MCID: CHR667
MIFTS: 44

Chromosome 3pter-P25 Deletion Syndrome

Categories: Eye diseases, Fetal diseases, Gastrointestinal diseases, Genetic diseases, Mental diseases, Nephrological diseases, Neuronal diseases, Rare diseases
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Aliases & Classifications for Chromosome 3pter-P25 Deletion Syndrome

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

Name: Chromosome 3pter-P25 Deletion Syndrome 57 11
3p- Syndrome 57 42 58 28 5
3p Deletion Syndrome 11 42 14
Chromosome 3, Monosomy 3p 42 71
Distal Monosomy 3p 11 58
Chromosome Deletion Syndrome 3pter-P25 38
Chromosome 3p Deletion Syndrome 42
3p Partial Monosomy Syndrome 42
Chromosome 3, Deletion 3p 42
Telomeric Monosomy 3p 58
Partial Monosomy 3p 42
Distal 3p Deletion 58
Monosomy 3pter 58
Del Syndrome 42
Deletion 3p 42
Monosomy 3p 42

Characteristics:


Inheritance:

Autosomal dominant 57

Prevelance:

Distal Monosomy 3p: <1/1000000 (Worldwide) 58

Age Of Onset:

Distal Monosomy 3p: Antenatal,Neonatal 58

OMIM®:

57 (Updated 24-Oct-2022)
Miscellaneous:
contiguous gene deletion syndrome


Classifications:

Orphanet: 58  
Rare neurological diseases
Rare eye diseases
Developmental anomalies during embryogenesis


Summaries for Chromosome 3pter-P25 Deletion Syndrome

MedlinePlus Genetics: 42 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 chromosome 3p- syndrome and intellectual developmental disorder with dysmorphic facies and ptosis, 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 are Post-translational modification: synthesis of GPI-anchored proteins and Signaling by Slit. Affiliated tissues include heart, eye and skin, and related phenotypes are ptosis and hypertelorism

OMIM®: 57 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) (Updated 24-Oct-2022)

Orphanet: 58 Distal monosomy 3p is a rare chromosomal anomaly syndrome, resulting from a partial deletion of the short arm of chromosome 3, with a highly variable phenotype typically characterized by pre- and post-natal growth retardation, intellectual disability, developmental delay and craniofacial dysmorphism (microcephaly, trigonocephaly, downslanting palpebral fissures, telecanthus, ptosis, micrognathia). Postaxial polydactyly, hypotonia, renal anomalies and congenital heart defects (e.g. atrioventricular septal defect) may be associated.

Disease Ontology: 11 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.

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 89)
# Related Disease Score Top Affiliating Genes
1 chromosome 3p- syndrome 11.5
2 intellectual developmental disorder with dysmorphic facies and ptosis 11.2
3 wolf-hirschhorn syndrome 10.9
4 chromosome 18q deletion syndrome 10.9
5 proximal chromosome 18q deletion syndrome 10.9
6 chromosome 16q duplication 10.2
7 lissencephaly 5 10.1 SRGAP3 SRGAP2
8 avoidant personality disorder 10.1 SRGAP3 SRGAP2
9 retinitis pigmentosa 23 10.1 SRGAP3 SRGAP2
10 ptosis 10.1
11 microcephaly 10.1
12 chromosome 3p duplication 10.1
13 fibrillary astrocytoma 10.1 SRGAP3 SRGAP2
14 laryngomalacia 10.1
15 pheochromocytoma 10.1
16 trichorhinophalangeal syndrome, type i 10.1
17 pancreatic cancer 10.1
18 hemangioma 10.1
19 trichorhinophalangeal syndrome 10.1
20 chromosome 8q duplication 10.1
21 chromosomal triplication 10.0
22 cerebellar angioblastoma 10.0 THUMPD3 SETD5 CNTN4
23 coarctation of aorta 10.0
24 pectus excavatum 10.0
25 cryptorchidism, unilateral or bilateral 10.0
26 scoliosis 10.0
27 inguinal hernia 10.0
28 anterior segment dysgenesis 10.0
29 chromosomal disease 10.0
30 enterocele 10.0
31 atrial heart septal defect 10.0
32 craniosynostosis 10.0
33 hypertrichosis 10.0
34 esotropia 10.0
35 1q duplications 10.0
36 chromosome 2p duplication 10.0
37 chromosome 5q duplication 10.0
38 interatrial communication 10.0
39 trisomy 1q 10.0
40 peripheral pulmonary stenosis 10.0
41 coffin-siris syndrome 6 10.0 CNTN6 CNTN5 CNTN4
42 intellectual developmental disorder, autosomal dominant 23 10.0 SETD5 CRELD1
43 atrial septal defect 6 10.0 CNTN6 CNTN5
44 hypertelorism 10.0
45 heart septal defect 10.0
46 cardiomyopathy, familial hypertrophic, 1 9.9
47 chromosome 13q14 deletion syndrome 9.9
48 pulmonary hypertension 9.9
49 patau syndrome 9.9
50 hypertrophic cardiomyopathy 9.9

