MCID: CHR594
MIFTS: 48

Chromosome 3q29 Deletion Syndrome

Categories: Rare diseases, Fetal diseases, Genetic diseases

Aliases & Classifications for Chromosome 3q29 Deletion Syndrome

MalaCards integrated aliases for Chromosome 3q29 Deletion Syndrome:

Name: Chromosome 3q29 Deletion Syndrome 53 24 41 69
3q29 Microdeletion Syndrome 12 72 49 24 55 28
Chromosome 3q29 Microdeletion Syndrome 53 12 49 13 14
3q Subtelomere Deletion Syndrome 12 49 24 55
3qter Deletion 12 49 55
Monosomy 3q29 49 24 55
Microdeletion 3q29 Syndrome 53 24
3q29 Deletion Syndrome 49 24
Monosomy 3qter 49 55
Del(3)(q29) 49 55
3q29 Recurrent Deletion 24
3q29 Deletion 49

Characteristics:

Orphanet epidemiological data:

55
3q29 microdeletion syndrome
Inheritance: Autosomal dominant; Age of onset: Infancy,Neonatal;

OMIM:

53
Inheritance:
isolated cases

Miscellaneous:
contiguous gene deletion syndrome
microdeletion is approximately 1.5mb in length


HPO:

31
chromosome 3q29 deletion syndrome:
Inheritance autosomal dominant inheritance sporadic


Classifications:



Summaries for Chromosome 3q29 Deletion Syndrome

NIH Rare Diseases : 49 3q29 microdeletion syndromeis a rare chromosome disorder. Symptoms may include delay reaching some developmental milestones such as sitting, walking or talking, frequent ear and respiratory infections, and a small head size (microcephaly). Some babies with this condition are born with a cleft lip or cleft palate, and a few have been reported to have heart defects. As children with this condition get older, they may develop behavioral difficulties such as autism, and they may have symptoms of mental illness. The severity of symptoms can vary, and some people with 3q29 microdeletion syndrome may have very mild symptoms or may not even know they are affected.  3q29 microdeletion syndrome is caused by the loss of a small piece of DNA in one copy of chromosome 3, one of the 23 pairs of chromosomes in each cell in our bodies. Most cases of 3q29 microdeletion syndrome are de novo, which means the deletion was not passed down from either parent. Some cases may be inherited from a parent who is only mildly affected by the condition. Diagnosis of 3q29 microdeletion syndrome may be suspected by symptoms but is confirmed by genetic testing. Treatment is based on signs and symptoms of each person and may include surgeries to repair any physical abnormalities, speech therapy, behavior therapy and special education. Last updated: 9/23/2016

MalaCards based summary : Chromosome 3q29 Deletion Syndrome, also known as 3q29 microdeletion syndrome, is related to 3q29 recurrent deletion and spastic paraplegia 14, autosomal recessive, and has symptoms including macrocephaly, low-set ears and pectus excavatum. An important gene associated with Chromosome 3q29 Deletion Syndrome is DEL3Q29 (Chromosome 3q29 Microdeletion Syndrome), and among its related pathways/superpathways are SALM protein interactions at the synapses and Abacavir transport and metabolism. Affiliated tissues include heart, testes and skin, and related phenotypes are cellular and endocrine/exocrine gland

Genetics Home Reference : 24 3q29 microdeletion syndrome (also known as 3q29 deletion syndrome) is a condition that results from the deletion of a small piece of chromosome 3 in each cell. The deletion occurs on the long (q) arm of the chromosome at a position designated q29.

Wikipedia : 72 3q29 microdeletion syndrome is a rare genetic disorder resulting from the deletion of a segment of... more...

Description from OMIM: 609425

Related Diseases for Chromosome 3q29 Deletion Syndrome

Diseases related to Chromosome 3q29 Deletion Syndrome via text searches within MalaCards or GeneCards Suite gene sharing:

# Related Disease Score Top Affiliating Genes
1 3q29 recurrent deletion 11.5
2 spastic paraplegia 14, autosomal recessive 10.3 CCDC50 SNCA
3 leukemia 10.2
4 myeloid leukemia 10.2
5 deafness, autosomal dominant 44 10.1 CCDC50 SNCA
6 type 1 diabetes mellitus 8 10.0 SLC22A2 SLC22A3
7 schizophrenia 10.0
8 bipolar disorder 10.0
9 scotoma 9.9 DLG3 SNCA
10 cerebral palsy, ataxic, autosomal recessive 9.8 IGF2R SLC22A2 SLC22A3

