KLEFS1
MCID: KLF004
MIFTS: 52

Kleefstra Syndrome 1 (KLEFS1)

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

Aliases & Classifications for Kleefstra Syndrome 1

MalaCards integrated aliases for Kleefstra Syndrome 1:

Name: Kleefstra Syndrome 1 57 12 72 29 6 15
9q Subtelomeric Deletion Syndrome 57 12 58
Kleefstra Syndrome 58 44 70
Chromosome 9q34.3 Deletion Syndrome 57 72
9q34 Deletion Syndrome 12 73
9q- Syndrome 57 72
Klefs1 57 72
Kleefstra Syndrome Due to 9q Subtelomeric Deletion 58
Kleefstra Syndrome Due to 9q34 Microdeletion 58
Chromosome 9q Subtelomeric Deletion Syndrome 72
Kleefstra Syndrome Due to Monosomy 9q34 58
Kleefstra Syndrome Due to Del(9)(q34) 58
Syndrome, Kleefstra, Type 1 39
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®:

57 (Updated 05-Apr-2021)
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® : 57 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) (Updated 05-Apr-2021)

MalaCards based summary : Kleefstra Syndrome 1, also known as 9q subtelomeric deletion syndrome, is related to kleefstra syndrome due to a point mutation and kleefstra 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 PKMTs methylate histone lysines. Affiliated tissues include tongue, heart and testis, and related phenotypes are intellectual disability and dysphasia

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 : 72 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 : 73 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 71)
# Related Disease Score Top Affiliating Genes
1 kleefstra syndrome due to a point mutation 32.3 KMT2C EHMT1
2 kleefstra syndrome 28.9 PAGR1 PAEP NR1I3 MBD5 KMT2C KDM4C
3 kleefstra syndrome 2 10.9
4 alacrima, achalasia, and mental retardation syndrome 10.6
5 hypotonia 10.5
6 autism spectrum disorder 10.3
7 microcephaly 10.3
8 waardenburg syndrome, type 2d 10.2 ZMYND19 PAGR1 ARRDC1-AS1
9 nut midline carcinoma 10.2 KMT2C KDM4C H2AC18
10 chromosome 9p deletion syndrome 10.2 FREM1 CER1
11 retinal cancer 10.2 PAGR1 KDM4C H2AC18
12 epicanthus 10.2
13 neural tube defects 10.2
14 branchiootic syndrome 1 10.2
15 neuroblastoma 10.2
16 exophthalmos 10.2
17 microtia 10.2
18 mental retardation, x-linked, syndromic, claes-jensen type 10.1 PWWP2B KDM4C
19 hypertelorism 10.1
20 autism 10.1
21 brain stem cancer 10.1 KDM4C H2AC18
22 hyperoxaluria, primary, type i 10.1 KDM4C H2AC18 EHMT2
23 chromosome 16p13.3 deletion syndrome, proximal 10.1 PAGR1 KDM4C H2AC18 EHMT1
24 carbohydrate metabolic disorder 10.1 KDM4C H2AC18 EHMT2
25 specific developmental disorder 10.1 PAGR1 KDM4C H2AC18
26 chromosomal deletion syndrome 10.1 PAGR1 KDM4C H2AC18 EHMT1
27 pervasive developmental disorder 10.1 PAGR1 KDM4C H2AC18
28 chromosomal triplication 10.1
29 chromosome 9q duplication 10.1
30 angelman syndrome 10.1
31 macroglossia 10.1
32 down syndrome 10.1
33 agenesis of corpus callosum, cardiac, ocular, and genital syndrome 10.1
34 pulmonary hypertension 10.1
35 kabuki syndrome 1 10.1 PAGR1 KMT2C KDM4C H2AC18 EHMT1
36 christianson syndrome 10.1 MBD5 EHMT1
37 primary hyperoxaluria 10.0 KDM4C H2AC18 EHMT2
38 weaver syndrome 10.0 PWWP2B KDM4C H2AC18 EHMT1
39 ring chromosome 9 10.0
40 ring chromosome 10.0
41 sotos syndrome 1 10.0 PWWP2B MBD5 H2AC18 EHMT1
42 gilles de la tourette syndrome 9.9
43 obsessive-compulsive disorder 9.9
44 prader-willi syndrome 9.9
45 smith-magenis syndrome 9.9
46 cryptorchidism, unilateral or bilateral 9.9
47 abnormal hair, joint laxity, and developmental delay 9.9
48 polydactyly 9.9
49 valproate embryopathy 9.9
50 koolen-de vries syndrome 9.9

