrent infections. Recurrent ear infections may be a predisposing factor to hearing loss (25%). Microcephaly is uncommon (20%). Other congenital malformations, while rare, can be severe and include cardiovascular malformations, congenital diaphragmatic hernia, intestinal atresia, imperforate anus, and myelomeningocele (see these terms). Etiology The syndrome is caused by a microdeletion of 1.7 to 6.1 Mb in size in chromosome 15q24 which usually results from nonallelic homologous recombination (NAHR). The smallest region of overlap (SRO) spans a 1.2 Mb region including several candidate genes that may predispose to many of the clinical features: CYP11A1, SEMA7A, CPLX3, ARID3B, STRA6, SIN3A and CSK. Diagnostic methods Oligonucleotide array CGH (aCGH) with confirmation by fluorescent in-situ hybridization (FISH) detects most, if not all, deletions of 15q24. Karyotypes are typically normal. Differential diagnosis Differential diagnoses include other genetic syndromes, particularly monosomy 22q11, Prader-Willi, and Noonan syndromes (see these terms). Antenatal diagnosis Deletion of 15q24 can be detected in amniotic fluid or chorionic villi samples. Since routine karyotyping is not sufficient to detect the deletion, aCGH should be performed. Genetic counseling The deletion occurred as a de novo event in all reported patients when parents were available for testing. Parental aCGH and/or FISH studies are recommended to provide accurate genetic counseling. Management and treatment Management should be multi-disciplinary with the primary care physician and clinical geneticist playing crucial roles in appropriate screening, surveillance, and care. At the time of diagnosis, baseline echocardiograms, audiologic, ophthalmologic, and developmental assessments are needed. Growth and feeding should be monitored closely. Prognosis The prognosis is variable and depends on the severity and extent of congenital malformations.

MalaCards based summary : Chromosome 15q24 Deletion Syndrome, also known as 15q24 microdeletion syndrome, is related to witteveen-kolk syndrome and alacrima, achalasia, and mental retardation syndrome. An important gene associated with Chromosome 15q24 Deletion Syndrome is SIN3A (SIN3 Transcription Regulator Family Member A). Affiliated tissues include eye and heart, and related phenotypes are global developmental delay and intellectual disability

Disease Ontology : 12 A chromosomal deletion syndrome that is characterized by dysmorphic facial features, intellectual disability and seizure, has material basis in autosomal dominant inheritance of mutation in the SIN3A gene causing partial deletion of the long arm of chromosome 15.

MedlinePlus Genetics : 43 15q24 microdeletion is a chromosomal change in which a small piece of chromosome 15 is deleted in each cell. The deletion occurs on the long (q) arm of the chromosome at a position designated q24.15q24 microdeletion is associated with mild to moderate intellectual disability and delayed speech development. Other common signs and symptoms include short stature, weak muscle tone (hypotonia), and skeletal abnormalities including loose (lax) joints. Affected males may have genital abnormalities, which can include an unusually small penis (micropenis) and the opening of the urethra on the underside of the penis (hypospadias). Affected individuals also have distinctive facial features such as a high front hairline, broad eyebrows, widely set eyes (hypertelorism), outside corners of the eyes that point downward (downslanting palpebral fissures), a broad nasal bridge, a full lower lip, and a long, smooth space between the upper lip and nose (philtrum).

Related Diseases for Chromosome 15q24 Deletion Syndrome

Graphical network of the top 20 diseases related to Chromosome 15q24 Deletion Syndrome:



Diseases related to Chromosome 15q24 Deletion Syndrome

Symptoms & Phenotypes for Chromosome 15q24 Deletion Syndrome

Human phenotypes related to Chromosome 15q24 Deletion Syndrome:

31 (show all 50)
# Description HPO Frequency HPO Source Accession
1 global developmental delay 31 hallmark (90%) HP:0001263
2 intellectual disability 31 frequent (33%) HP:0001249
3 behavioral abnormality 31 frequent (33%) HP:0000708
4 smooth philtrum 31 frequent (33%) HP:0000319
5 short stature 31 frequent (33%) HP:0004322
6 postnatal growth retardation 31 frequent (33%) HP:0008897
7 epicanthus 31 frequent (33%) HP:0000286
8 joint laxity 31 frequent (33%) HP:0001388
9 downslanted palpebral fissures 31 frequent (33%) HP:0000494
10 brachydactyly 31 frequent (33%) HP:0001156
11 long philtrum 31 frequent (33%) HP:0000343
12 high anterior hairline 31 frequent (33%) HP:0009890
13 recurrent infections 31 frequent (33%) HP:0002719
14 small for gestational age 31 frequent (33%) HP:0001518
15 abnormality of the outer ear 31 frequent (33%) HP:0000356
16 broad eyebrow 31 frequent (33%) HP:0011229
17 hypotonia 31 frequent (33%) HP:0001252
18 failure to thrive 31 occasional (7.5%) HP:0001508
19 scoliosis 31 occasional (7.5%) HP:0002650
20 nystagmus 31 occasional (7.5%) HP:0000639
21 kyphosis 31 occasional (7.5%) HP:0002808
22 hearing impairment 31 occasional (7.5%) HP:0000365
23 depressed nasal bridge 31 occasional (7.5%) HP:0005280
24 hypertelorism 31 occasional (7.5%) HP:0000316
25 abnormality of the dentition 31 occasional (7.5%) HP:0000164
26 microcephaly 31 occasional (7.5%) HP:0000252
27 thick lower lip vermilion 31 occasional (7.5%) HP:0000179
28 strabismus 31 occasional (7.5%) HP:0000486
29 cryptorchidism 31 occasional (7.5%) HP:0000028
30 obesity 31 occasional (7.5%) HP:0001513
31 narrow mouth 31 occasional (7.5%) HP:0000160
32 anal atresia 31 occasional (7.5%) HP:0002023
33 facial asymmetry 31 occasional (7.5%) HP:0000324
34 long face 31 occasional (7.5%) HP:0000276
35 prominent nasal bridge 31 occasional (7.5%) HP:0000426
36 hypospadias 31 occasional (7.5%) HP:0000047
37 congenital diaphragmatic hernia 31 occasional (7.5%) HP:0000776
38 small hand 31 occasional (7.5%) HP:0200055
39 proximal placement of thumb 31 occasional (7.5%) HP:0009623
40 intestinal atresia 31 occasional (7.5%) HP:0011100
41 abnormal palate morphology 31 occasional (7.5%) HP:0000174
42 feeding difficulties 31 occasional (7.5%) HP:0011968
43 abnormal heart morphology 31 occasional (7.5%) HP:0001627
44 coloboma 31 occasional (7.5%) HP:0000589
45 clinodactyly 31 occasional (7.5%) HP:0030084
46 wide nasal base 31 occasional (7.5%) HP:0012810
47 abnormality of toe 31 occasional (7.5%) HP:0001780
48 microphallus 31 occasional (7.5%) HP:0030260
49 decreased response to growth hormone stimuation test 31 occasional (7.5%) HP:0000824
50 myelomeningocele 31 very rare (1%) HP:0002475

Drugs & Therapeutics for Chromosome 15q24 Deletion Syndrome

Search Clinical Trials , NIH Clinical Center for Chromosome 15q24 Deletion Syndrome

Cochrane evidence based reviews: 15q24 microdeletion

Genetic Tests for Chromosome 15q24 Deletion Syndrome

Anatomical Context for Chromosome 15q24 Deletion Syndrome

MalaCards organs/tissues related to Chromosome 15q24 Deletion Syndrome:

40
Eye, Heart

Publications for Chromosome 15q24 Deletion Syndrome

Articles related to Chromosome 15q24 Deletion Syndrome:

(show all 21)
# Title Authors PMID Year
1
Novel SIN3A mutation identified in a Japanese patient with Witteveen-Kolk syndrome. 6
30267900 2019
2
Haploinsufficiency of MeCP2-interacting transcriptional co-repressor SIN3A causes mild intellectual disability by affecting the development of cortical integrity. 6
27399968 2016
3
Coexistence of urogenital malformations in a female fetus with de novo 15q24 microdeletion and a literature review. 61
32400031 2020
4
Refining critical regions in 15q24 microdeletion syndrome pertaining to autism. 61
31953991 2020
5
[Clinical and genetic analysis of three pediatric patients with 15q24 microdeletion syndrome]. 61
31302908 2019
6
Application of chromosome microarray analysis in patients with unexplained developmental delay/intellectual disability in South China. 61
29631977 2019
7
15q24.1 BP4-BP1 microdeletion unmasking paternally inherited functional polymorphisms combined with distal 15q24.2q24.3 duplication in a patient with epilepsy, psychomotor delay, overweight, ventricular arrhythmia. 61
29549028 2018
8
A Novel Case of 15q24 Microdeletion Syndrome Detected by MLPA in a Chinese Family. 61
28879703 2017
9
[Application of chromosome microarray analysis in 489 children with developmental delay/intellectual disability]. 61
28777852 2017
10
An inferential study of the phenotype for the chromosome 15q24 microdeletion syndrome: a bootstrap analysis. 61
26925314 2016
11
Inherited 15q24 microdeletion syndrome in twins and their father with phenotypic variability. 61
25527279 2015
12
Maturation of cortical circuits requires Semaphorin 7A. 61
25201975 2014
13
Genomic Analyses of Patients With Unexplained Early-Onset Scoliosis. 61
27927329 2014
14
Further clinical and molecular delineation of the 15q24 microdeletion syndrome. 61
22180641 2012
15
15q24 Microdeletion Syndrome – RETIRED CHAPTER, FOR HISTORICAL REFERENCE ONLY 61
22359776 2012
16
Chromosome 15q24 microdeletion syndrome. 61
22216833 2012
17
A large-scale survey of the novel 15q24 microdeletion syndrome in autism spectrum disorders identifies an atypical deletion that narrows the critical region. 61
20678247 2010
18
Congenital diaphragmatic hernia is part of the new 15q24 microdeletion syndrome. 61
19233321 2009
19
A 15q24 microduplication, reciprocal to the recently described 15q24 microdeletion, in a boy sharing clinical features with 15q24 microdeletion syndrome patients. 61
18755302 2008
20
A further case of the recurrent 15q24 microdeletion syndrome, detected by array CGH. 61
17932688 2008
21
Characterization of a recurrent 15q24 microdeletion syndrome. 61
17360722 2007

Variations for Chromosome 15q24 Deletion Syndrome

ClinVar genetic disease variations for Chromosome 15q24 Deletion Syndrome:

6 (show all 14)
# Gene Name Type Significance ClinVarId dbSNP ID Position
1 SIN3A NM_001145358.2(SIN3A):c.2949_2950GA[3] (p.Glu985fs) Microsatellite Pathogenic 253073 rs886037847 GRCh37: 15:75682058-75682059
GRCh38: 15:75389717-75389718
2 SIN3A NM_001145358.2(SIN3A):c.803dup (p.Leu269fs) Duplication Pathogenic 253070 rs879255618 GRCh37: 15:75704037-75704038
GRCh38: 15:75411696-75411697
3 SIN3A NM_001145358.2(SIN3A):c.3114_3115CA[2] (p.Gln1040fs) Microsatellite Pathogenic 431101 rs1135401768 GRCh37: 15:75676681-75676682
GRCh38: 15:75384340-75384341
4 SIN3A NM_001145358.2(SIN3A):c.848dup (p.His283fs) Duplication Pathogenic 560386 rs1567368243 GRCh37: 15:75703992-75703993
GRCh38: 15:75411651-75411652
5 SIN3A NM_001145357.1(SIN3A):c.1010_1013del (p.Lys337Serfs) Deletion Pathogenic 253071 rs879255619 GRCh37: 15:75702623-75702626
GRCh38: 15:75410282-75410285
6 SIN3A NM_001145358.2(SIN3A):c.3310C>T (p.Arg1104Ter) SNV Pathogenic 253074 rs879255621 GRCh37: 15:75673043-75673043
GRCh38: 15:75380702-75380702
7 SIN3A NM_001145358.2(SIN3A):c.1759del (p.Ser587fs) Deletion Pathogenic 253072 rs879255620 GRCh37: 15:75692476-75692476
GRCh38: 15:75400135-75400135
8 SIN3A NM_001145358.2(SIN3A):c.1229del (p.Lys410fs) Deletion Pathogenic 1031165 GRCh37: 15:75702265-75702265
GRCh38: 15:75409924-75409924
9 SIN3A NM_001145358.2(SIN3A):c.2258_2259dup (p.Glu754fs) Duplication Pathogenic 1031167 GRCh37: 15:75687038-75687039
GRCh38: 15:75394697-75394698
10 SIN3A NM_001145358.2(SIN3A):c.2005C>T (p.Leu669Phe) SNV Likely pathogenic 1031166 GRCh37: 15:75688687-75688687
GRCh38: 15:75396346-75396346
11 SIN3A NM_001145358.2(SIN3A):c.2006T>A (p.Leu669His) SNV Likely pathogenic 803108 rs1595897117 GRCh37: 15:75688686-75688686
GRCh38: 15:75396345-75396345
12 SIN3A NM_001145358.2(SIN3A):c.866C>A (p.Ser289Ter) SNV Likely pathogenic 930683 GRCh37: 15:75703975-75703975
GRCh38: 15:75411634-75411634
13 overlap with 10 genes Duplication Uncertain significance 560141 GRCh37: 15:75600108-76063285
GRCh38:
14 SIN3A NM_001145358.2(SIN3A):c.776A>C (p.His259Pro) SNV Uncertain significance 1031168 GRCh37: 15:75704065-75704065
GRCh38: 15:75411724-75411724

