MCID: CHR667
MIFTS: 41

Chromosome 3pter-P25 Deletion Syndrome

Categories: Fetal diseases, Gastrointestinal diseases, Genetic diseases, Neuronal diseases, Rare diseases

Aliases & Classifications for Chromosome 3pter-P25 Deletion Syndrome

MalaCards integrated aliases for Chromosome 3pter-P25 Deletion Syndrome:

Name: Chromosome 3pter-P25 Deletion Syndrome 56 12 52 29 6
3p- Syndrome 56 52 25 58 13
Chromosome 3, Monosomy 3p 25 29 71
3p Deletion Syndrome 12 25 15
Distal Monosomy 3p 12 52 58
Telomeric Monosomy 3p 52 58
Distal 3p Deletion 52 58
Monosomy 3pter 52 58
Del Syndrome 52 25
Deletion Syndrome, Chromosome 3pter-P25 39
Chromosome 3p Deletion Syndrome 25
3p Partial Monosomy Syndrome 25
Chromosome 3, Monosomy 3p25 52
Chromosome 3, Deletion 3p 25
Chromosome 3p- Syndrome 52
Partial Monosomy 3p 25
Deletion 3p25 52
Deletion 3p 25
Monosomy 3p 25

Characteristics:

OMIM:

56
Inheritance:
autosomal dominant

Miscellaneous:
contiguous gene deletion syndrome


HPO:

31
chromosome 3pter-p25 deletion syndrome:
Inheritance autosomal dominant inheritance


Classifications:

Orphanet: 58  
Rare neurological diseases
Developmental anomalies during embryogenesis


Summaries for Chromosome 3pter-P25 Deletion Syndrome

Genetics Home Reference : 25 3p deletion syndrome is a condition that results from a chromosomal change in which a small piece of chromosome 3 is deleted in each cell. The deletion occurs at the end of the short (p) arm of the chromosome. This chromosomal change often leads to intellectual disability, developmental delay, and abnormal physical features. Individuals with 3p deletion syndrome typically have severe to profound intellectual disability. Most have delayed development of language skills as well as motor skills such as crawling and walking. While affected individuals learn to walk in childhood, their language ability usually remains limited. Some individuals with 3p deletion syndrome have obsessive-compulsive disorder (OCD) or features of autism spectrum disorders, which are conditions characterized by impaired communication and social interaction. The physical signs and symptoms of 3p deletion syndrome vary greatly. Many affected individuals have slow growth, an abnormally small head (microcephaly), a small jaw (micrognathia), droopy eyelids (ptosis), malformed ears or nose, and widely spaced eyes (hypertelorism). Other frequent features include skin folds covering the inner corner of the eyes (epicanthal folds), extra fingers or toes (polydactyly), and an opening in the roof of the mouth (cleft palate). Additionally, individuals with 3p deletion syndrome may have seizures, weak muscle tone (hypotonia), intestinal abnormalities, or congenital heart defects.

MalaCards based summary : Chromosome 3pter-P25 Deletion Syndrome, also known as 3p- syndrome, is related to patent ductus arteriosus 1 and partial deletion of the short arm of chromosome 3, and has symptoms including muscle spasticity An important gene associated with Chromosome 3pter-P25 Deletion Syndrome is DEL3PTERP25 (3p- Syndrome), and among its related pathways/superpathways is Signaling by Slit. Affiliated tissues include heart, eye and skin, and related phenotypes are hypertelorism and short stature

Disease Ontology : 12 A chromosomal deletion syndrome that has material basis in a contiguous gene deletion syndrome involving chromosome 3pter-p25 and is characterized by low birth weight, microcephaly, trigonocephaly, hypotonia, psychomotor and growth retardation, ptosis, telecanthus, downslanting palpebral fissures, and micrognathia.

