CSS3
MCID: CFF010
MIFTS: 42

Coffin-Siris Syndrome 3 (CSS3)

Categories: Bone diseases, Eye diseases, Fetal diseases, Genetic diseases, Mental diseases, Neuronal diseases, Rare diseases, Smell/Taste diseases

Aliases & Classifications for Coffin-Siris Syndrome 3

MalaCards integrated aliases for Coffin-Siris Syndrome 3:

Name: Coffin-Siris Syndrome 3 56 12 73 15
Mental Retardation, Autosomal Dominant 15 56 73 29 13 6 71
Mrd15 56 12 73
Css3 56 12 73
Mental Retardation, Autosomal Dominant 15; Mrd15 56
Autosomal Dominant Mental Retardation 15 12
Coffin-Siris Syndrome, Type 3 39

Characteristics:

OMIM:

56
Inheritance:
autosomal dominant


HPO:

31
coffin-siris syndrome 3:
Inheritance autosomal dominant inheritance


Classifications:



Summaries for Coffin-Siris Syndrome 3

OMIM : 56 Coffin-Siris syndrome is a congenital malformation syndrome characterized by developmental delay, intellectual disability, coarse facial features, feeding difficulties, and hypoplastic or absent fifth fingernails and fifth distal phalanges. Other more variable features may also occur. Patients with SMARCB1 mutations may have more severe neurodevelopmental deficits including severe intellectual disability, brain structural abnormalities, and no expressive words, as well as scoliosis (summary by Kosho et al., 2014). For a general phenotypic description and a discussion of genetic heterogeneity of Coffin-Siris syndrome, see CSS1 (135900). (614608)

MalaCards based summary : Coffin-Siris Syndrome 3, also known as mental retardation, autosomal dominant 15, is related to peripheral nerve schwannoma and spinal canal and spinal cord meningioma, and has symptoms including seizures An important gene associated with Coffin-Siris Syndrome 3 is SMARCB1 (SWI/SNF Related, Matrix Associated, Actin Dependent Regulator Of Chromatin, Subfamily B, Member 1), and among its related pathways/superpathways are Glycosaminoglycan metabolism and Chondroitin sulfate/dermatan sulfate metabolism. Affiliated tissues include brain, bone and heart, and related phenotypes are seizures and microcephaly

Disease Ontology : 12 A Coffin-Siris syndrome that has material basis in an autosomal dominant mutation of SMARCB1 on chromosome 22q11.23.

UniProtKB/Swiss-Prot : 73 Coffin-Siris syndrome 3: A form of Coffin-Siris syndrome, a congenital multiple malformation syndrome with broad phenotypic and genetic variability. Cardinal features are intellectual disability, coarse facial features, hypertrichosis, and hypoplastic or absent fifth digit nails or phalanges. Additional features include malformations of the cardiac, gastrointestinal, genitourinary, and/or central nervous systems. Sucking/feeding difficulties, poor growth, ophthalmologic abnormalities, hearing impairment, and spinal anomalies are common findings. Both autosomal dominant and autosomal recessive inheritance patterns have been reported.

Related Diseases for Coffin-Siris Syndrome 3

Diseases in the Coffin-Siris Syndrome 1 family:

Coffin-Siris Syndrome 2 Coffin-Siris Syndrome 3
Coffin-Siris Syndrome 4 Coffin-Siris Syndrome 9
Coffin-Siris Syndrome 5 Coffin-Siris Syndrome 6
Coffin-Siris Syndrome 7 Coffin-Siris Syndrome 8
Coffin-Siris Syndrome 10

Diseases related to Coffin-Siris Syndrome 3 via text searches within MalaCards or GeneCards Suite gene sharing:

(show all 18)
# Related Disease Score Top Affiliating Genes
1 peripheral nerve schwannoma 10.3 SMARCE1 SMARCB1
2 spinal canal and spinal cord meningioma 10.2 SMARCE1 SMARCB1
3 spinal meningioma 10.2 SMARCE1 SMARCB1
4 clear cell meningioma 10.2 SMARCE1 SMARCB1
5 spinal cancer 10.1 SMARCE1 SMARCB1
6 neurilemmomatosis 10.1 SMARCE1 SMARCB1 ARID2
7 urofacial syndrome 1 10.0 CHPF2 CHPF
8 hypertrichosis 10.0 SMARCE1 SMARCB1 ARID2
9 non-syndromic intellectual disability 9.9 SMARCE1 SMARCB1 H2AC18 ARID2
10 rhabdoid cancer 9.9 SMARCE1 SMARCB1 H2AC18 ARID2
11 breast pericanalicular fibroadenoma 9.9 CSGALNACT1 CHSY1 CHPF
12 coffin-siris syndrome 4 9.9 SMARCE1 H2AC18 CMAS ARID2
13 temtamy preaxial brachydactyly syndrome 9.7 CSGALNACT1 CHSY1 CHPF2 CHPF
14 meningioma, familial 9.7 SMARCE1 SMARCB1 H2AC18
15 chromosome 22q11.2 deletion syndrome, distal 9.2 TMEM156 KLHL5 FAM114A1
16 coffin-siris syndrome 2 8.5 SMARCE1 H2AC18 CSGALNACT2 CSGALNACT1 CMAS CHSY3
17 coffin-siris syndrome 1 8.3 SMARCE1 SMARCB1 H2AC18 CSGALNACT2 CSGALNACT1 CMAS
18 autosomal dominant non-syndromic intellectual disability 5.9 TSPAN5 TMEM156 STXBP6 SNORD11 SMARCE1 SMARCB1

