KLEFS1
MCID: KLF004
MIFTS: 55

Kleefstra Syndrome 1 (KLEFS1)

Categories: Eye diseases, Fetal diseases, Genetic diseases, Mental diseases, Metabolic diseases, Neuronal diseases, Rare diseases

Aliases & Classifications for Kleefstra Syndrome 1

MalaCards integrated aliases for Kleefstra Syndrome 1:

Name: Kleefstra Syndrome 1 56 12 73 6
Kleefstra Syndrome 58 43 15 71
9q Subtelomeric Deletion Syndrome 56 12 58
Chromosome 9q34.3 Deletion Syndrome 56 73
9q34 Deletion Syndrome 12 74
9q- Syndrome 56 73
Klefs1 56 73
Kleefstra Syndrome Due to 9q Subtelomeric Deletion 58
Kleefstra Syndrome Due to 9q34 Microdeletion 58
Chromosome 9q Subtelomeric Deletion Syndrome 73
Kleefstra Syndrome Due to Monosomy 9q34 58
Kleefstra Syndrome Due to Del(9)(q34) 58
9q-Syndrome 12
9qstds 58

Characteristics:

Orphanet epidemiological data:

58
kleefstra syndrome
Inheritance: Autosomal dominant; Prevalence: <1/1000000 (Worldwide); Age of onset: Infancy,Neonatal; Age of death: elderly;
kleefstra syndrome due to 9q34 microdeletion
Prevalence: <1/1000000 (Worldwide); Age of onset: Infancy,Neonatal;

OMIM:

56
Inheritance:
autosomal dominant

Miscellaneous:
de novo mutation in most cases
many cases have submicroscopic subtelomeric deletions of chromosome 9q leading to haploinsufficiency of ehmt1


HPO:

31
kleefstra syndrome 1:
Inheritance autosomal dominant inheritance sporadic


Classifications:

Orphanet: 58  
Rare neurological diseases
Developmental anomalies during embryogenesis


Summaries for Kleefstra Syndrome 1

OMIM : 56 Submicroscopic subtelomeric deletions of chromosome 9q are associated with a recognizable mental retardation syndrome (Harada et al., 2004; Iwakoshi et al., 2004; Stewart et al., 2004; Neas et al., 2005). Common features in patients with 9q subtelomeric deletion syndrome are severe mental retardation, hypotonia, brachy(micro)cephaly, epileptic seizures, flat face with hypertelorism, synophrys, anteverted nares, everted lower lip, carp mouth with macroglossia, and heart defects. (610253)

MalaCards based summary : Kleefstra Syndrome 1, also known as kleefstra syndrome, is related to kleefstra syndrome due to a point mutation and alacrima, achalasia, and mental retardation syndrome, and has symptoms including seizures An important gene associated with Kleefstra Syndrome 1 is EHMT1 (Euchromatic Histone Lysine Methyltransferase 1), and among its related pathways/superpathways are Chromatin organization and Chromatin Regulation / Acetylation. Affiliated tissues include heart, brain and testis, and related phenotypes are hypertelorism and intellectual disability

Disease Ontology : 12 A syndrome that is characterized by severe mental retardation, hypotonia, brachy(micro)cephaly, epileptic seizures, flat face with hypertelorism, synophrys, anteverted nares, everted lower lip, carp mouth with macroglossia, and heart defects and that has material basis in a microdeletion in the chromosome region 9q34.3 or by a point mutation in the EHMT1 gene located in that region.

UniProtKB/Swiss-Prot : 73 Kleefstra syndrome 1: A form of Kleefstra syndrome, an autosomal dominant disease characterized by variable mental retardation, psychomotor developmental delay, seizures, behavioral abnormalities, and facial dysmorphisms. KLEFS1 patients additionally manifest brachy(micro)cephaly, congenital heart defects, and urogenital defects.

Wikipedia : 74 9q34 deletion syndrome is a rare genetic disorder. Terminal deletions of chromosome 9q34 have been... more...

Related Diseases for Kleefstra Syndrome 1

Diseases in the Kleefstra Syndrome family:

Kleefstra Syndrome 1 Kleefstra Syndrome 2
Kleefstra Syndrome Due to a Point Mutation

Diseases related to Kleefstra Syndrome 1 via text searches within MalaCards or GeneCards Suite gene sharing:

(show top 50) (show all 92)
# Related Disease Score Top Affiliating Genes
1 kleefstra syndrome due to a point mutation 34.2 KMT2C EHMT1
2 alacrima, achalasia, and mental retardation syndrome 31.1 UBE3A RAI1 MECP2 KMT2C KDM5C EHMT1
3 kleefstra syndrome 30.7 PAEP NR1I3 KMT2C EHMT1
4 angelman syndrome 30.5 UBE3A MECP2 H2AC18 CDKL5
5 autism spectrum disorder 30.4 UBE3A RAI1 MECP2 MBD5 KMT2D KMT2C
6 smith-magenis syndrome 30.4 RAI1 MECP2 KMT2D KDM5C
7 autism 30.2 UBE3A RAI1 MECP2 MBD5 KDM5C KDM4C
8 kleefstra syndrome 2 11.3
9 hypotonia 10.5
10 nut midline carcinoma 10.4 KMT2C KDM4C H2AC18
11 syndromic intellectual disability 10.4 SLC9A7 MECP2 H2AC18
12 chromosomal duplication syndrome 10.4 RAI1 MECP2 KDM4C
13 hypotrichosis 2 10.4 WIZ H3-2 H2AC18
14 potocki-lupski syndrome 10.4 RAI1 MECP2 KDM4C
15 infratentorial cancer 10.4 KMT2D KDM4C H2AC18
16 kbg syndrome 10.4 MECP2 KMT2D KDM6A
17 gait apraxia 10.4 MECP2 CDKL5
18 syndromic x-linked intellectual disability siderius type 10.3 KDM5C KDM4C
19 fetal alcohol spectrum disorder 10.3 MECP2 KDM4C H2AC18 EHMT2
20 brain stem glioma 10.3 KDM6A KDM4C H3-2
21 chromosomal deletion syndrome 10.3 RAI1 MECP2 H2AC18
22 retinal cancer 10.3 KDM4C H3-2 H2AC18
23 bruxism 10.3 UBE3A MECP2 CDKL5
24 alpha thalassemia-x-linked intellectual disability syndrome 10.3 MECP2 KDM5C H3-2 H2AC18
25 microcephaly 10.3
26 cornelia de lange syndrome 10.3 MECP2 MBD5 H3-2 H2AC18
27 syndromic x-linked intellectual disability 10.3 SLC9A7 MECP2 H2AC18
28 chromosomal disease 10.3 UBE3A RAI1 MECP2 H2AC18
29 beckwith-wiedemann syndrome 10.3 UBE3A KDM4C H2AC18 EHMT2
30 physical disorder 10.3 MECP2 KDM4C H2AC18
31 biliary tract disease 10.3 NR1I3 KDM4C H2AC18
32 congenital nervous system abnormality 10.3 UBE3A MECP2 H2AC18 CDKL5
33 lubs x-linked mental retardation syndrome 10.2 UBE3A PCDHB1 MECP2 CDKL5
34 immunodeficiency-centromeric instability-facial anomalies syndrome 10.2 PCDHB1 MECP2 H3-2 H2AC18 EHMT2
35 epileptic encephalopathy, early infantile, 6 10.2 UBE3A SLC9A7 MECP2 CDKL5
36 wolf-hirschhorn syndrome 10.2 H3-2 H2AC18 EHMT1
37 epicanthus 10.2
38 hypertelorism 10.2
39 neural tube defects 10.2
40 branchiootic syndrome 1 10.2
41 neuroblastoma 10.2
42 exophthalmos 10.2
43 hypopituitarism 10.2
44 microtia 10.2
45 specific developmental disorder 10.2 UBE3A MECP2 KDM4C H2AC18 CDKL5
46 macroglossia 10.2
47 down syndrome 10.2
48 pulmonary hypertension 10.2
49 mowat-wilson syndrome 10.1 UBE3A SLC9A7 MECP2 MBD5 CDKL5
50 early infantile epileptic encephalopathy 10.1 UBE3A SLC9A7 MECP2 CDKL5

Graphical network of the top 20 diseases related to Kleefstra Syndrome 1:



Diseases related to Kleefstra Syndrome 1

Symptoms & Phenotypes for Kleefstra Syndrome 1

Human phenotypes related to Kleefstra Syndrome 1:

58 31 (show top 50) (show all 109)
# Description HPO Frequency Orphanet Frequency HPO Source Accession
1 hypertelorism 58 31 frequent (33%) Very frequent (99-80%),Very frequent (99-80%) HP:0000316
2 intellectual disability 58 31 hallmark (90%) Very frequent (99-80%) HP:0001249
3 dysphasia 58 31 hallmark (90%) Very frequent (99-80%) HP:0002357
4 muscular hypotonia 58 31 hallmark (90%) Very frequent (99-80%),Very frequent (99-80%) HP:0001252
5 global developmental delay 58 31 hallmark (90%) Very frequent (99-80%),Very frequent (99-80%) HP:0001263
6 short nose 58 31 hallmark (90%) Very frequent (99-80%),Very frequent (99-80%) HP:0003196
7 anteverted nares 58 31 frequent (33%) Very frequent (99-80%),Very frequent (99-80%) HP:0000463
8 brachycephaly 58 31 frequent (33%) Frequent (79-30%),Very frequent (99-80%) HP:0000248
9 highly arched eyebrow 58 31 hallmark (90%) Frequent (79-30%),Very frequent (99-80%) HP:0002553
10 everted lower lip vermilion 58 31 frequent (33%) Very frequent (99-80%),Very frequent (99-80%) HP:0000232
11 specific learning disability 58 31 hallmark (90%) Very frequent (99-80%) HP:0001328
12 aphasia 58 31 hallmark (90%) Very frequent (99-80%) HP:0002381
13 echolalia 58 31 hallmark (90%) Very frequent (99-80%) HP:0010529
14 flat occiput 58 31 hallmark (90%) Very frequent (99-80%) HP:0005469
15 mutism 58 31 hallmark (90%) Very frequent (99-80%) HP:0002300
16 malar flattening 58 31 frequent (33%) Very frequent (99-80%) HP:0000272
17 obesity 58 31 frequent (33%) Frequent (79-30%),Frequent (79-30%) HP:0001513
18 sleep disturbance 58 31 frequent (33%) Frequent (79-30%),Occasional (29-5%) HP:0002360
19 macroglossia 58 31 frequent (33%) Frequent (79-30%),Frequent (79-30%) HP:0000158
20 coarse facial features 58 31 frequent (33%) Very frequent (99-80%) HP:0000280
21 mandibular prognathia 58 31 frequent (33%) Frequent (79-30%) HP:0000303
22 recurrent respiratory infections 58 31 frequent (33%) Occasional (29-5%) HP:0002205
23 delayed speech and language development 58 31 frequent (33%) Very frequent (99-80%) HP:0000750
24 cryptorchidism 58 31 frequent (33%) Occasional (29-5%),Frequent (79-30%) HP:0000028
25 microcephaly 58 31 very rare (1%) Frequent (79-30%),Frequent (79-30%) HP:0000252
26 midface retrusion 58 31 frequent (33%) Frequent (79-30%) HP:0011800
27 stereotypy 58 31 frequent (33%) Occasional (29-5%) HP:0000733
28 autism 58 31 frequent (33%) Frequent (79-30%) HP:0000717
29 hypospadias 58 31 frequent (33%) Occasional (29-5%) HP:0000047
30 micropenis 58 31 frequent (33%) Occasional (29-5%) HP:0000054
31 upslanted palpebral fissure 58 31 frequent (33%) Frequent (79-30%) HP:0000582
32 synophrys 58 31 frequent (33%) Frequent (79-30%),Frequent (79-30%) HP:0000664
33 aggressive behavior 58 31 frequent (33%) Frequent (79-30%) HP:0000718
34 downturned corners of mouth 58 31 frequent (33%) Occasional (29-5%),Frequent (79-30%) HP:0002714
35 absence seizure 58 31 frequent (33%) Frequent (79-30%) HP:0002121
36 status epilepticus 58 31 frequent (33%) Frequent (79-30%) HP:0002133
37 abnormal cardiac septum morphology 58 31 frequent (33%) Frequent (79-30%) HP:0001671
38 protruding tongue 58 31 frequent (33%) Frequent (79-30%) HP:0010808
39 epileptic spasms 58 31 frequent (33%) Frequent (79-30%) HP:0011097
40 abnormality of the pinna 31 frequent (33%) HP:0000377
41 u-shaped upper lip vermilion 31 frequent (33%) HP:0010806
42 agenesis of corpus callosum 58 31 occasional (7.5%) Occasional (29-5%),Occasional (29-5%) HP:0001274
43 failure to thrive 58 31 occasional (7.5%) Occasional (29-5%) HP:0001508
44 depressivity 58 31 occasional (7.5%) Occasional (29-5%) HP:0000716
45 hearing impairment 58 31 very rare (1%) Frequent (79-30%),Occasional (29-5%) HP:0000365
46 inguinal hernia 58 31 occasional (7.5%) Occasional (29-5%) HP:0000023
47 feeding difficulties 58 31 occasional (7.5%) Occasional (29-5%) HP:0011968
48 gastroesophageal reflux 58 31 occasional (7.5%) Occasional (29-5%) HP:0002020
49 renal insufficiency 58 31 occasional (7.5%) Occasional (29-5%),Occasional (29-5%) HP:0000083
50 irritability 58 31 occasional (7.5%) Occasional (29-5%) HP:0000737

Symptoms via clinical synopsis from OMIM:

56
Head And Neck Eyes:
hypertelorism
synophrys
upslanting palpebral fissures

Neurologic Central Nervous System:
seizures
hypotonia
mental retardation, severe

Skeletal Hands:
brachydactyly
single transverse palmar creases

Head And Neck Nose:
anteverted nares

Skin Nails Hair Hair:
synophrys

Head And Neck Ears:
hearing loss
malformed ears

Growth Weight:
obesity

Head And Neck Mouth:
macroglossia
everted lower lip
carp-shaped mouth

Head And Neck Head:
microcephaly
brachycephaly

Head And Neck Face:
flat face
midface hypoplasia
prognathism
coarse facies

Neurologic Behavioral Psychiatric Manifestations:
aggressive behavior
stereotypic movements
behavioral problems
obsessive-compulsive disorder
sleep disorders

Cardiovascular Heart:
conotruncal heart defects

Clinical features from OMIM:

610253

UMLS symptoms related to Kleefstra Syndrome 1:


seizures

MGI Mouse Phenotypes related to Kleefstra Syndrome 1:

45
# Description MGI Source Accession Score Top Affiliating Genes
1 growth/size/body region MP:0005378 9.93 EHMT1 EHMT2 KDM4C KDM5C KDM6A KMT2C
2 mortality/aging MP:0010768 9.8 EHMT1 EHMT2 KDM4C KDM5C KDM6A KMT2C
3 nervous system MP:0003631 9.36 CDKL5 EHMT1 EHMT2 KDM5C KDM6A KMT2D

Drugs & Therapeutics for Kleefstra Syndrome 1

Search Clinical Trials , NIH Clinical Center for Kleefstra Syndrome 1

Cochrane evidence based reviews: kleefstra syndrome

Genetic Tests for Kleefstra Syndrome 1

Anatomical Context for Kleefstra Syndrome 1

MalaCards organs/tissues related to Kleefstra Syndrome 1:

40
Heart, Brain, Testis, Tongue, Bone, Eye, Lung

Publications for Kleefstra Syndrome 1

Articles related to Kleefstra Syndrome 1:

(show top 50) (show all 68)
# Title Authors PMID Year
1
Disruption of an EHMT1-associated chromatin-modification module causes intellectual disability. 61 56 6
22726846 2012
2
Further clinical and molecular delineation of the 9q subtelomeric deletion syndrome supports a major contribution of EHMT1 haploinsufficiency to the core phenotype. 56 6
19264732 2009
3
Loss-of-function mutations in euchromatin histone methyl transferase 1 (EHMT1) cause the 9q34 subtelomeric deletion syndrome. 56 6
16826528 2006
4
Kleefstra syndrome in three adult patients: further delineation of the behavioral and neurological phenotype shows aspects of a neurodegenerative course. 61 56
21910222 2011
5
Familial Kleefstra syndrome due to maternal somatic mosaicism for interstitial 9q34.3 microdeletions. 61 56
21204793 2011
6
Kleefstra Syndrome 61 6
20945554 2010
7
Molecular mechanisms for subtelomeric rearrangements associated with the 9q34.3 microdeletion syndrome. 56
19293338 2009
8
Three patients with terminal deletions within the subtelomeric region of chromosome 9q. 56
15633179 2005
9
Subtelomeric deletions of chromosome 9q: a novel microdeletion syndrome. 56
15264279 2004
10
9q34.3 deletion syndrome in three unrelated children. 56
15054842 2004
11
A 1-Mb critical region in six patients with 9q34.3 terminal deletion syndrome. 56
15258833 2004
12
KMT2C/D COMPASS complex-associated diseases [KCDCOM-ADs]: an emerging class of congenital regulopathies. 61
31924266 2020
13
Distinct Pathogenic Genes Causing Intellectual Disability and Autism Exhibit a Common Neuronal Network Hyperactivity Phenotype. 61
31914384 2020
14
Otopathology in Kleefstra Syndrome: A Case Report. 61
31750954 2019
15
Neuronal network dysfunction in a model for Kleefstra syndrome mediated by enhanced NMDAR signaling. 61
31666522 2019
16
[Kleefstra syndrome 1 and ring chromosome 9 in a case]. 61
31400141 2019
17
9q34.3 microduplications lead to neurodevelopmental disorders through EHMT1 overexpression. 61
31209758 2019
18
Chromosomal microarray analysis in fetuses with an isolated congenital heart defect: A retrospective, nationwide, multicenter study in France. 61
30896039 2019
19
Histone 4 Lysine 20 Methylation: A Case for Neurodevelopmental Disease. 61
30832413 2019
20
Shone's complex in a patient with chromosome 9q34.3 deletion (Kleefstra syndrome). 61
30585561 2019
21
Fetal valproate syndrome as a phenocopy of Kleefstra syndrome. 61
30151876 2018
22
Pulmonary hypertension in patients with 9q34.3 microdeletion-associated Kleefstra syndrome. 61
30063093 2018
23
Increased H3K9 methylation and impaired expression of Protocadherins are associated with the cognitive dysfunctions of the Kleefstra syndrome. 61
29554304 2018
24
Biochemical validation of EHMT1 missense mutations in Kleefstra syndrome. 61
29459631 2018
25
First prenatal diagnosis of a 'pure' 9q34.3 deletion (Kleefstra syndrome): A case report and literature review. 61
29160022 2018
26
EHMT1 mosaicism in apparently unaffected parents is associated with autism spectrum disorder and neurocognitive dysfunction. 61
29416845 2018
27
New Insights into Kleefstra Syndrome: Report of Two Novel Cases with Previously Unreported Features and Literature Review. 61
30448833 2018
28
Hypogonadotropic Hypogonadism and Kleefstra Syndrome due to a Pathogenic Variant in the EHMT1 Gene: An Underrecognized Association. 61
30370152 2018
29
Kleefstra Syndrome: The First Case Report From Iran. 61
29228531 2017
30
Functional convergence of histone methyltransferases EHMT1 and KMT2C involved in intellectual disability and autism spectrum disorder. 61
29069077 2017
31
Genotype-phenotype evaluation of MED13L defects in the light of a novel truncating and a recurrent missense mutation. 61
28645799 2017
32
Adaptive and maladaptive functioning in Kleefstra syndrome compared to other rare genetic disorders with intellectual disabilities. 61
28498556 2017
33
Sleep Disturbance as a Precursor of Severe Regression in Kleefstra Syndrome Suggests a Need for Firm and Rapid Pharmacological Treatment. 61
28622207 2017
34
Altered neurite morphology and cholinergic function of induced pluripotent stem cell-derived neurons from a patient with Kleefstra syndrome and autism. 61
28742076 2017
35
Increased first-trimester nuchal translucency associated with a dicentric chromosome and 9q34.3 microdeletion syndrome. 61
27966372 2017
36
A novel de novo frameshift deletion in EHMT1 in a patient with Kleefstra Syndrome results in decreased H3K9 dimethylation. 61
28361100 2017
37
A de novo splice site mutation in EHMT1 resulting in Kleefstra syndrome with pharmacogenomics screening and behavior therapy for regressive behaviors. 61
28361099 2017
38
A Novel Kleefstra Syndrome-associated Variant That Affects the Conserved TPLX Motif within the Ankyrin Repeat of EHMT1 Leads to Abnormal Protein Folding. 61
28057753 2017
39
Haploinsufficiency of EHMT1 improves pattern separation and increases hippocampal cell proliferation. 61
28071689 2017
40
Targeted next generation sequencing of a panel of autism-related genes identifies an EHMT1 mutation in a Kleefstra syndrome patient with autism and normal intellectual performance. 61
27651234 2016
41
Establishment of EHMT1 mutant induced pluripotent stem cell (iPSC) line from a 11-year-old Kleefstra syndrome (KS) patient with autism and normal intellectual performance. 61
27789404 2016
42
Euchromatin histone methyltransferase 1 regulates cortical neuronal network development. 61
27767173 2016
43
Histone Methylation by the Kleefstra Syndrome Protein EHMT1 Mediates Homeostatic Synaptic Scaling. 61
27373831 2016
44
Expanding the phenotypic profile of Kleefstra syndrome: A female with low-average intelligence and childhood apraxia of speech. 61
26833960 2016
45
Reversible white matter lesions associated with mutant EHMT1 and Kleefstra syndrome. 61
27123477 2016
46
A structured assessment of motor function and behavior in patients with Kleefstra syndrome. 61
26808425 2016
47
Kleefstra syndrome in Hungarian patients: additional symptoms besides the classic phenotype. 61
26918030 2016
48
Multiple Coronary Artery Microfistulas in a Girl with Kleefstra Syndrome. 61
27239352 2016
49
Pregnancy with de novo 9q34.3 microdeletion and Kleefstra syndrome in the fetus may be associated with an abnormal maternal serum screening result. 61
26384070 2015
50
Deep brain stimulation for the obsessive-compulsive and Tourette-like symptoms of Kleefstra syndrome. 61
26030700 2015

Variations for Kleefstra Syndrome 1

ClinVar genetic disease variations for Kleefstra Syndrome 1:

6 (show top 50) (show all 268) ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎
# Gene Name Type Significance ClinVarId dbSNP ID GRCh37 Pos GRCh38 Pos
1 EHMT1 NM_024757.5(EHMT1):c.391del (p.Ala131fs)deletion Pathogenic 209152 rs797045043 9:140611382-140611382 9:137716930-137716930
2 EHMT1 NM_024757.5(EHMT1):c.3413G>A (p.Trp1138Ter)SNV Pathogenic 221980 rs886037776 9:140711929-140711929 9:137817477-137817477
3 EHMT1 NM_024757.5(EHMT1):c.1413_1425del (p.Pro473fs)deletion Pathogenic 3606 rs137852715 9:140652371-140652383 9:137757919-137757931
4 EHMT1 NM_024757.5(EHMT1):c.3218G>A (p.Cys1073Tyr)SNV Pathogenic 3607 rs137852726 9:140708920-140708920 9:137814468-137814468
5 EHMT1 NM_024757.5(EHMT1):c.871C>T (p.Arg291Ter)SNV Pathogenic 3608 rs137852714 9:140637870-140637870 9:137743418-137743418
6 EHMT1 NM_024757.5(EHMT1):c.3502C>T (p.Arg1168Ter)SNV Pathogenic 3605 rs121918301 9:140712552-140712552 9:137818100-137818100
7 EHMT1 NM_024757.5(EHMT1):c.3181-80_3233deldeletion Pathogenic 41267 rs1554896943 9:140708803-140708935 9:137814351-137814483
8 EHMT1 NM_024757.5(EHMT1):c.1529_1532AGAC[1] (p.Asp512fs)short repeat Pathogenic 65726 rs137852716 9:140657154-140657157 9:137762702-137762705
9 EHMT1 NM_024757.5(EHMT1):c.1810C>T (p.Gln604Ter)SNV Pathogenic 65728 rs137852717 9:140671088-140671088 9:137776636-137776636
10 EHMT1 NM_024757.5(EHMT1):c.1858C>T (p.Arg620Ter)SNV Pathogenic 65729 rs137852718 9:140671136-140671136 9:137776684-137776684
11 EHMT1 NM_024757.5(EHMT1):c.2028dup (p.Pro677fs)duplication Pathogenic 65730 rs1554879411 9:140672340-140672341 9:137777888-137777889
12 EHMT1 NM_024757.5(EHMT1):c.2193-1G>CSNV Pathogenic 65731 rs137852720 9:140674086-140674086 9:137779634-137779634
13 EHMT1 NM_024757.5(EHMT1):c.2861_2862GT[1] (p.Val955fs)short repeat Pathogenic 65732 rs137852721 9:140706060-140706061 9:137811608-137811609
14 EHMT1 NM_024757.5(EHMT1):c.2873_2876TTCT[1] (p.Ser960fs)short repeat Pathogenic 65734 rs786205129 9:140707460-140707463 9:137813008-137813011
15 EHMT1 NM_024757.5(EHMT1):c.3180+1G>TSNV Pathogenic 65735 rs137852724 9:140707983-140707983 9:137813531-137813531
16 EHMT1 NM_024757.5(EHMT1):c.3229C>T (p.Gln1077Ter)SNV Pathogenic 65736 rs137852725 9:140708931-140708931 9:137814479-137814479
17 EHMT1 NM_024757.5(EHMT1):c.2868-1G>ASNV Pathogenic 65733 rs137852722 9:140707457-140707457 9:137813005-137813005
18 EHMT1 NM_024757.5(EHMT1):c.1434_1435del (p.Tyr479fs)deletion Pathogenic 431703 rs1554867189 9:140652396-140652397 9:137757944-137757945
19 EHMT1 NM_024757.5(EHMT1):c.2214_2230dup (p.Phe744fs)duplication Pathogenic 438289 rs1554880275 9:140674107-140674108 9:137779655-137779656
20 EHMT1 NM_024757.5(EHMT1):c.2224del (p.Leu742fs)deletion Pathogenic 560999 rs1564744631 9:140674118-140674118 9:137779666-137779666
21 EHMT1 NM_024757.5(EHMT1):c.3046C>T (p.Arg1016Ter)SNV Pathogenic 566937 rs1429360126 9:140707848-140707848 9:137813396-137813396
22 EHMT1 NM_024757.5(EHMT1):c.1495del (p.Ala499fs)deletion Pathogenic 620057 rs1564704457 9:140652457-140652457 9:137758005-137758005
23 EHMT1 NC_000009.11:g.(?_140605399)_(140652483_?)dupduplication Pathogenic 662276 9:140605399-140652483 9:137710947-137758031
24 EHMT1 NM_024757.5(EHMT1):c.2566C>T (p.Gln856Ter)SNV Pathogenic 666593 9:140693325-140693325 9:137798873-137798873
25 PAEP NM_002571.4(PAEP):c.311-444_*248deldeletion Pathogenic 666598 9:138455646-138458646 9:135563800-135566800
26 EHMT1 NM_024757.5(EHMT1):c.3443del (p.Pro1148fs)deletion Pathogenic 694702 9:140711958-140711958 9:137817506-137817506