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 113)
# Description HPO Frequency Orphanet Frequency HPO Source Accession
1 intellectual disability 58 31 hallmark (90%) Very frequent (99-80%) HP:0001249
2 dysphasia 58 31 hallmark (90%) Very frequent (99-80%) HP:0002357
3 global developmental delay 58 31 hallmark (90%) Very frequent (99-80%),Very frequent (99-80%) HP:0001263
4 hypertelorism 58 31 frequent (33%) Very frequent (99-80%),Very frequent (99-80%) HP:0000316
5 short nose 58 31 hallmark (90%) Very frequent (99-80%),Very frequent (99-80%) HP:0003196
6 anteverted nares 58 31 frequent (33%) Very frequent (99-80%),Very frequent (99-80%) HP:0000463
7 brachycephaly 58 31 frequent (33%) Very frequent (99-80%),Frequent (79-30%) HP:0000248
8 everted lower lip vermilion 58 31 frequent (33%) Very frequent (99-80%),Very frequent (99-80%) HP:0000232
9 specific learning disability 58 31 hallmark (90%) Very frequent (99-80%) HP:0001328
10 highly arched eyebrow 58 31 hallmark (90%) Very frequent (99-80%),Frequent (79-30%) HP:0002553
11 flat occiput 58 31 hallmark (90%) Very frequent (99-80%) HP:0005469
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 mutism 58 31 hallmark (90%) Very frequent (99-80%) HP:0002300
15 hypotonia 31 hallmark (90%) HP:0001252
16 sleep disturbance 58 31 frequent (33%) Occasional (29-5%),Frequent (79-30%) HP:0002360
17 macroglossia 58 31 frequent (33%) Frequent (79-30%),Frequent (79-30%) HP:0000158
18 coarse facial features 58 31 frequent (33%) Very frequent (99-80%) HP:0000280
19 mandibular prognathia 58 31 frequent (33%) Frequent (79-30%) HP:0000303
20 recurrent respiratory infections 58 31 frequent (33%) Occasional (29-5%) HP:0002205
21 delayed speech and language development 58 31 frequent (33%) Very frequent (99-80%) HP:0000750
22 microcephaly 58 31 very rare (1%) Frequent (79-30%),Frequent (79-30%) HP:0000252
23 stereotypy 58 31 frequent (33%) Occasional (29-5%) HP:0000733
24 cryptorchidism 58 31 frequent (33%) Frequent (79-30%),Occasional (29-5%) HP:0000028
25 autism 58 31 frequent (33%) Frequent (79-30%) HP:0000717
26 obesity 58 31 frequent (33%) Frequent (79-30%),Frequent (79-30%) HP:0001513
27 upslanted palpebral fissure 58 31 frequent (33%) Frequent (79-30%) HP:0000582
28 downturned corners of mouth 58 31 frequent (33%) Frequent (79-30%),Occasional (29-5%) HP:0002714
29 protruding tongue 58 31 frequent (33%) Frequent (79-30%) HP:0010808
30 micropenis 58 31 frequent (33%) Occasional (29-5%) HP:0000054
31 abnormal cardiac septum morphology 58 31 frequent (33%) Frequent (79-30%) HP:0001671
32 malar flattening 58 31 frequent (33%) Very frequent (99-80%) HP:0000272
33 hypospadias 58 31 frequent (33%) Occasional (29-5%) HP:0000047
34 midface retrusion 58 31 frequent (33%) Frequent (79-30%) HP:0011800
35 synophrys 58 31 frequent (33%) Frequent (79-30%),Frequent (79-30%) HP:0000664
36 status epilepticus 58 31 frequent (33%) Frequent (79-30%) HP:0002133
37 aggressive behavior 58 31 frequent (33%) Frequent (79-30%) HP:0000718
38 u-shaped upper lip vermilion 31 frequent (33%) HP:0010806
39 abnormality of the pinna 31 frequent (33%) HP:0000377
40 generalized non-motor (absence) seizure 31 frequent (33%) HP:0002121
41 epileptic spasm 31 frequent (33%) HP:0011097
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%) Occasional (29-5%),Frequent (79-30%) HP:0000365
46 inguinal hernia 58 31 occasional (7.5%) Occasional (29-5%) HP:0000023
47 gastroesophageal reflux 58 31 occasional (7.5%) Occasional (29-5%) HP:0002020
48 renal insufficiency 58 31 occasional (7.5%) Occasional (29-5%),Occasional (29-5%) HP:0000083
49 growth delay 58 31 occasional (7.5%) Occasional (29-5%) HP:0001510
50 anxiety 58 31 occasional (7.5%) Occasional (29-5%) HP:0000739