NIH Rare Diseases : 52 Chromosome 3p- syndrome is a rare chromosome abnormality that occurs when there is a missing copy of the genetic material located towards the end of the short arm (p) of chromosome 3 . The severity of the condition and the signs and symptoms depend on the exact size and location of the deletion and which genes are involved. Some affected people appear to have no features or mild features, while others are more severely affected. Common symptoms shared by many people with this deletion include poor growth, developmental delay , intellectual disability , distinctive facial features, autism spectrum disorder , an unusually small head (microcephaly ), and poor muscle tone (hypotonia ). Most cases are not inherited , but people can pass the deletion on to their children. Treatment is based on the signs and symptoms present in each person.

OMIM : 56 Characteristic features of the distal 3p- syndrome include low birth weight, microcephaly, trigonocephaly, hypotonia, psychomotor and growth retardation, ptosis, telecanthus, downslanting palpebral fissures, and micrognathia. Postaxial polydactyly, renal anomalies, cleft palate, congenital heart defects (especially atrioventricular septal defects), preauricular pits, sacral dimple, and gastrointestinal anomalies are variable features. Although intellectual deficits are almost invariably associated with cytogenetically visible 3p deletions, rare patients with a 3p26-p25 deletion and normal intelligence or only mild abnormalities have been described (summary by Shuib et al., 2009). (613792)

Related Diseases for Chromosome 3pter-P25 Deletion Syndrome

Diseases related to Chromosome 3pter-P25 Deletion Syndrome via text searches within MalaCards or GeneCards Suite gene sharing:

(show top 50) (show all 59)
# Related Disease Score Top Affiliating Genes
1 patent ductus arteriosus 1 28.6 PTER CRELD1
2 partial deletion of the short arm of chromosome 3 11.5
3 intellectual developmental disorder with dysmorphic facies and ptosis 11.4
4 ohdo syndrome 11.2
5 wolf-hirschhorn syndrome 11.0
6 distal chromosome 18q deletion syndrome 11.0
7 proximal chromosome 18q deletion syndrome 11.0
8 chromosome 16q duplication 10.2
9 trichorhinophalangeal syndrome, type i 10.2
10 hemangioma 10.2
11 trichorhinophalangeal syndrome 10.2
12 chromosome 8q duplication 10.2
13 ptosis 10.1
14 microcephaly 10.1
15 chromosomal triplication 10.1
16 chromosome 3p duplication 10.1
17 pectus excavatum 10.1
18 uvula, bifid 10.1
19 cryptorchidism, unilateral or bilateral 10.1
20 scoliosis 10.1
21 inguinal hernia 10.1
22 anterior segment dysgenesis 10.1
23 atrial heart septal defect 10.1
24 craniosynostosis 10.1
25 hypertrichosis 10.1
26 chromosome 10q duplication 10.1
27 chromosome 2p duplication 10.1
28 chromosome 5q duplication 10.1
29 trisomy 1q 10.1
30 peripheral pulmonary stenosis 10.1
31 chromosome 1p duplication 10.0
32 atrial septal defect 6 10.0 CNTN6 CNTN5
33 hypertelorism 9.9
34 telecanthus 9.9
35 cleft lip 9.9
36 coffin-siris syndrome 6 9.9 CNTN6 CNTN5 CNTN4
37 cleft palate, isolated 9.9
38 tetralogy of fallot 9.9
39 velocardiofacial syndrome 9.9
40 clubfoot 9.9
41 hemangioblastoma 9.9
42 hypotonia 9.9
43 renal cell carcinoma, nonpapillary 9.8
44 small cell cancer of the lung 9.8
45 adenocarcinoma 9.8
46 childhood pilocytic astrocytoma 9.8 SRGAP3 SRGAP2
47 epicanthus 9.8
48 congenital anomalies of kidney and urinary tract 2 9.8
49 branchiootic syndrome 1 9.8
50 atrioventricular septal defect 9.8

Graphical network of the top 20 diseases related to Chromosome 3pter-P25 Deletion Syndrome:



Diseases related to Chromosome 3pter-P25 Deletion Syndrome

Symptoms & Phenotypes for Chromosome 3pter-P25 Deletion Syndrome

Human phenotypes related to Chromosome 3pter-P25 Deletion Syndrome:

58 31 (show top 50) (show all 60)
# Description HPO Frequency Orphanet Frequency HPO Source Accession
1 hypertelorism 58 31 hallmark (90%) Very frequent (99-80%) HP:0000316
2 short stature 58 31 hallmark (90%) Very frequent (99-80%) HP:0004322
3 cognitive impairment 58 31 hallmark (90%) Very frequent (99-80%) HP:0100543
4 micrognathia 58 31 hallmark (90%) Very frequent (99-80%) HP:0000347
5 ptosis 58 31 hallmark (90%) Very frequent (99-80%) HP:0000508
6 long philtrum 58 31 hallmark (90%) Very frequent (99-80%) HP:0000343
7 telecanthus 58 31 hallmark (90%) Very frequent (99-80%) HP:0000506
8 hearing impairment 58 31 occasional (7.5%) Frequent (79-30%) HP:0000365
9 muscular hypotonia 58 31 frequent (33%) Frequent (79-30%) HP:0001252
10 microcephaly 58 31 frequent (33%) Frequent (79-30%) HP:0000252
11 brachycephaly 58 31 frequent (33%) Frequent (79-30%) HP:0000248
12 cleft palate 58 31 frequent (33%) Frequent (79-30%) HP:0000175
13 cryptorchidism 58 31 occasional (7.5%) Frequent (79-30%) HP:0000028
14 intrauterine growth retardation 58 31 frequent (33%) Frequent (79-30%) HP:0001511
15 high palate 58 31 frequent (33%) Frequent (79-30%) HP:0000218
16 epicanthus 58 31 frequent (33%) Frequent (79-30%) HP:0000286
17 downturned corners of mouth 58 31 frequent (33%) Frequent (79-30%) HP:0002714
18 low-set, posteriorly rotated ears 58 31 frequent (33%) Frequent (79-30%) HP:0000368
19 atrioventricular canal defect 58 31 occasional (7.5%) Frequent (79-30%) HP:0006695
20 postaxial hand polydactyly 58 31 frequent (33%) Frequent (79-30%) HP:0001162
21 inguinal hernia 58 31 occasional (7.5%) Occasional (29-5%) HP:0000023
22 short neck 58 31 occasional (7.5%) Occasional (29-5%) HP:0000470
23 umbilical hernia 58 31 occasional (7.5%) Occasional (29-5%) HP:0001537
24 anteverted nares 58 31 occasional (7.5%) Occasional (29-5%) HP:0000463
25 spasticity 58 31 occasional (7.5%) Occasional (29-5%) HP:0001257
26 clinodactyly of the 5th finger 58 31 occasional (7.5%) Occasional (29-5%) HP:0004209
27 ventriculomegaly 58 31 occasional (7.5%) Occasional (29-5%) HP:0002119
28 blepharophimosis 58 31 occasional (7.5%) Occasional (29-5%) HP:0000581
29 sacral dimple 58 31 occasional (7.5%) Occasional (29-5%) HP:0000960
30 thin vermilion border 58 31 occasional (7.5%) Occasional (29-5%) HP:0000233
31 triangular face 58 31 occasional (7.5%) Occasional (29-5%) HP:0000325
32 preauricular pit 58 31 occasional (7.5%) Occasional (29-5%) HP:0004467
33 abnormal vestibulo-ocular reflex 58 31 occasional (7.5%) Occasional (29-5%) HP:0007670
34 prominent nasal bridge 31 occasional (7.5%) HP:0000426
35 macular hypoplasia 31 occasional (7.5%) HP:0001104
36 abnormal renal morphology 31 occasional (7.5%) HP:0012210
37 seizure 31 occasional (7.5%) HP:0001250
38 global developmental delay 31 HP:0001263
39 depressed nasal bridge 31 HP:0005280
40 wide nasal bridge 31 HP:0000431
41 seizures 58 Occasional (29-5%)
42 feeding difficulties 31 HP:0011968
43 strabismus 31 HP:0000486
44 absent speech 31 HP:0001344
45 postnatal growth retardation 31 HP:0008897
46 retrognathia 31 HP:0000278
47 low-set ears 31 HP:0000369
48 upslanted palpebral fissure 31 HP:0000582
49 highly arched eyebrow 31 HP:0002553
50 flat occiput 31 HP:0005469