Graphical network of the top 20 diseases related to Chromosome 3q29 Deletion Syndrome:



Diseases related to Chromosome 3q29 Deletion Syndrome

Symptoms & Phenotypes for Chromosome 3q29 Deletion Syndrome

Symptoms via clinical synopsis from OMIM:

53
Neurologic Central Nervous System:
gait ataxia
mental retardation, mild to moderate

Chest RibsSternum Clavicles And Scapulae:
pectus excavatum
pectus carinatum

Growth Other:
failure to thrive

Head And Neck Face:
short philtrum
long, narrow face

Head And Neck Nose:
high nasal bridge

Skeletal Hands:
long, tapered fingers

Head And Neck Ears:
low-set ears
posteriorly rotated ears
large ears

Skeletal Feet:
clinodactyly

Neurologic Behavioral Psychiatric Manifestations:
autism
anxiety
psychosis
hyperactivity
aggression

Head And Neck Mouth:
thin upper lip

Growth Weight:
low birth weight

Laboratory Abnormalities:
subtelomeric deletion of long arm of chromosome 3 (3q29)


Clinical features from OMIM:

609425

Human phenotypes related to Chromosome 3q29 Deletion Syndrome:

55 31 (show top 50) (show all 52)
# Description HPO Frequency Orphanet Frequency HPO Source Accession
1 macrocephaly 55 31 occasional (7.5%) Occasional (29-5%) HP:0000256
2 low-set ears 55 31 frequent (33%) Frequent (79-30%) HP:0000369
3 pectus excavatum 55 31 occasional (7.5%) Occasional (29-5%) HP:0000767
4 high palate 55 31 occasional (7.5%) Occasional (29-5%) HP:0000218
5 intellectual disability 55 31 hallmark (90%) Very frequent (99-80%) HP:0001249
6 gait disturbance 55 31 occasional (7.5%) Occasional (29-5%) HP:0001288
7 failure to thrive 55 31 occasional (7.5%) Occasional (29-5%) HP:0001508
8 macrotia 55 31 frequent (33%) Frequent (79-30%) HP:0000400
9 cataract 55 31 occasional (7.5%) Occasional (29-5%) HP:0000518
10 global developmental delay 55 31 hallmark (90%) Very frequent (99-80%) HP:0001263
11 delayed speech and language development 55 31 frequent (33%) Frequent (79-30%) HP:0000750
12 pectus carinatum 55 31 occasional (7.5%) Occasional (29-5%) HP:0000768
13 short nose 55 31 occasional (7.5%) Occasional (29-5%) HP:0003196
14 microcephaly 55 31 frequent (33%) Frequent (79-30%) HP:0000252
15 gastroesophageal reflux 55 31 occasional (7.5%) Occasional (29-5%) HP:0002020
16 pulmonary arterial hypertension 55 31 occasional (7.5%) Occasional (29-5%) HP:0002092
17 patent ductus arteriosus 55 31 occasional (7.5%) Occasional (29-5%) HP:0001643
18 joint hyperflexibility 55 31 occasional (7.5%) Occasional (29-5%) HP:0005692
19 everted lower lip vermilion 55 31 frequent (33%) Frequent (79-30%) HP:0000232
20 autism 55 31 occasional (7.5%) Occasional (29-5%) HP:0000717
21 attention deficit hyperactivity disorder 55 31 occasional (7.5%) Occasional (29-5%) HP:0007018
22 anxiety 55 31 occasional (7.5%) Occasional (29-5%) HP:0000739
23 horseshoe kidney 55 31 occasional (7.5%) Occasional (29-5%) HP:0000085
24 prominent nasal bridge 55 31 frequent (33%) Frequent (79-30%) HP:0000426
25 short philtrum 55 31 frequent (33%) Frequent (79-30%) HP:0000322
26 microphthalmia 55 31 occasional (7.5%) Occasional (29-5%) HP:0000568
27 hypospadias 55 31 occasional (7.5%) Occasional (29-5%) HP:0000047
28 psychosis 55 31 occasional (7.5%) Occasional (29-5%) HP:0000709
29 clinodactyly of the 5th finger 55 31 occasional (7.5%) Occasional (29-5%) HP:0004209
30 narrow face 55 31 occasional (7.5%) Occasional (29-5%) HP:0000275
31 dental crowding 55 31 occasional (7.5%) Occasional (29-5%) HP:0000678
32 downslanted palpebral fissures 55 31 occasional (7.5%) Occasional (29-5%) HP:0000494
33 long face 55 31 occasional (7.5%) Occasional (29-5%) HP:0000276
34 nasal speech 55 31 occasional (7.5%) Occasional (29-5%) HP:0001611
35 bipolar affective disorder 55 31 occasional (7.5%) Occasional (29-5%) HP:0007302
36 aggressive behavior 55 31 occasional (7.5%) Occasional (29-5%) HP:0000718
37 abnormality of skin pigmentation 55 31 occasional (7.5%) Occasional (29-5%) HP:0001000
38 facial asymmetry 55 31 occasional (7.5%) Occasional (29-5%) HP:0000324
39 tapered finger 55 31 occasional (7.5%) Occasional (29-5%) HP:0001182
40 oral cleft 55 31 occasional (7.5%) Occasional (29-5%) HP:0000202
41 six lumbar vertebrae 55 31 occasional (7.5%) Occasional (29-5%) HP:0008416
42 gait ataxia 31 HP:0002066
43 depression 55 Occasional (29-5%)
44 abnormality of the dentition 55 Occasional (29-5%)
45 stereotypy 31 HP:0000733
46 thin upper lip vermilion 31 HP:0000219
47 hyperactivity 31 HP:0000752
48 posteriorly rotated ears 31 HP:0000358
49 small for gestational age 31 HP:0001518
50 subaortic stenosis 55 Occasional (29-5%)