Symptoms via clinical synopsis from OMIM®:

57 (Updated 05-Apr-2021)
Neurologic Central Nervous System:
seizures
hypotonia
mental retardation, severe

Head And Neck Eyes:
hypertelorism
synophrys
upslanting palpebral fissures

Head And Neck Nose:
anteverted nares

Growth Weight:
obesity

Skin Nails Hair Hair:
synophrys

Head And Neck Ears:
hearing loss
malformed ears

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

Skeletal Hands:
brachydactyly
single transverse palmar creases

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 (Updated 05-Apr-2021)

UMLS symptoms related to Kleefstra Syndrome 1:


seizures

GenomeRNAi Phenotypes related to Kleefstra Syndrome 1 according to GeneCards Suite gene sharing:

26
# Description GenomeRNAi Source Accession Score Top Affiliating Genes
1 Decreased viability GR00106-A-0 9.77 CACNA1B
2 Decreased viability GR00221-A-1 9.77 NR1I3
3 Decreased viability GR00221-A-2 9.77 NR1I3
4 Decreased viability GR00249-S 9.77 ABCC9 KMT2C NR1I3
5 Decreased viability GR00301-A 9.77 NR1I3
6 Decreased viability GR00381-A-1 9.77 CACNA1B PAGR1
7 Decreased viability GR00386-A-1 9.77 ARRDC1 GALNT1 NR1I3
8 Decreased viability GR00402-S-2 9.77 FREM1
9 Increased the percentage of infected cells GR00402-S-1 8.32 CER1

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

Genetic tests related to Kleefstra Syndrome 1:

# Genetic test Affiliating Genes
1 Kleefstra Syndrome 1 29 EHMT1

Anatomical Context for Kleefstra Syndrome 1

MalaCards organs/tissues related to Kleefstra Syndrome 1:

40
Tongue, Heart, Testis

Publications for Kleefstra Syndrome 1

Articles related to Kleefstra Syndrome 1:

(show all 18)
# Title Authors PMID Year
1
Further clinical and molecular delineation of the 9q subtelomeric deletion syndrome supports a major contribution of EHMT1 haploinsufficiency to the core phenotype. 57 6
19264732 2009
2
Loss-of-function mutations in euchromatin histone methyl transferase 1 (EHMT1) cause the 9q34 subtelomeric deletion syndrome. 57 6
16826528 2006
3
A Novel Kleefstra Syndrome-associated Variant That Affects the Conserved TPLX Motif within the Ankyrin Repeat of EHMT1 Leads to Abnormal Protein Folding. 6
28057753 2017
4
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. 6
27651234 2016
5
Molecular diagnostic experience of whole-exome sequencing in adult patients. 6
26633545 2016
6
Expanding the phenotypic profile of Kleefstra syndrome: A female with low-average intelligence and childhood apraxia of speech. 6
26833960 2016
7
Enrichment of small pathogenic deletions at chromosome 9p24.3 and 9q34.3 involving DOCK8, KANK1, EHMT1 genes identified by using high-resolution oligonucleotide-single nucleotide polymorphism array analysis. 6
27891178 2016
8
Disruption of an EHMT1-associated chromatin-modification module causes intellectual disability. 57
22726846 2012
9
Update on Kleefstra Syndrome. 6
22670141 2012
10
Kleefstra syndrome in three adult patients: further delineation of the behavioral and neurological phenotype shows aspects of a neurodegenerative course. 57
21910222 2011
11
Familial Kleefstra syndrome due to maternal somatic mosaicism for interstitial 9q34.3 microdeletions. 57
21204793 2011
12
Kleefstra Syndrome 6
20945554 2010
13
Molecular mechanisms for subtelomeric rearrangements associated with the 9q34.3 microdeletion syndrome. 57
19293338 2009
14
Three patients with terminal deletions within the subtelomeric region of chromosome 9q. 57
15633179 2005
15
Subtelomeric deletions of chromosome 9q: a novel microdeletion syndrome. 57
15264279 2004
16
9q34.3 deletion syndrome in three unrelated children. 57
15054842 2004
17
A 1-Mb critical region in six patients with 9q34.3 terminal deletion syndrome. 57
15258833 2004
18
[Kleefstra syndrome 1 and ring chromosome 9 in a case]. 61
31400141 2019

Variations for Kleefstra Syndrome 1

ClinVar genetic disease variations for Kleefstra Syndrome 1:

6 (show top 50) (show all 534)
# Gene Name Type Significance ClinVarId dbSNP ID Position
1 EHMT1 NM_024757.5(EHMT1):c.1413_1425del (p.Pro473fs) Deletion Pathogenic 3606 rs137852715 GRCh37: 9:140652371-140652383
GRCh38: 9:137757919-137757931
2 EHMT1 NM_024757.5(EHMT1):c.3218G>A (p.Cys1073Tyr) SNV Pathogenic 3607 rs137852726 GRCh37: 9:140708920-140708920
GRCh38: 9:137814468-137814468
3 EHMT1 NM_024757.5(EHMT1):c.871C>T (p.Arg291Ter) SNV Pathogenic 3608 rs137852714 GRCh37: 9:140637870-140637870
GRCh38: 9:137743418-137743418
4 EHMT1 NM_024757.5(EHMT1):c.3181-80_3233del Deletion Pathogenic 41267 rs1554896943 GRCh37: 9:140708803-140708935
GRCh38: 9:137814351-137814483
5 EHMT1 NM_024757.5(EHMT1):c.1529_1532AGAC[1] (p.Asp512fs) Microsatellite Pathogenic 65726 rs137852716 GRCh37: 9:140657154-140657157
GRCh38: 9:137762702-137762705
6 EHMT1 NM_024757.5(EHMT1):c.1810C>T (p.Gln604Ter) SNV Pathogenic 65728 rs137852717 GRCh37: 9:140671088-140671088
GRCh38: 9:137776636-137776636
7 EHMT1 NM_024757.5(EHMT1):c.1858C>T (p.Arg620Ter) SNV Pathogenic 65729 rs137852718 GRCh37: 9:140671136-140671136
GRCh38: 9:137776684-137776684
8 EHMT1 NM_024757.5(EHMT1):c.2028dup (p.Pro677fs) Duplication Pathogenic 65730 rs1554879411 GRCh37: 9:140672340-140672341
GRCh38: 9:137777888-137777889
9 EHMT1 NM_024757.5(EHMT1):c.2193-1G>C SNV Pathogenic 65731 rs137852720 GRCh37: 9:140674086-140674086
GRCh38: 9:137779634-137779634
10 EHMT1 NM_024757.5(EHMT1):c.2861_2862GT[1] (p.Val955fs) Microsatellite Pathogenic 65732 rs137852721 GRCh37: 9:140706060-140706061
GRCh38: 9:137811608-137811609
11 EHMT1 NM_024757.5(EHMT1):c.2868-1G>A SNV Pathogenic 65733 rs137852722 GRCh37: 9:140707457-140707457
GRCh38: 9:137813005-137813005
12 EHMT1 NM_024757.5(EHMT1):c.3180+1G>T SNV Pathogenic 65735 rs137852724 GRCh37: 9:140707983-140707983
GRCh38: 9:137813531-137813531
13 EHMT1 NM_024757.5(EHMT1):c.3229C>T (p.Gln1077Ter) SNV Pathogenic 65736 rs137852725 GRCh37: 9:140708931-140708931
GRCh38: 9:137814479-137814479
14 EHMT1 NM_024757.5(EHMT1):c.391del (p.Ala131fs) Deletion Pathogenic 209152 rs797045043 GRCh37: 9:140611382-140611382
GRCh38: 9:137716930-137716930
15 EHMT1 NM_024757.5(EHMT1):c.3413G>A (p.Trp1138Ter) SNV Pathogenic 221980 rs886037776 GRCh37: 9:140711929-140711929
GRCh38: 9:137817477-137817477
16 EHMT1 NM_024757.5(EHMT1):c.2214_2230dup (p.Phe744fs) Duplication Pathogenic 438289 rs1554880275 GRCh37: 9:140674107-140674108
GRCh38: 9:137779655-137779656
17 EHMT1 NM_024757.5(EHMT1):c.3046C>T (p.Arg1016Ter) SNV Pathogenic 566937 rs1429360126 GRCh37: 9:140707848-140707848
GRCh38: 9:137813396-137813396
18 EHMT1 NM_024757.5(EHMT1):c.1434_1435del (p.Tyr479fs) Deletion Pathogenic 431703 rs1554867189 GRCh37: 9:140652396-140652397
GRCh38: 9:137757944-137757945
19 EHMT1 NM_024757.5(EHMT1):c.2224del (p.Leu742fs) Deletion Pathogenic 560999 rs1564744631 GRCh37: 9:140674118-140674118
GRCh38: 9:137779666-137779666
20 EHMT1 NM_024757.5(EHMT1):c.1495del (p.Ala499fs) Deletion Pathogenic 620057 GRCh37: 9:140652457-140652457
GRCh38: 9:137758005-137758005
21 EHMT1 NM_024757.5(EHMT1):c.1647+2T>C SNV Pathogenic 374120 rs1057518913 GRCh37: 9:140657274-140657274
GRCh38: 9:137762822-137762822
22 EHMT1 NM_024757.5(EHMT1):c.3443del (p.Pro1148fs) Deletion Pathogenic 694702 rs1588875719 GRCh37: 9:140711958-140711958
GRCh38: 9:137817506-137817506
23 EHMT1 NM_024757.5(EHMT1):c.2566C>T (p.Gln856Ter) SNV Pathogenic 666593 rs1588770875 GRCh37: 9:140693325-140693325
GRCh38: 9:137798873-137798873
24 PAEP NM_002571.4(PAEP):c.311-444_*248del Deletion Pathogenic 666598 GRCh37: 9:138455646-138458646
GRCh38: 9:135563800-135566800