Symptoms via clinical synopsis from OMIM:

56
Head And Neck Eyes:
hypertelorism
strabismus
ptosis
blepharophimosis
synophrys
more
Growth Height:
short stature

Muscle Soft Tissue:
spasticity
muscle hypotonia
muscle hypertonicity

Head And Neck Face:
retrognathia
micrognathia
long philtrum
triangular face
mandible small

Head And Neck Mouth:
downturned corners of mouth
high-arched palate
thin lips

Skeletal Hands:
postaxial polydactyly
tapering fingers

Genitourinary Internal Genitalia Male:
cryptorchidism (in some patients)

Abdomen Gastrointestinal:
feeding problems

Neurologic Central Nervous System:
seizures (rare)
poor or absent speech
psychomotor retardation, severe to profound

Genitourinary Kidneys:
renal malformation (in some patients)

Head And Neck Nose:
anteverted nares
broad nasal tip
broad nasal bridge
flat nasal bridge
prominent columella
more
Head And Neck Head:
brachycephaly
flat occiput
trigonocephaly
microcephaly (up to -3.4 sd)

Growth Other:
postnatal growth retardation

Head And Neck Ears:
low-set ears
preauricular fistulas
preauricular pits
hearing loss (in some patients)
poorly shaped ears

Skeletal Spine:
sacral dimple

Skeletal Feet:
postaxial polydactyly

Skeletal Skull:
prominent metopic suture

Growth Weight:
low birth weight

Cardiovascular Heart:
congenital heart disease (in some patients)
atrioventricular septal defect (in some patients)

Clinical features from OMIM:

613792

UMLS symptoms related to Chromosome 3pter-P25 Deletion Syndrome:


muscle spasticity

MGI Mouse Phenotypes related to Chromosome 3pter-P25 Deletion Syndrome:

45
# Description MGI Source Accession Score Top Affiliating Genes
1 nervous system MP:0003631 9.23 CNTN4 CNTN5 CNTN6 CRBN CRELD1 SETD5

Drugs & Therapeutics for Chromosome 3pter-P25 Deletion Syndrome

Search Clinical Trials , NIH Clinical Center for Chromosome 3pter-P25 Deletion Syndrome

Genetic Tests for Chromosome 3pter-P25 Deletion Syndrome

Genetic tests related to Chromosome 3pter-P25 Deletion Syndrome:

# Genetic test Affiliating Genes
1 Chromosome 3pter-P25 Deletion Syndrome 29
2 Chromosome 3, Monosomy 3p 29

Anatomical Context for Chromosome 3pter-P25 Deletion Syndrome

MalaCards organs/tissues related to Chromosome 3pter-P25 Deletion Syndrome:

40
Heart, Eye, Skin, Brain

Publications for Chromosome 3pter-P25 Deletion Syndrome

Articles related to Chromosome 3pter-P25 Deletion Syndrome:

(show all 50)
# Title Authors PMID Year
1
Microarray based analysis of 3p25-p26 deletions (3p- syndrome). 61 56
19760623 2009
2
The novel Rho-GTPase activating gene MEGAP/ srGAP3 has a putative role in severe mental retardation. 56 61
12195014 2002
3
Molecular cytogenetic characterization of a subtle interstitial del(3)(p25.3p26.2) in a patient with deletion 3p syndrome. 56 61
11977162 2002
4
Detailed mapping of a congenital heart disease gene in chromosome 3p25. 61 56
10922384 2000
5
CALL gene is haploinsufficient in a 3p- syndrome patient. 56 61
10508992 1999
6
Precise localisation of 3p25 breakpoints in four patients with the 3p-syndrome. 61 56
8933338 1996
7
Molecular genetic analysis of the 3p- syndrome. 61 56
7951234 1994
8
Loss of the 3p25.3 band is critical in the manifestation of del(3p) syndrome: karyotype-phenotype correlation in cases with deficiency of the distal portion of the short arm of chromosome 3. 56 61
2178418 1990
9
Terminal deletion of the short arm of chromosome 3, del(3pter-p25): a recognizable syndrome. 56 61
3443553 1987
10
Mutations in Histone Acetylase Modifier BRPF1 Cause an Autosomal-Dominant Form of Intellectual Disability with Associated Ptosis. 56
27939639 2017
11
Loss-of-function variants of SETD5 cause intellectual disability and the core phenotype of microdeletion 3p25.3 syndrome. 56
25138099 2015
12
Distal 3p deletion syndrome: detailed molecular cytogenetic and clinical characterization of three small distal deletions and review. 56
17696125 2007
13
Chromosome 3p25 deletion in mother and daughter with minimal phenotypic effect. 56
16770804 2006
14
Analysis of CRELD1 as a candidate 3p25 atrioventicular septal defect locus (AVSD2). 56
15857420 2005
15
Disruption of contactin 4 (CNTN4) results in developmental delay and other features of 3p deletion syndrome. 56
15106122 2004
16
A terminal deletion of the short arm of chromosome 3: karyotype 46, XY, del (3) (p25-pter); a case report and literature review. 56
11074119 2000
17
Clinical and molecular analyses of deletion 3p25-pter syndrome. 56
8103286 1993
18
Infant with del(3) (p25-pter): karyotype-phenotype correlation and review of previously reported cases. 56
1481811 1992
19
Two infants with del(3)(p25pter) and a review of previously reported cases. 56
2665488 1989
20
A patient with a partial deletion of the short arm of chromosome 3. 56
623063 1978
21
3p25.3 microdeletion of GABA transporters SLC6A1 and SLC6A11 results in intellectual disability, epilepsy and stereotypic behavior. 61
25256099 2014
22
Complex translocation among chromosomes 2, 3, 9, 15, 18, 20 in a patient with 3p-syndrome. 61
24979567 2014
23
A case of partial trisomy 3p syndrome with rare clinical manifestations. 61
22474466 2012
24
Microarray based analysis of an inherited terminal 3p26.3 deletion, containing only the CHL1 gene, from a normal father to his two affected children. 61
21457564 2011
25
Molecular characterization and clinical features of a patient with an interstitial deletion of 3p25.3-p26.1. 61
21082655 2010
26
"CRASH"ing with the worm: insights into L1CAM functions and mechanisms. 61
20225255 2010
27
3p-- syndrome defines a hearing loss locus in 3p25.3. 61
17208398 2007
28
FISH and array-CGH analysis of a complex chromosome 3 aberration suggests that loss of CNTN4 and CRBN contributes to mental retardation in 3pter deletions. 61
17036314 2006
29
Blepharophimosis-mental retardation (BMR) syndromes: A proposed clinical classification of the so-called Ohdo syndrome, and delineation of two new BMR syndromes, one X-linked and one autosomal recessive. 61
16700052 2006
30
Aberrant neuronal connectivity in CHL1-deficient mice is associated with altered information processing-related immediate early gene expression. 61
12973829 2003
31
Loss of WAVE-1 causes sensorimotor retardation and reduced learning and memory in mice. 61
12578964 2003
32
Misguided axonal projections, neural cell adhesion molecule 180 mRNA upregulation, and altered behavior in mice deficient for the close homolog of L1. 61
12391163 2002
33
Identification, genomic organization and mRNA expression of CRELD1, the founding member of a unique family of matricellular proteins. 61
12137942 2002
34
A novel splice variant of the cell adhesion molecule contactin 4 ( CNTN4) is mainly expressed in human brain. 61
12202991 2002
35
A gene for nonsyndromic mental retardation maps to chromosome 3p25-pter. 61
10932263 2000
36
Does the taurine transporter gene play a role in 3p-syndrome? 61
11787648 2000
37
The taurine transporter gene and its role in renal development. 61
11140355 2000
38
Localization of the human caveolin-3 gene to the D3S18/D3S4163/D3S4539 locus (3p25), in close proximity to the human oxytocin receptor gene. Identification of the caveolin-3 gene as a candidate for deletion in 3p-syndrome. 61
10386585 1999
39
Detection of a concomitant distal deletion in an inverted duplication of chromosome 3. Is there an overall mechanism for the origin of such duplications/deficiencies? 61
9801868 1998
40
In silico-initiated cloning and molecular characterization of a novel human member of the L1 gene family of neural cell adhesion molecules. 61
9799093 1998
41
Anaesthesia and trisomy 3p syndrome. 61
8909680 1996
42
Del(3) (p25.3) without phenotypic effect. 61
8825934 1995
43
Molecular characterization of trisomic segment 3p24.1-->3pter: a case with review of the literature. 61
7586645 1995
44
Mapping of the taurine transporter gene to mouse chromosome 6 and to the short arm of human chromosome 3. 61
7774940 1995
45
Double mitral valve, complete atrioventricular canal, and tricuspid atresia in chromosomal 3P-syndrome. 61
3601739 1987
46
Partial trisomy 3p syndrome. 61
3757296 1986
47
Trisomy 3p syndrome. Report of a new case, due to a chromosomal insertion. 61
6335373 1984
48
The dup(3)(p25 leads to pter) syndrome: a case with holoprosencephaly. 61
6846406 1983
49
Clinical and cytogenetic spectrum of duplication 3p. 61
7094943 1982
50
Duplication 3p syndrome: report of a new case and review of the literature. 61
7246613 1981