Graphical network of the top 20 diseases related to Coffin-Siris Syndrome 3:



Diseases related to Coffin-Siris Syndrome 3

Symptoms & Phenotypes for Coffin-Siris Syndrome 3

Human phenotypes related to Coffin-Siris Syndrome 3:

31 (show all 29)
# Description HPO Frequency HPO Source Accession
1 seizures 31 very rare (1%) HP:0001250
2 microcephaly 31 very rare (1%) HP:0000252
3 cerebellar hypoplasia 31 very rare (1%) HP:0001321
4 hirsutism 31 very rare (1%) HP:0001007
5 intellectual disability 31 HP:0001249
6 scoliosis 31 HP:0002650
7 macroglossia 31 HP:0000158
8 coarse facial features 31 HP:0000280
9 hearing impairment 31 HP:0000365
10 global developmental delay 31 HP:0001263
11 delayed skeletal maturation 31 HP:0002750
12 depressed nasal bridge 31 HP:0005280
13 short stature 31 HP:0004322
14 feeding difficulties 31 HP:0011968
15 intrauterine growth retardation 31 HP:0001511
16 anteverted nares 31 HP:0000463
17 visual impairment 31 HP:0000505
18 thick eyebrow 31 HP:0000574
19 generalized hypotonia 31 HP:0001290
20 wide mouth 31 HP:0000154
21 sparse scalp hair 31 HP:0002209
22 abnormal heart morphology 31 HP:0001627
23 wide nose 31 HP:0000445
24 long eyelashes 31 HP:0000527
25 abnormality of cardiovascular system morphology 31 HP:0030680
26 hypertrichosis 31 HP:0000998
27 abnormal corpus callosum morphology 31 HP:0001273
28 delayed eruption of permanent teeth 31 HP:0000696
29 aplasia/hypoplasia of the distal phalanges of the hand 31 HP:0009835

Symptoms via clinical synopsis from OMIM:

56
Neurologic Central Nervous System:
seizures
hypotonia
mental retardation
delayed psychomotor development, severe
small cerebellum
more
Head And Neck Mouth:
macroglossia
large mouth
thin upper vermilion
thick lower vermilion

Growth Height:
short stature

Head And Neck Head:
microcephaly

Skin Nails Hair Hair:
sparse scalp hair
hypertrichosis

Skeletal:
delayed bone age

Cardiovascular Heart:
congenital heart defects

Abdomen Gastrointestinal:
feeding problems

Skeletal Feet:
hypoplastic to absent terminal phalanges (especially fifth toe)

Skeletal Spine:
scoliosis

Head And Neck Ears:
hearing impairment

Growth Other:
intrauterine growth retardation
poor overall growth

Head And Neck Eyes:
visual impairment
long eyelashes
thick eyebrows

Head And Neck Nose:
anteverted nostrils
broad nose
flat nasal bridge

Head And Neck Face:
coarse facies

Head And Neck Teeth:
delayed dentition

Skeletal Hands:
hypoplastic to absent terminal phalanges (especially fifth finger)

Skin Nails Hair Nails:
hypoplastic or absent nails

Clinical features from OMIM:

614608

UMLS symptoms related to Coffin-Siris Syndrome 3:


seizures

GenomeRNAi Phenotypes related to Coffin-Siris Syndrome 3 according to GeneCards Suite gene sharing:

26
# Description GenomeRNAi Source Accession Score Top Affiliating Genes
1 Decreased IL-13 protein expression GR00219-A 8.62 CSGALNACT1 SMARCB1

Drugs & Therapeutics for Coffin-Siris Syndrome 3

Search Clinical Trials , NIH Clinical Center for Coffin-Siris Syndrome 3

Genetic Tests for Coffin-Siris Syndrome 3

Genetic tests related to Coffin-Siris Syndrome 3:

# Genetic test Affiliating Genes
1 Mental Retardation, Autosomal Dominant 15 29 SMARCB1

Anatomical Context for Coffin-Siris Syndrome 3

MalaCards organs/tissues related to Coffin-Siris Syndrome 3:

40
Brain, Bone, Heart, Breast, Cerebellum, Eye, Spinal Cord

Publications for Coffin-Siris Syndrome 3

Articles related to Coffin-Siris Syndrome 3:

(show all 22)
# Title Authors PMID Year
1
Disruption of an EHMT1-associated chromatin-modification module causes intellectual disability. 56 6
22726846 2012
2
Mutations affecting components of the SWI/SNF complex cause Coffin-Siris syndrome. 56 6
22426308 2012
3
Genotype-phenotype correlation of Coffin-Siris syndrome caused by mutations in SMARCB1, SMARCA4, SMARCE1, and ARID1A. 56
25168959 2014
4
A comprehensive molecular study on Coffin-Siris and Nicolaides-Baraitser syndromes identifies a broad molecular and clinical spectrum converging on altered chromatin remodeling. 56
23906836 2013
5
Coffin-Siris syndrome and the BAF complex: genotype-phenotype study in 63 patients. 56
23929686 2013
6
Persistence of Nasopharyngeal Pneumococcal Vaccine Serotypes and Increase of Nonvaccine Serotypes Among Vaccinated Infants and Their Mothers 5 Years After Introduction of Pneumococcal Conjugate Vaccine 13 in The Gambia. 61
30165376 2019
7
[OISO, automatic treatment of patients management in oncogenetics]. 61
28689638 2017
8
A computer-human interaction model to improve the diagnostic accuracy and clinical decision-making during 12-lead electrocardiogram interpretation. 61
27687552 2016
9
User Interface Design in Medical Distributed Web Applications. 61
27139407 2016
10
Is Speed Reserve Related to Critical Speed and Anaerobic Distance Capacity in Swimming? 61
24513615 2015
11
Presentation and response timing accuracy in Adobe Flash and HTML5/JavaScript Web experiments. 61
24903687 2015
12
Marky: a tool supporting annotation consistency in multi-user and iterative document annotation projects. 61
25480679 2015
13
PoopMD, a Mobile Health Application, Accurately Identifies Infant Acholic Stools. 61
26221719 2015
14
Chemozart: a web-based 3D molecular structure editor and visualizer platform. 61
26587057 2015
15
SeqReporter: automating next-generation sequencing result interpretation and reporting workflow in a clinical laboratory. 61
24220144 2014
16
SU-E-J-114: Web-Browser Medical Physics Applications Using HTML5 and Javascript. 61
28519822 2012
17
DNA methylation changes in a human cell model of breast cancer progression. 61
20193695 2010
18
Estrogen and xenoestrogens in breast cancer. 61
19933552 2010
19
Identification of chondroitin sulfate glucuronyltransferase as chondroitin synthase-3 involved in chondroitin polymerization: chondroitin polymerization is achieved by multiple enzyme complexes consisting of chondroitin synthase family members. 61
18316376 2008
20
Involvement of chondroitin sulfate synthase-3 (chondroitin synthase-2) in chondroitin polymerization through its interaction with chondroitin synthase-1 or chondroitin-polymerizing factor. 61
17253960 2007
21
Chondroitin sulfate synthase-3. Molecular cloning and characterization. 61
12907687 2003
22
Calcium responses to thyrotropin-releasing hormone, gonadotropin-releasing hormone and somatostatin in phospholipase css3 knockout mice. 61
11145744 2001

Variations for Coffin-Siris Syndrome 3

ClinVar genetic disease variations for Coffin-Siris Syndrome 3:

6 ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎
# Gene Name Type Significance ClinVarId dbSNP ID GRCh37 Pos GRCh38 Pos
1 SMARCB1 NM_003073.5(SMARCB1):c.1130G>A (p.Arg377His)SNV Pathogenic 30203 rs387906812 22:24176339-24176339 22:23834152-23834152
2 SMARCB1 NM_003073.5(SMARCB1):c.1085_1087AGA[2] (p.Lys364del)short repeat Pathogenic/Likely pathogenic 30201 rs875989800 22:24175857-24175859 22:23833670-23833672
3 SMARCB1 NM_003073.5(SMARCB1):c.1121G>A (p.Arg374Gln)SNV Pathogenic/Likely pathogenic 372511 rs1057517825 22:24176330-24176330 22:23834143-23834143
4 SMARCB1 NM_003073.5(SMARCB1):c.602G>A (p.Arg201Gln)SNV Likely pathogenic 438304 rs1555877287 22:24145583-24145583 22:23803396-23803396
5 SMARCB1 NM_003073.5(SMARCB1):c.1070C>G (p.Thr357Arg)SNV Likely pathogenic 559897 rs1555881567 22:24175842-24175842 22:23833655-23833655
6 SMARCB1 NM_003073.5(SMARCB1):c.1087A>G (p.Lys363Glu)SNV Likely pathogenic 212263 rs797045989 22:24175859-24175859 22:23833672-23833672
7 SMARCB1 NM_003073.5(SMARCB1):c.110G>A (p.Arg37His)SNV Conflicting interpretations of pathogenicity 88893 rs398122368 22:24133959-24133959 22:23791772-23791772
8 SMARCB1 NM_003073.5(SMARCB1):c.1089G>T (p.Lys363Asn)SNV Uncertain significance 561114 rs1568963037 22:24175861-24175861 22:23833674-23833674