27 EHMT1 NM_024757.5(EHMT1):c.2976del (p.Ser992fs)deletion Pathogenic 802552 9:140707566-140707566 9:137813114-137813114
28 EHMT1 NM_024757.5(EHMT1):c.3709C>T (p.Gln1237Ter)SNV Pathogenic 802554 9:140728969-140728969 9:137834517-137834517
29 EHMT1 NM_024757.5(EHMT1):c.1647+2T>CSNV Pathogenic/Likely pathogenic 374120 rs1057518913 9:140657274-140657274 9:137762822-137762822
30 EHMT1 NM_024757.5(EHMT1):c.673C>T (p.Arg225Ter)SNV Pathogenic/Likely pathogenic 252987 rs879255531 9:140622831-140622831 9:137728379-137728379
31 EHMT1 NM_024757.5(EHMT1):c.3310G>A (p.Glu1104Lys)SNV Likely pathogenic 268206 rs886041093 9:140710450-140710450 9:137815998-137815998
32 EHMT1 NM_024757.5(EHMT1):c.3589C>T (p.Arg1197Trp)SNV Likely pathogenic 65737 rs137852727 9:140728849-140728849 9:137834397-137834397
33 EHMT1 NM_024757.5(EHMT1):c.3583_3594del (p.Val1195_Phe1198del)deletion Likely pathogenic 435046 rs1554908290 9:140728842-140728853 9:137834390-137834401
34 EHMT1 NM_024757.5(EHMT1):c.2516G>T (p.Gly839Val)SNV Likely pathogenic 522804 rs1554888939 9:140693275-140693275 9:137798823-137798823
35 EHMT1 NM_024757.5(EHMT1):c.1042_1043dup (p.Asp349fs)duplication Likely pathogenic 666585 9:140638412-140638413 9:137743960-137743961
36 EHMT1 NM_024757.5(EHMT1):c.3252C>G (p.Tyr1084Ter)SNV Likely pathogenic 802553 9:140708954-140708954 9:137814502-137814502
37 EHMT1 NM_024757.5(EHMT1):c.13_21+153deldeletion Likely pathogenic 573983 rs1564509503 9:140513484-140513645 9:137619032-137619193
38 EHMT1 NM_024757.5(EHMT1):c.1249-2A>GSNV Likely pathogenic 619987 rs1564697048 9:140648621-140648621 9:137754169-137754169
39 EHMT1 NM_024757.5(EHMT1):c.23C>T (p.Ala8Val)SNV Conflicting interpretations of pathogenicity 531856 rs375391530 9:140605420-140605420 9:137710968-137710968
40 EHMT1 NM_024757.5(EHMT1):c.499G>A (p.Ala167Thr)SNV Conflicting interpretations of pathogenicity 531857 rs141282876 9:140611491-140611491 9:137717039-137717039
41 EHMT1 NM_024757.5(EHMT1):c.2026G>A (p.Gly676Arg)SNV Conflicting interpretations of pathogenicity 599476 rs757416132 9:140672341-140672341 9:137777889-137777889
42 EHMT1 NM_024757.5(EHMT1):c.1814C>T (p.Pro605Leu)SNV Conflicting interpretations of pathogenicity 567822 rs373640528 9:140671092-140671092 9:137776640-137776640
43 EHMT1 NM_024757.5(EHMT1):c.3355G>A (p.Val1119Ile)SNV Conflicting interpretations of pathogenicity 567063 rs139394414 9:140710495-140710495 9:137816043-137816043
44 EHMT1 NM_024757.5(EHMT1):c.1655G>A (p.Arg552Gln)SNV Conflicting interpretations of pathogenicity 462980 rs747623277 9:140669568-140669568 9:137775116-137775116
45 EHMT1 NM_024757.5(EHMT1):c.1433G>A (p.Gly478Glu)SNV Conflicting interpretations of pathogenicity 462979 rs376787713 9:140652395-140652395 9:137757943-137757943
46 EHMT1 NM_024757.5(EHMT1):c.3894A>G (p.Leu1298=)SNV Conflicting interpretations of pathogenicity 366036 rs886063743 9:140729402-140729402 9:137834950-137834950
47 EHMT1 NM_024757.5(EHMT1):c.1402G>A (p.Ala468Thr)SNV Conflicting interpretations of pathogenicity 366009 rs202097707 9:140652364-140652364 9:137757912-137757912
48 EHMT1 NM_024757.5(EHMT1):c.3377C>T (p.Ala1126Val)SNV Conflicting interpretations of pathogenicity 366029 rs560251933 9:140711893-140711893 9:137817441-137817441
49 EHMT1 NM_024757.5(EHMT1):c.153C>T (p.Asp51=)SNV Conflicting interpretations of pathogenicity 365991 rs765396242 9:140611145-140611145 9:137716693-137716693
50 EHMT1 NM_024757.5(EHMT1):c.2142A>G (p.Gly714=)SNV Conflicting interpretations of pathogenicity 366013 rs758845539 9:140672457-140672457 9:137778005-137778005