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 30 (show top 50) (show all 69)
# Description HPO Frequency Orphanet Frequency HPO Source Accession
1 ptosis 58 30 Very rare (1%) Very frequent (99-80%)
HP:0000508
2 hypertelorism 58 30 Very rare (1%) Very frequent (99-80%)
HP:0000316
3 short stature 58 30 Hallmark (90%) Very frequent (99-80%)
HP:0004322
4 cognitive impairment 58 30 Hallmark (90%) Very frequent (99-80%)
HP:0100543
5 micrognathia 58 30 Very rare (1%) Very frequent (99-80%)
HP:0000347
6 long philtrum 58 30 Very rare (1%) Very frequent (99-80%)
HP:0000343
7 telecanthus 58 30 Hallmark (90%) Very frequent (99-80%)
HP:0000506
8 high palate 58 30 Frequent (33%) Frequent (79-30%)
HP:0000218
9 hearing impairment 58 30 Occasional (7.5%) Frequent (79-30%)
HP:0000365
10 microcephaly 58 30 Very rare (1%) Frequent (79-30%)
HP:0000252
11 brachycephaly 58 30 Frequent (33%) Frequent (79-30%)
HP:0000248
12 cleft palate 58 30 Frequent (33%) Frequent (79-30%)
HP:0000175
13 cryptorchidism 58 30 Occasional (7.5%) Frequent (79-30%)
HP:0000028
14 intrauterine growth retardation 58 30 Very rare (1%) Frequent (79-30%)
HP:0001511
15 epicanthus 58 30 Very rare (1%) Frequent (79-30%)
HP:0000286
16 downturned corners of mouth 58 30 Frequent (33%) Frequent (79-30%)
HP:0002714
17 low-set, posteriorly rotated ears 58 30 Frequent (33%) Frequent (79-30%)
HP:0000368
18 atrioventricular canal defect 58 30 Occasional (7.5%) Frequent (79-30%)
HP:0006695
19 postaxial hand polydactyly 58 30 Frequent (33%) Frequent (79-30%)
HP:0001162
20 hypotonia 30 Very rare (1%) HP:0001252
21 spasticity 58 30 Occasional (7.5%) Occasional (29-5%)
HP:0001257
22 short neck 58 30 Occasional (7.5%) Occasional (29-5%)
HP:0000470
23 inguinal hernia 58 30 Occasional (7.5%) Occasional (29-5%)
HP:0000023
24 umbilical hernia 58 30 Occasional (7.5%) Occasional (29-5%)
HP:0001537
25 anteverted nares 58 30 Occasional (7.5%) Occasional (29-5%)
HP:0000463
26 clinodactyly of the 5th finger 58 30 Occasional (7.5%) Occasional (29-5%)
HP:0004209
27 ventriculomegaly 58 30 Occasional (7.5%) Occasional (29-5%)
HP:0002119
28 blepharophimosis 58 30 Very rare (1%) Occasional (29-5%)
HP:0000581
29 sacral dimple 58 30 Very rare (1%) Occasional (29-5%)
HP:0000960
30 thin vermilion border 58 30 Occasional (7.5%) Occasional (29-5%)
HP:0000233
31 triangular face 58 30 Very rare (1%) Occasional (29-5%)
HP:0000325
32 preauricular pit 58 30 Very rare (1%) Occasional (29-5%)
HP:0004467
33 abnormal vestibulo-ocular reflex 58 30 Occasional (7.5%) Occasional (29-5%)
HP:0007670
34 prominent nasal bridge 30 Occasional (7.5%) HP:0000426
35 macular hypoplasia 30 Occasional (7.5%) HP:0001104
36 abnormal renal morphology 30 Occasional (7.5%) HP:0012210
37 seizure 30 Occasional (7.5%) HP:0001250
38 intellectual disability 30 Very rare (1%) HP:0001249
39 eeg abnormality 30 Very rare (1%) HP:0002353
40 global developmental delay 30 Very rare (1%) HP:0001263
41 depressed nasal bridge 30 Very rare (1%) HP:0005280
42 wide nasal bridge 30 Very rare (1%) HP:0000431
43 gastroesophageal reflux 30 Very rare (1%) HP:0002020
44 postnatal growth retardation 30 Very rare (1%) HP:0008897
45 low-set ears 30 Very rare (1%) HP:0000369
46 dolichocephaly 30 Very rare (1%) HP:0000268
47 anal atresia 30 Very rare (1%) HP:0002023
48 overfolded helix 30 Very rare (1%) HP:0000396
49 thin upper lip vermilion 30 Very rare (1%) HP:0000219
50 flat occiput 30 Very rare (1%) HP:0005469