25 EHMT1 NM_024757.5(EHMT1):c.2976del (p.Ser992fs) Deletion Pathogenic 802552 rs1588854011 GRCh37: 9:140707566-140707566
GRCh38: 9:137813114-137813114
26 overlap with 29 genes NC_000009.12:g.(?_137139467)_(137834973_?)del Deletion Pathogenic 830975 GRCh37: 9:140033919-140729425
GRCh38:
27 EHMT1 NM_024757.5(EHMT1):c.3709C>T (p.Gln1237Ter) SNV Pathogenic 802554 rs1325669112 GRCh37: 9:140728969-140728969
GRCh38: 9:137834517-137834517
28 EHMT1 NM_024757.5(EHMT1):c.40dup (p.Glu14fs) Duplication Pathogenic 852882 GRCh37: 9:140605431-140605432
GRCh38: 9:137710979-137710980
29 EHMT1 NM_024757.5(EHMT1):c.2608-1G>A SNV Pathogenic 939737 GRCh37: 9:140695331-140695331
GRCh38: 9:137800879-137800879
30 EHMT1 NM_024757.5(EHMT1):c.2079dup (p.Glu694fs) Duplication Pathogenic 973221 GRCh37: 9:140672391-140672392
GRCh38: 9:137777939-137777940
31 EHMT1 NM_024757.5(EHMT1):c.2018+1G>C SNV Pathogenic 981202 GRCh37: 9:140671297-140671297
GRCh38: 9:137776845-137776845
32 EHMT1 NM_024757.5(EHMT1):c.3462-1G>A SNV Pathogenic 984655 GRCh37: 9:140712511-140712511
GRCh38: 9:137818059-137818059
33 EHMT1 NC_000009.12:g.137729445_137745564dup Duplication Pathogenic 988097 GRCh37:
GRCh38: 9:137729444-137745563
34 EHMT1 NM_024757.5(EHMT1):c.1597del (p.Thr533fs) Deletion Pathogenic 992396 GRCh37: 9:140657222-140657222
GRCh38: 9:137762770-137762770
35 EHMT1 NM_024757.5(EHMT1):c.2873_2876TTCT[1] (p.Ser960fs) Microsatellite Pathogenic 65734 rs786205129 GRCh37: 9:140707460-140707463
GRCh38: 9:137813008-137813011
36 EHMT1 NM_024757.5(EHMT1):c.2712+1G>A SNV Pathogenic 374034 rs1057518849 GRCh37: 9:140695437-140695437
GRCh38: 9:137800985-137800985
37 overlap with 75 genes NC_000009.11:g.(?_139018777)_(141018984_?)del Deletion Pathogenic 986753 GRCh37: 9:139018777-141018984
GRCh38:
38 overlap with 79 genes NC_000009.11:g.(?_138645763)_(140729425_?)del Deletion Pathogenic 831360 GRCh37: 9:138645763-140729425
GRCh38:
39 EHMT1 NM_024757.5(EHMT1):c.508del (p.Gln170fs) Deletion Pathogenic 976695 GRCh37: 9:140611497-140611497
GRCh38: 9:137717045-137717045
40 EHMT1 NM_024757.5(EHMT1):c.3000del (p.Asp1001fs) Deletion Pathogenic 1031404 GRCh37: 9:140707586-140707586
GRCh38: 9:137813134-137813134
41 KMT2C NM_170606.3(KMT2C):c.8543del (p.Asn2848fs) Deletion Pathogenic 1033181 GRCh37: 7:151873995-151873995
GRCh38: 7:152176910-152176910
42 EHMT1 NM_024757.5(EHMT1):c.1059_1060AG[1] (p.Glu354fs) Microsatellite Pathogenic 422908 rs1064796085 GRCh37: 9:140638431-140638432
GRCh38: 9:137743979-137743980
43 EHMT1 NM_024757.5(EHMT1):c.673C>T (p.Arg225Ter) SNV Pathogenic/Likely pathogenic 252987 rs879255531 GRCh37: 9:140622831-140622831
GRCh38: 9:137728379-137728379
44 EHMT1 NM_024757.5(EHMT1):c.824-2del Deletion Likely pathogenic 992223 GRCh37: 9:140637821-140637821
GRCh38: 9:137743369-137743369
45 ABCC9 NM_005691.3(ABCC9):c.3346C>T (p.Arg1116Cys) SNV Likely pathogenic 35534 rs387907228 GRCh37: 12:21995375-21995375
GRCh38: 12:21842441-21842441
46 EHMT1 NM_024757.5(EHMT1):c.3627_3633dup (p.Val1212fs) Duplication Likely pathogenic 977309 GRCh37: 9:140728885-140728886
GRCh38: 9:137834433-137834434
47 EHMT1 NM_024757.5(EHMT1):c.3343T>G (p.Cys1115Gly) SNV Likely pathogenic 979188 GRCh37: 9:140710483-140710483
GRCh38: 9:137816031-137816031
48 EHMT1 NM_024757.5(EHMT1):c.3578G>A (p.Gly1193Glu) SNV Likely pathogenic 981477 GRCh37: 9:140728838-140728838
GRCh38: 9:137834386-137834386
49 EHMT1 NM_024757.5(EHMT1):c.2530C>T (p.His844Tyr) SNV Likely pathogenic 981734 GRCh37: 9:140693289-140693289
GRCh38: 9:137798837-137798837
50 EHMT1 NM_024757.5(EHMT1):c.870dup (p.Arg291fs) Duplication Likely pathogenic 973220 GRCh37: 9:140637863-140637864
GRCh38: 9:137743411-137743412