UMLS symptoms related to Chromosome 3q29 Deletion Syndrome:


gait ataxia

MGI Mouse Phenotypes related to Chromosome 3q29 Deletion Syndrome:

43
# Description MGI Source Accession Score Top Affiliating Genes
1 cellular MP:0005384 9.81 DLG1 ETS1 HES1 IGF2R MPP3 PTEN
2 endocrine/exocrine gland MP:0005379 9.5 IGF2R PTEN RNF168 SNCA DLG1 ETS1
3 taste/olfaction MP:0005394 8.8 HES1 PTEN SNCA

Drugs & Therapeutics for Chromosome 3q29 Deletion Syndrome

Interventional clinical trials:


# Name Status NCT ID Phase Drugs
1 Characterization of 3q29 Deletion Syndrome and 3q29 Duplication Syndrome Recruiting NCT02447861

Search NIH Clinical Center for Chromosome 3q29 Deletion Syndrome

Cochrane evidence based reviews: chromosome 3q29 deletion syndrome

Genetic Tests for Chromosome 3q29 Deletion Syndrome

Genetic tests related to Chromosome 3q29 Deletion Syndrome:

# Genetic test Affiliating Genes
1 3q29 Microdeletion Syndrome 28

Anatomical Context for Chromosome 3q29 Deletion Syndrome

MalaCards organs/tissues related to Chromosome 3q29 Deletion Syndrome:

38
Heart, Testes, Skin, Kidney

Publications for Chromosome 3q29 Deletion Syndrome

Articles related to Chromosome 3q29 Deletion Syndrome:

# Title Authors Year
1
3q29 microdeletion syndrome: Cognitive and behavioral phenotype in four patients. ( 24214349 )
2013
2
A case of 3q29 microdeletion syndrome involving oral cleft inherited from a nonaffected mosaic parent: molecular analysis and ethical implications. ( 20500065 )
2011
3
Mutation screening of the 3q29 microdeletion syndrome candidate genes DLG1 and PAK2 in schizophrenia. ( 21850710 )
2011
4
The 3q29 microdeletion syndrome: report of three new unrelated patients and in silico "RNA binding" analysis of the 3q29 region. ( 21626679 )
2011
5
Autistic and psychiatric findings associated with the 3q29 microdeletion syndrome: case report and review. ( 20830797 )
2010
6
Familial 3q29 microdeletion syndrome providing further evidence of involvement of the 3q29 region in bipolar disorder. ( 20453639 )
2010
7
[Identification of a novel deletion region in 3q29 microdeletion syndrome by oligonucleotide array comparative genomic hybridization]. ( 20197726 )
2010
8
Expanding the clinical phenotype of the 3q29 microdeletion syndrome and characterization of the reciprocal microduplication. ( 18471269 )
2008
9
3q29 microdeletion syndrome: clinical and molecular characterization of a new syndrome. ( 15918153 )
2005

Variations for Chromosome 3q29 Deletion Syndrome

ClinVar genetic disease variations for Chromosome 3q29 Deletion Syndrome:

6
# Gene Variation Type Significance SNP ID Assembly Location
1 subset of 21 genes:PAK2 GRCh37/hg19 3q29(chr3: 195756054-197344665)x1 copy number loss Pathogenic GRCh37 Chromosome 3, 195756054: 197344665