UniProtKB/Swiss-Prot genetic disease variations for Kleefstra Syndrome 1:

73
# Symbol AA change Variation ID SNP ID
1 EHMT1 p.Cys1075Tyr VAR_069183

Expression for Kleefstra Syndrome 1

Search GEO for disease gene expression data for Kleefstra Syndrome 1.

Pathways for Kleefstra Syndrome 1

Pathways related to Kleefstra Syndrome 1 according to GeneCards Suite gene sharing:

# Super pathways Score Top Affiliating Genes
1
Show member pathways
12.07 KMT2D KMT2C KDM6A KDM5C KDM4C H2AC18
2 11.96 MECP2 KDM6A KDM5C EHMT2
3
Show member pathways
11.61 KMT2D KMT2C EHMT2 EHMT1
4 11.04 KMT2D KMT2C EHMT2 EHMT1

GO Terms for Kleefstra Syndrome 1

Cellular components related to Kleefstra Syndrome 1 according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 nucleus GO:0005634 10.16 WIZ UBE3A RAI1 NR1I3 MECP2 MBD5
2 nucleoplasm GO:0005654 9.97 WIZ RAI1 NR1I3 MECP2 MBD5 KMT2D
3 chromosome GO:0005694 9.72 MBD5 H3-2 H2AC18 EHMT2 EHMT1
4 MLL3/4 complex GO:0044666 9.13 KMT2D KMT2C KDM6A
5 histone methyltransferase complex GO:0035097 9.02 KMT2D KMT2C KDM6A KDM5C KDM4C

Biological processes related to Kleefstra Syndrome 1 according to GeneCards Suite gene sharing:

(show all 11)
# Name GO ID Score Top Affiliating Genes
1 methylation GO:0032259 9.73 KMT2D KMT2C EHMT2 EHMT1
2 chromatin remodeling GO:0006338 9.65 KDM6A KDM5C KDM4C
3 chromatin silencing GO:0006342 9.49 MECP2 KMT2D
4 histone H3-K9 methylation GO:0051567 9.46 EHMT2 EHMT1
5 histone H3-K4 methylation GO:0051568 9.43 KMT2D KMT2C KDM6A
6 peptidyl-lysine dimethylation GO:0018027 9.4 EHMT2 EHMT1
7 response to fungicide GO:0060992 9.37 EHMT2 EHMT1
8 histone methylation GO:0016571 9.33 MECP2 EHMT2 EHMT1
9 histone H3-K27 methylation GO:0070734 9.32 EHMT2 EHMT1
10 histone lysine methylation GO:0034968 9.26 KMT2D KMT2C EHMT2 EHMT1
11 chromatin organization GO:0006325 9.23 KMT2D KMT2C KDM6A KDM5C KDM4C H2AC18

Molecular functions related to Kleefstra Syndrome 1 according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 metal ion binding GO:0046872 10.06 WIZ UBE3A RAI1 NR1I3 KMT2D KMT2C
2 transcription coactivator activity GO:0003713 9.73 UBE3A NR1I3 KMT2D KMT2C
3 dioxygenase activity GO:0051213 9.54 KDM6A KDM5C KDM4C
4 histone methyltransferase activity (H3-K4 specific) GO:0042800 9.48 KMT2D KMT2C
5 histone demethylase activity GO:0032452 9.46 KDM5C KDM4C
6 methyltransferase activity GO:0008168 9.46 KMT2D KMT2C EHMT2 EHMT1
7 C2H2 zinc finger domain binding GO:0070742 9.4 EHMT2 EHMT1
8 histone methyltransferase activity (H3-K9 specific) GO:0046974 9.26 EHMT2 EHMT1
9 histone methyltransferase activity (H3-K27 specific) GO:0046976 8.96 EHMT2 EHMT1
10 histone-lysine N-methyltransferase activity GO:0018024 8.92 KMT2D KMT2C EHMT2 EHMT1

Sources for Kleefstra Syndrome 1

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
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48 NCI
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50 NDF-RT
53 NINDS
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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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