UniProtKB/Swiss-Prot genetic disease variations for Coffin-Siris Syndrome 3:

73
# Symbol AA change Variation ID SNP ID
1 SMARCB1 p.Arg377His VAR_068179 rs387906812
2 SMARCB1 p.Arg366Cys VAR_076934 rs886039520
3 SMARCB1 p.Arg374Gln VAR_076935 rs105751782

Expression for Coffin-Siris Syndrome 3

Search GEO for disease gene expression data for Coffin-Siris Syndrome 3.

Pathways for Coffin-Siris Syndrome 3

Pathways related to Coffin-Siris Syndrome 3 according to GeneCards Suite gene sharing:

# Super pathways Score Top Affiliating Genes
1
Show member pathways
12.18 CSGALNACT2 CSGALNACT1 CHSY3 CHSY1 CHPF2 CHPF
2
Show member pathways
11.61 CSGALNACT2 CSGALNACT1 CHSY3 CHSY1 CHPF2 CHPF

GO Terms for Coffin-Siris Syndrome 3

Cellular components related to Coffin-Siris Syndrome 3 according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 Golgi apparatus GO:0005794 9.7 FAM114A1 CSGALNACT2 CSGALNACT1 CHSY3 CHSY1 CHPF2
2 Golgi membrane GO:0000139 9.43 CSGALNACT2 CSGALNACT1 CHSY3 CHSY1 CHPF2 CHPF
3 SWI/SNF complex GO:0016514 9.37 SMARCE1 SMARCB1
4 nBAF complex GO:0071565 9.32 SMARCE1 SMARCB1
5 npBAF complex GO:0071564 9.26 SMARCE1 SMARCB1
6 Golgi cisterna membrane GO:0032580 9.1 CSGALNACT2 CSGALNACT1 CHSY3 CHSY1 CHPF2 CHPF

Biological processes related to Coffin-Siris Syndrome 3 according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 chromatin organization GO:0006325 9.71 SMARCE1 SMARCB1 H2AC18 ARID2
2 ATP-dependent chromatin remodeling GO:0043044 9.43 SMARCE1 SMARCB1
3 proteoglycan biosynthetic process GO:0030166 9.37 CSGALNACT2 CSGALNACT1
4 chondroitin sulfate proteoglycan biosynthetic process GO:0050650 9.32 CSGALNACT2 CSGALNACT1
5 dermatan sulfate proteoglycan biosynthetic process GO:0050651 9.26 CSGALNACT2 CSGALNACT1
6 chondroitin sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process GO:0050653 9.16 CSGALNACT2 CSGALNACT1
7 nucleosome disassembly GO:0006337 9.13 SMARCE1 SMARCB1 ARID2
8 chondroitin sulfate biosynthetic process GO:0030206 9.1 CSGALNACT2 CSGALNACT1 CHSY3 CHSY1 CHPF2 CHPF

Molecular functions related to Coffin-Siris Syndrome 3 according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 transferase activity GO:0016740 9.87 CSGALNACT2 CSGALNACT1 CMAS CHSY3 CHSY1 CHPF2
2 N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity GO:0050510 9.46 CHSY3 CHSY1 CHPF2 CHPF
3 nucleosomal DNA binding GO:0031492 9.37 SMARCE1 SMARCB1
4 glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase activity GO:0047237 9.26 CSGALNACT2 CSGALNACT1
5 glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity GO:0047238 9.26 CSGALNACT1 CHSY3 CHSY1 CHPF
6 acetylgalactosaminyltransferase activity GO:0008376 9.1 CSGALNACT2 CSGALNACT1 CHSY3 CHSY1 CHPF2 CHPF

Sources for Coffin-Siris Syndrome 3

3 CDC
7 CNVD
9 Cosmic
10 dbSNP
11 DGIdb
17 EFO
18 ExPASy
19 FMA
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
43 MeSH
44 MESH via Orphanet
45 MGI
48 NCI
49 NCIt
50 NDF-RT
53 NINDS
54 Novoseek
56 OMIM
57 OMIM via Orphanet
61 PubMed
63 QIAGEN
68 SNOMED-CT via HPO
69 TGDB
70 Tocris
71 UMLS
72 UMLS via Orphanet
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