Symptoms via clinical synopsis from OMIM®:

57 (Updated 24-Oct-2022)
Muscle Soft Tissue:
spasticity
muscle hypotonia
muscle hypertonicity

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)

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 Eyes:
ptosis
hypertelorism
strabismus
blepharophimosis
synophrys
more
Growth Height:
short stature

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 (Updated 24-Oct-2022)

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


muscle spasticity

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 3p- Syndrome 28

Anatomical Context for Chromosome 3pter-P25 Deletion Syndrome

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

MalaCards : Heart, Eye, Skin, Lung, Brain

Publications for Chromosome 3pter-P25 Deletion Syndrome

Articles related to Chromosome 3pter-P25 Deletion Syndrome:

(show top 50) (show all 108)
# Title Authors PMID Year
1
Microarray based analysis of 3p25-p26 deletions (3p- syndrome). 62 57
19760623 2009
2
Distal 3p deletion syndrome: detailed molecular cytogenetic and clinical characterization of three small distal deletions and review. 62 57
17696125 2007
3
Disruption of contactin 4 (CNTN4) results in developmental delay and other features of 3p deletion syndrome. 62 57
15106122 2004
4
The novel Rho-GTPase activating gene MEGAP/ srGAP3 has a putative role in severe mental retardation. 62 57
12195014 2002
5
Molecular cytogenetic characterization of a subtle interstitial del(3)(p25.3p26.2) in a patient with deletion 3p syndrome. 62 57
11977162 2002
6
A terminal deletion of the short arm of chromosome 3: karyotype 46, XY, del (3) (p25-pter); a case report and literature review. 62 57
11074119 2000
7
Detailed mapping of a congenital heart disease gene in chromosome 3p25. 62 57
10922384 2000
8
CALL gene is haploinsufficient in a 3p- syndrome patient. 62 57
10508992 1999
9
Precise localisation of 3p25 breakpoints in four patients with the 3p-syndrome. 62 57
8933338 1996
10
Molecular genetic analysis of the 3p- syndrome. 62 57
7951234 1994
11
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. 62 57
2178418 1990
12
Terminal deletion of the short arm of chromosome 3, del(3pter-p25): a recognizable syndrome. 62 57
3443553 1987
13
Mutations in Histone Acetylase Modifier BRPF1 Cause an Autosomal-Dominant Form of Intellectual Disability with Associated Ptosis. 57
27939639 2017
14
Loss-of-function variants of SETD5 cause intellectual disability and the core phenotype of microdeletion 3p25.3 syndrome. 57
25138099 2015
15
Chromosome 3p25 deletion in mother and daughter with minimal phenotypic effect. 57
16770804 2006
16
Analysis of CRELD1 as a candidate 3p25 atrioventicular septal defect locus (AVSD2). 57
15857420 2005
17
Clinical and molecular analyses of deletion 3p25-pter syndrome. 57
8103286 1993
18
Infant with del(3) (p25-pter): karyotype-phenotype correlation and review of previously reported cases. 57
1481811 1992
19
Two infants with del(3)(p25pter) and a review of previously reported cases. 57
2665488 1989
20
A patient with a partial deletion of the short arm of chromosome 3. 57
623063 1978
21
Adapted whole-body surveillance for von Hippel-Lindau-associated tumors in 3p deletion syndrome with VHL deletion: A case report. 62
35441425 2022
22
Iris and Ciliary Body Melanocytomas Are Defined by Solitary GNAQ Mutation Without Additional Oncogenic Alterations. 62
35835335 2022
23
Analysis of the functional sequences in the promoter region of the human adhesion molecule close homolog of L1. 62
33054469 2022
24
Pulmonary artery sling in a 22-month-old boy with 18q deletion syndrome: A rare but possible association. 62
35434845 2022
25
Partial Trisomy 13q/Monosomy 3p Resulting from a Paternal Reciprocal 3p;13q Translocation in a Boy with Facial Dysmorphism and Hypertrophic Cardiomyopathy. 62
34602958 2021
26
A new phenomenon of cochlear otosclerosis: an acquired or congenital disease? - A clinical report of cochlear otosclerosis. 62
33819124 2021
27
Familiar del3p syndrome: The uncertainty of the prognosis. A case report. 62
33936696 2021
28
Case Report: A Case Report and Literature Review of 3p Deletion Syndrome. 62
33643973 2021
29
Fetal Cystic Hygroma Associated with Terminal 2p25.1 Duplication and Terminal 3p25.3 Deletion: Cytogenetic, Fluorescent in Situ Hybridization and Microarray Familial Characterization of Two Different Chromosomal Structural Rearrangements. 62
33816076 2020
30
Cell Adhesion Molecules Involved in Neurodevelopmental Pathways Implicated in 3p-Deletion Syndrome and Autism Spectrum Disorder. 62
33519384 2020
31
Diagnostic and clinical utility of whole genome sequencing in a cohort of undiagnosed Chinese families with rare diseases. 62
31852928 2019
32
Prenatal diagnosis and molecular cytogenetic characterization of de novo partial monosomy 3p (3p26.3→pter) and partial trisomy 16q (16q23.1→qter). 62
27125417 2016
33
A case of 3p deletion syndrome associated with cerebellar hemangioblastoma. 62
26365017 2016
34
Chromosome r(3)(p25.3q29) in a Patient with Developmental Delay and Congenital Heart Defects: A Case Report and a Brief Literature Review. 62
27077748 2016
35
A large Indian family with rearrangement of chromosome 4p16 and 3p26.3 and divergent clinical presentations. 62
26554554 2015
36
3p25.3 microdeletion of GABA transporters SLC6A1 and SLC6A11 results in intellectual disability, epilepsy and stereotypic behavior. 62
25256099 2014
37
Trisomy 1q41-qter and monosomy 3p26.3-pter in a family with a translocation (1;3): further delineation of the syndromes. 62
25223409 2014
38
Complex translocation among chromosomes 2, 3, 9, 15, 18, 20 in a patient with 3p-syndrome. 62
24979567 2014
39
Intrachromosomal 3p insertion as a cause of reciprocal pure interstitial deletion and duplication in two siblings: further delineation of the emerging proximal 3p deletion syndrome. 62
25720458 2014
40
Interstitial 3p25 deletion in a patient with features of 3p deletion syndrome: further evidence for the role of SRGAP3 in mental retardation. 62
24300292 2014
41
3p deletion syndrome. 62
24036645 2013
42
Prenatal diagnosis of a distal 3p deletion associated with fetoplacental chromosomal discrepancy and confined placental mosaicism detected by array comparative genomic hybridization. 62
23915866 2013
43
Deletion of 3p25.3 in a patient with intellectual disability and dysmorphic features with further definition of a critical region. 62
23613140 2013
44
Monosomy 3pter-p25.3 and trisomy 1q42.13-qter in a boy with profound growth and developmental restriction, multiple congenital anomalies, and early death. 62
23597526 2013
45
3p deletion syndrome: implications for cochlear implantation. 62
22449389 2012
46
Microdeletion on 3p25 in a patient with features of 3p deletion syndrome. 62
22903836 2012
47
Bilateral anterior segment dysgenesis in an infant with partial trisomy 16q and partial monosomy 3p. 62
23084388 2012
48
Disruption of Contactin 4 in two subjects with autism in Chinese population. 62
22750301 2012
49
Pure partial monosomy 3p (3p25.3 → pter): prenatal diagnosis and array comparative genomic hybridization characterization. 62
23040932 2012
50
A case of partial trisomy 3p syndrome with rare clinical manifestations. 62
22474466 2012