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

72
# 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
12.2 KMT2C KDM4C H2AC18 EHMT2 EHMT1
2
Show member pathways
11.48 KMT2C EHMT2 EHMT1
3 10.6 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 MLL3/4 complex GO:0044666 8.96 PAGR1 KMT2C
2 histone methyltransferase complex GO:0035097 8.8 PAGR1 KMT2C KDM4C

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

# Name GO ID Score Top Affiliating Genes
1 chromatin organization GO:0006325 9.67 KMT2C KDM4C EHMT2 EHMT1
2 histone H3-K4 methylation GO:0051568 9.43 PAGR1 KMT2C
3 histone lysine methylation GO:0034968 9.4 EHMT2 EHMT1
4 histone methylation GO:0016571 9.32 EHMT2 EHMT1
5 histone H3-K9 methylation GO:0051567 9.26 EHMT2 EHMT1
6 peptidyl-lysine dimethylation GO:0018027 9.16 EHMT2 EHMT1
7 response to fungicide GO:0060992 8.96 EHMT2 EHMT1
8 histone H3-K27 methylation GO:0070734 8.62 EHMT2 EHMT1

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

# Name GO ID Score Top Affiliating Genes
1 RNA polymerase II transcription corepressor binding GO:0001226 9.26 EHMT2 EHMT1
2 C2H2 zinc finger domain binding GO:0070742 9.16 EHMT2 EHMT1
3 histone methyltransferase activity (H3-K9 specific) GO:0046974 8.96 EHMT2 EHMT1
4 histone methyltransferase activity (H3-K27 specific) GO:0046976 8.62 EHMT2 EHMT1

Sources for Kleefstra Syndrome 1

3 CDC
7 CNVD
9 Cosmic
10 dbSNP
11 DGIdb
17 EFO
18 ExPASy
19 FMA
20 GARD
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
44 MeSH
45 MESH via Orphanet
46 MGI
49 NCI
50 NCIt
51 NDF-RT
53 NINDS
54 Novoseek
56 OMIM via Orphanet
57 OMIM® (Updated 05-Apr-2021)
61 PubMed
63 QIAGEN
68 SNOMED-CT via HPO
69 Tocris
70 UMLS
71 UMLS via Orphanet
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