Copy number variations for Chromosome 3q29 Deletion Syndrome from CNVD:

7
# CNVD ID Chromosom Start End Type Gene Symbol CNVD Disease
1 173445 3 193800000 199501827 Microdeletion 3q29 microdeletion syndrome
2 173448 3 193800000 199501827 Microdeletion DLG1 3q29 microdeletion syndrome
3 173449 3 193800000 199501827 Microdeletions RNF168 3q29 microdeletion syndrome

Expression for Chromosome 3q29 Deletion Syndrome

Search GEO for disease gene expression data for Chromosome 3q29 Deletion Syndrome.

Pathways for Chromosome 3q29 Deletion Syndrome

Pathways related to Chromosome 3q29 Deletion Syndrome according to GeneCards Suite gene sharing:

# Super pathways Score Top Affiliating Genes
1 10.58 DLG1 DLG3
2
Show member pathways
10.46 SLC22A2 SLC22A3
3 10.21 SLC22A2 SLC22A3
4 9.4 SLC22A2 SLC22A3

GO Terms for Chromosome 3q29 Deletion Syndrome

Cellular components related to Chromosome 3q29 Deletion Syndrome according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 synapse GO:0045202 9.26 DLG1 DLG3 SLC22A2 SNCA
2 ionotropic glutamate receptor complex GO:0008328 8.62 DLG1 DLG3

Biological processes related to Chromosome 3q29 Deletion Syndrome according to GeneCards Suite gene sharing:

(show all 13)
# Name GO ID Score Top Affiliating Genes
1 response to interleukin-1 GO:0070555 9.52 ETS1 SNCA
2 pituitary gland development GO:0021983 9.51 ETS1 HES1
3 drug transmembrane transport GO:0006855 9.49 SLC22A2 SLC22A3
4 organic anion transport GO:0015711 9.48 SLC22A2 SLC22A3
5 receptor clustering GO:0043113 9.46 DLG1 DLG3
6 organic cation transport GO:0015695 9.43 SLC22A2 SLC22A3
7 establishment or maintenance of epithelial cell apical/basal polarity GO:0045197 9.4 DLG1 DLG3
8 ammonium transmembrane transport GO:0072488 9.37 SLC22A2 SLC22A3
9 receptor localization to synapse GO:0097120 9.32 DLG1 DLG3
10 dopamine transport GO:0015872 9.26 SLC22A2 SLC22A3
11 quaternary ammonium group transport GO:0015697 9.16 SLC22A2 SLC22A3
12 GMP metabolic process GO:0046037 9.13 DLG1 DLG3 MPP3
13 GDP metabolic process GO:0046710 8.8 DLG1 DLG3 MPP3

Molecular functions related to Chromosome 3q29 Deletion Syndrome according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 PDZ domain binding GO:0030165 9.54 DLG3 MPP3 PTEN
2 phosphoprotein binding GO:0051219 9.46 IGF2R SNCA
3 ligand-gated ion channel activity GO:0015276 9.43 DLG1 DLG3
4 organic anion transmembrane transporter activity GO:0008514 9.4 SLC22A2 SLC22A3
5 organic cation transmembrane transporter activity GO:0015101 9.32 SLC22A2 SLC22A3
6 quaternary ammonium group transmembrane transporter activity GO:0015651 9.26 SLC22A2 SLC22A3
7 dopamine transmembrane transporter activity GO:0005329 9.16 SLC22A2 SLC22A3
8 ionotropic glutamate receptor binding GO:0035255 9.13 DLG1 DLG3 PTEN
9 guanylate kinase activity GO:0004385 8.8 DLG1 DLG3 MPP3

Sources for Chromosome 3q29 Deletion Syndrome

3 CDC
7 CNVD
9 Cosmic
10 dbSNP
11 DGIdb
16 ExPASy
18 FMA
27 GO
28 GTR
29 HGMD
30 HMDB
31 HPO
32 ICD10
33 ICD10 via Orphanet
34 ICD9CM
35 IUPHAR
36 KEGG
37 LifeMap
39 MedGen
41 MeSH
42 MESH via Orphanet
43 MGI
45 NCI
46 NCIt
47 NDF-RT
50 NINDS
51 Novoseek
53 OMIM
54 OMIM via Orphanet
58 PubMed
60 QIAGEN
65 SNOMED-CT via HPO
66 SNOMED-CT via Orphanet
67 TGDB
68 Tocris
69 UMLS
70 UMLS via Orphanet
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