Variations for Chromosome 3pter-P25 Deletion Syndrome

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

5
# Gene Name Type Significance ClinVarId dbSNP ID Position
1 overlap with 87 genes DEL Pathogenic
1703229 GRCh37:
GRCh38: 3:13371737-20095506
2 overlap with 2 genes NC_000003.11:g.9387774_9503839del116066 DEL Pathogenic
818229 GRCh37: 3:9387774-9503839
GRCh38:

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
Show member pathways
11.2 CNTN5 CNTN4 CNTN3
2 10.84 SRGAP3 SRGAP2
3 9.53 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 obsolete anchored component of presynaptic membrane GO:0099026 8.96 CNTN6 CNTN5
2 obsolete anchored component of membrane GO:0031225 8.92 CNTN6 CNTN5 CNTN4 CNTN3

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 8.92 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 cell-cell adhesion mediator activity GO:0098632 9.1 CNTN6 CNTN5 CNTN4

Sources for Chromosome 3pter-P25 Deletion Syndrome

2 CDC
6 CNVD
8 Cosmic
9 dbSNP
10 DGIdb
16 EFO
17 ExPASy
18 FMA
19 GARD
27 GO
28 GTR
29 HMDB
30 HPO
31 ICD10
32 ICD10 via Orphanet
33 ICD11
34 ICD9CM
35 IUPHAR
36 LifeMap
38 LOVD
40 MedGen
43 MeSH
44 MESH via Orphanet
45 MGI
48 NCI
49 NCIt
50 NDF-RT
52 NINDS
53 Novoseek
55 ODiseA
56 OMIM via Orphanet
57 OMIM® (Updated 24-Oct-2022)
61 PubChem
62 PubMed
64 QIAGEN
69 SNOMED-CT via HPO
70 Tocris
71 UMLS
72 UMLS via Orphanet
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