Variations for Chromosome 3pter-P25 Deletion Syndrome

ClinVar genetic disease variations for Chromosome 3pter-P25 Deletion Syndrome:

6 ‎‎
# Gene Name Type Significance ClinVarId dbSNP ID GRCh37 Pos GRCh38 Pos
1 NC_000003.11:g.9387774_9503839del116066deletion Pathogenic 818229

Expression for Chromosome 3pter-P25 Deletion Syndrome

Search GEO for disease gene expression data for Chromosome 3pter-P25 Deletion Syndrome.

Pathways for Chromosome 3pter-P25 Deletion Syndrome

Pathways related to Chromosome 3pter-P25 Deletion Syndrome according to GeneCards Suite gene sharing:

# Super pathways Score Top Affiliating Genes
1 10.3 SRGAP3 SRGAP2

GO Terms for Chromosome 3pter-P25 Deletion Syndrome

Cellular components related to Chromosome 3pter-P25 Deletion Syndrome according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 anchored component of membrane GO:0031225 9.13 CNTN6 CNTN5 CNTN4
2 anchored component of presynaptic membrane GO:0099026 8.62 CNTN6 CNTN5

Biological processes related to Chromosome 3pter-P25 Deletion Syndrome according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 dendrite self-avoidance GO:0070593 8.62 CNTN6 CNTN4

Molecular functions related to Chromosome 3pter-P25 Deletion Syndrome according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 Rac GTPase binding GO:0048365 8.96 SRGAP3 SRGAP2
2 cell-cell adhesion mediator activity GO:0098632 8.62 CNTN6 CNTN4

Sources for Chromosome 3pter-P25 Deletion Syndrome

3 CDC
7 CNVD
9 Cosmic
10 dbSNP
11 DGIdb
17 EFO
18 ExPASy
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28 GO
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30 HMDB
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32 ICD10
33 ICD10 via Orphanet
34 ICD9CM
35 IUPHAR
36 KEGG
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43 MeSH
44 MESH via Orphanet
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48 NCI
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57 OMIM via Orphanet
61 PubMed
63 QIAGEN
68 SNOMED-CT via HPO
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72 UMLS via Orphanet
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