Copy number variations for Chromosome 15q24 Deletion Syndrome from CNVD:

7 (show all 17)
# CNVD ID Chromosome Start End Type Gene Symbol CNVD Disease
1 94771 15 70400000 76100000 Microdeletion 15q24 microdeletion syndrome
2 94772 15 70400000 76100000 Microdeletion 15q24 microdeletion syndrome
3 94773 15 70400000 76100000 Microdeletion 15q24 microdeletion syndrome
4 94776 15 70400000 76100000 Microdeletion ARID3B 15q24 microdeletion syndrome
5 94777 15 70400000 76100000 Microdeletion COMMD4 15q24 microdeletion syndrome
6 94778 15 70400000 76100000 Microdeletion CPLX3 15q24 microdeletion syndrome
7 94779 15 70400000 76100000 Microdeletion CSK 15q24 microdeletion syndrome
8 94780 15 70400000 76100000 Microdeletion CYP11A1 15q24 microdeletion syndrome
9 94781 15 70400000 76100000 Microdeletion CYP1A1 15q24 microdeletion syndrome
10 94782 15 70400000 76100000 Microdeletion MAN2C1 15q24 microdeletion syndrome
11 94783 15 70400000 76100000 Microdeletion NEIL1 15q24 microdeletion syndrome
12 94784 15 70400000 76100000 Microdeletion PTPN9 15q24 microdeletion syndrome
13 94785 15 70400000 76100000 Microdeletion SEMA7A 15q24 microdeletion syndrome
14 94786 15 70400000 76100000 Microdeletion SEMA7A 15q24 microdeletion syndrome
15 94787 15 70400000 76100000 Microdeletion SIN3A 15q24 microdeletion syndrome
16 94788 15 70400000 76100000 Microdeletion SIN3A 15q24 microdeletion syndrome
17 94789 15 70400000 76100000 Microdeletion STRA6 15q24 microdeletion syndrome

Expression for Chromosome 15q24 Deletion Syndrome

Search GEO for disease gene expression data for Chromosome 15q24 Deletion Syndrome.

Pathways for Chromosome 15q24 Deletion Syndrome

GO Terms for Chromosome 15q24 Deletion Syndrome

Molecular functions related to Chromosome 15q24 Deletion Syndrome according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 RNA polymerase II repressing transcription factor binding GO:0001103 8.62 SIN3A BBS4

Sources for Chromosome 15q24 Deletion Syndrome

3 CDC
7 CNVD
9 Cosmic
10 dbSNP
11 DGIdb
17 EFO
18 ExPASy
19 FMA
20 GARD
28 GO
29 GTR
30 HMDB
31 HPO
32 ICD10
33 ICD10 via Orphanet
34 ICD9CM
35 IUPHAR
36 KEGG
37 LifeMap
39 LOVD
41 MedGen
44 MeSH
45 MESH via Orphanet
46 MGI
49 NCI
50 NCIt
51 NDF-RT
53 NINDS
54 Novoseek
56 OMIM via Orphanet
57 OMIM® (Updated 20-May-2021)
61 PubMed
63 QIAGEN
68 SNOMED-CT via HPO
69 Tocris
70 UMLS
71 UMLS via Orphanet
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