SCKL4
MCID: SCK010
MIFTS: 39

Seckel Syndrome 4 (SCKL4)

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

Aliases & Classifications for Seckel Syndrome 4

MalaCards integrated aliases for Seckel Syndrome 4:

Name: Seckel Syndrome 4 57 12 72 29 13 6 15 70
Sckl4 57 12 72
Seckel Syndrome, Type 4 39

Characteristics:

OMIM®:

57 (Updated 20-May-2021)
Inheritance:
autosomal recessive


HPO:

31
seckel syndrome 4:
Inheritance autosomal recessive inheritance


Classifications:



External Ids:

Disease Ontology 12 DOID:0070010
OMIM® 57 613676
OMIM Phenotypic Series 57 PS210600
UMLS 70 C3888212

Summaries for Seckel Syndrome 4

OMIM® : 57 Seckel syndrome is a rare autosomal recessive disorder characterized by severe pre- and postnatal growth retardation, severe microcephaly with mental retardation, and specific dysmorphic features (Faivre et al., 2002). For a general description and a discussion of genetic heterogeneity of Seckel syndrome, see 210600. (613676) (Updated 20-May-2021)

MalaCards based summary : Seckel Syndrome 4, also known as sckl4, is related to microcephaly 14, primary, autosomal recessive and microcephaly 11, primary, autosomal recessive. An important gene associated with Seckel Syndrome 4 is CENPJ (Centromere Protein J), and among its related pathways/superpathways are Cell Cycle, Mitotic and Organelle biogenesis and maintenance. Affiliated tissues include eye and brain, and related phenotypes are cognitive impairment and microcephaly

Disease Ontology : 12 A Seckel syndrome that has material basis in homozygous mutation in the CENPJ gene on chromosome 13q12.

UniProtKB/Swiss-Prot : 72 Seckel syndrome 4: A rare autosomal recessive disorder characterized by proportionate dwarfism of prenatal onset associated with low birth weight, growth retardation, severe microcephaly with a bird-headed like appearance, and mental retardation.

Related Diseases for Seckel Syndrome 4

Diseases in the Seckel Syndrome family:

Seckel Syndrome 1 Seckel Syndrome 2
Seckel Syndrome 4 Seckel Syndrome 5
Seckel Syndrome 6 Seckel Syndrome 7
Seckel Syndrome 8 Seckel Syndrome 9
Seckel Syndrome 10

Diseases related to Seckel Syndrome 4 via text searches within MalaCards or GeneCards Suite gene sharing:

(show all 36)
# Related Disease Score Top Affiliating Genes
1 microcephaly 14, primary, autosomal recessive 10.1 CEP152 CENPJ
2 microcephaly 11, primary, autosomal recessive 10.1 MCPH1 CEP152 CENPJ
3 microcephaly 10, primary, autosomal recessive 10.1 CEP152 CENPJ
4 mosaic variegated aneuploidy syndrome 10.0 PCNT CNTLN CEP152
5 miller-dieker lissencephaly syndrome 9.9 RFC2 MCPH1 CDK5RAP2
6 microcephaly 8, primary, autosomal recessive 9.9 MCPH1 CEP152 CENPJ CDK5RAP2
7 microcephaly 12, primary, autosomal recessive 9.9 MCPH1 CEP152 CENPJ CDK5RAP2
8 microcephaly 9, primary, autosomal recessive 9.9 MCPH1 CEP152 CENPJ CDK5RAP2
9 neurodevelopmental disorder with progressive microcephaly, spasticity, and brain imaging abnormalities 9.9 PGAP2 CEP152
10 microcephaly 13, primary, autosomal recessive 9.9 MCPH1 CEP152
11 microcephaly 18, primary, autosomal dominant 9.9 MCPH1 CEP152 CENPJ ASPM
12 microcephaly 1, primary, autosomal recessive 9.9 MCPH1 CEP152 CENPJ ASPM
13 band heterotopia 9.8 MCPH1 CENPJ CDK5RAP2 ASPM
14 periventricular nodular heterotopia 9.8 MCPH1 CENPJ CDK5RAP2 ASPM
15 microcephaly 17, primary, autosomal recessive 9.7 MCPH1 CEP152 CENPJ CDK5RAP2 ASPM
16 microcephaly 3, primary, autosomal recessive 9.7 MCPH1 CEP152 CENPJ CDK5RAP2 ASPM
17 microcephaly 7, primary, autosomal recessive 9.7 MCPH1 CEP152 CENPJ CDK5RAP2 ASPM
18 microcephaly 4, primary, autosomal recessive 9.7 MCPH1 CEP152 CENPJ CDK5RAP2 ASPM
19 microcephaly 5, primary, autosomal recessive 9.7 MCPH1 CEP152 CENPJ CDK5RAP2 ASPM
20 joubert syndrome 1 9.7 PCNT CNTLN CEP152 CENPJ CDK5RAP2
21 primary microcephaly 9.7 MCPH1 CEP152 CENPJ CDK5RAP2 ASPM
22 isolated growth hormone deficiency 9.6 PCNT CNTLN CEP152 CENPJ CDK5RAP2 ASPM
23 microcephaly 2, primary, autosomal recessive, with or without cortical malformations 9.6 MCPH1 CNTLN CEP152 CENPJ CDK5RAP2 ASPM
24 microcephaly 6, primary, autosomal recessive 9.5 RNF17 MCPH1 CNTLN CEP152 CENPJ CDK5RAP2
25 microcephalic osteodysplastic primordial dwarfism, type ii 9.5 PCNT MCPH1 CNTLN CEP152 CENPJ CDK5RAP2
26 congenital nervous system abnormality 9.5 PCNT MCPH1 CNTLN CEP152 CENPJ CDK5RAP2
27 physical disorder 9.5 PCNT MCPH1 CNTLN CEP152 CENPJ CDK5RAP2
28 microcephaly 9.5 RBBP8 PCNT MCPH1 CEP152 CENPJ CDK5RAP2
29 autosomal recessive non-syndromic intellectual disability 9.4 PGAP2 MCPH1 IRF4 CEP152 CDK5RAP2
30 seckel syndrome 2 9.4 RFC2 RBBP8 PCNT MCPH1 CNTLN CEP152
31 seckel syndrome 1 9.4 RFC2 RBBP8 PCNT MCPH1 CNTLN CEP152
32 isolated growth hormone deficiency, type ia 9.3 RBBP8 PCNT MCPH1 CNTLN CEP152 CENPJ
33 seckel syndrome 5 9.3 TCP10L3 RNF17 RBBP8 PCNT MCPH1 CWH43
34 seckel syndrome 9.0 RNF17 RFC2 RBBP8 PCNT MCPH1 CNTLN
35 seckel syndrome 8 8.9 TTBK1 RBBP8 PGAP2 NUP85 CWH43 CEP152
36 primary autosomal recessive microcephaly 8.4 TTBK1 RNF17 RBBP8 PGAP2 PCNT MCPH1

Graphical network of the top 20 diseases related to Seckel Syndrome 4:



Diseases related to Seckel Syndrome 4

Symptoms & Phenotypes for Seckel Syndrome 4

Human phenotypes related to Seckel Syndrome 4:

31 (show all 11)
# Description HPO Frequency HPO Source Accession
1 cognitive impairment 31 occasional (7.5%) HP:0100543
2 microcephaly 31 HP:0000252
3 short stature 31 HP:0004322
4 intrauterine growth retardation 31 HP:0001511
5 retrognathia 31 HP:0000278
6 low-set ears 31 HP:0000369
7 high forehead 31 HP:0000348
8 decreased body weight 31 HP:0004325
9 underdeveloped nasal alae 31 HP:0000430
10 11 pairs of ribs 31 HP:0000878
11 steep acetabular roof 31 HP:0010455

Symptoms via clinical synopsis from OMIM®:

57 (Updated 20-May-2021)
Head And Neck Head:
microcephaly
high forehead

Head And Neck Ears:
low-set ears

Skeletal Pelvis:
steep acetabular roof

Growth Weight:
low weight

Growth Other:
intrauterine growth retardation (iugr)

Growth Height:
short stature

Chest Ribs Sternum Clavicles And Scapulae:
11 pairs of ribs

Head And Neck Nose:
hypoplastic alae nasi
prominent nasal spine

Head And Neck Mouth:
receding chin

Neurologic Central Nervous System:
intellectual impairment (rare)

Clinical features from OMIM®:

613676 (Updated 20-May-2021)

Drugs & Therapeutics for Seckel Syndrome 4

Search Clinical Trials , NIH Clinical Center for Seckel Syndrome 4

Genetic Tests for Seckel Syndrome 4

Genetic tests related to Seckel Syndrome 4:

# Genetic test Affiliating Genes
1 Seckel Syndrome 4 29 CENPJ

Anatomical Context for Seckel Syndrome 4

MalaCards organs/tissues related to Seckel Syndrome 4:

40
Eye, Brain

Publications for Seckel Syndrome 4

Articles related to Seckel Syndrome 4:

# Title Authors PMID Year
1
Novel CENPJ mutation causes Seckel syndrome. 57 6
20522431 2010
2
Disruption of mouse Cenpj, a regulator of centriole biogenesis, phenocopies Seckel syndrome. 61
23166506 2012
3
Primary Autosomal Recessive Microcephalies and Seckel Syndrome Spectrum Disorders – RETIRED CHAPTER, FOR HISTORICAL REFERENCE ONLY 61
20301772 2009

Variations for Seckel Syndrome 4

ClinVar genetic disease variations for Seckel Syndrome 4:

6 (show top 50) (show all 126)
# Gene Name Type Significance ClinVarId dbSNP ID Position
1 CENPJ , RNF17 NM_018451.5(CENPJ):c.3302-1G>C SNV Pathogenic 18417 rs864321658 GRCh37: 13:25459809-25459809
GRCh38: 13:24885671-24885671
2 CENPJ NM_018451.5(CENPJ):c.1339A>T (p.Lys447Ter) SNV Pathogenic 210655 rs797045447 GRCh37: 13:25480837-25480837
GRCh38: 13:24906699-24906699
3 CENPJ NM_018451.5(CENPJ):c.1850_1851del (p.Pro617fs) Deletion Pathogenic 210658 rs797045448 GRCh37: 13:25480325-25480326
GRCh38: 13:24906187-24906188
4 CENPJ NM_018451.5(CENPJ):c.898_899del (p.Glu300fs) Deletion Pathogenic 210670 rs797045454 GRCh37: 13:25482231-25482232
GRCh38: 13:24908093-24908094
5 CENPJ NM_018451.5(CENPJ):c.3007dup (p.Ile1003fs) Duplication Pathogenic 210665 rs797045452 GRCh37: 13:25466989-25466990
GRCh38: 13:24892851-24892852
6 CENPJ NM_018451.5(CENPJ):c.1404_1407del (p.Ser469fs) Deletion Pathogenic 210657 rs777893196 GRCh37: 13:25480769-25480772
GRCh38: 13:24906631-24906634
7 CENPJ NM_018451.5(CENPJ):c.1882del (p.Ala628fs) Deletion Pathogenic 210660 rs797045449 GRCh37: 13:25480294-25480294
GRCh38: 13:24906156-24906156
8 CENPJ NM_018451.5(CENPJ):c.1969C>T (p.Gln657Ter) SNV Pathogenic 210661 rs797045450 GRCh37: 13:25480207-25480207
GRCh38: 13:24906069-24906069
9 CENPJ NM_018451.5(CENPJ):c.2872C>T (p.Arg958Ter) SNV Pathogenic 432139 rs749343808 GRCh37: 13:25473676-25473676
GRCh38: 13:24899538-24899538
10 CENPJ NM_018451.5(CENPJ):c.1434del (p.Lys479fs) Deletion Pathogenic 1032801 GRCh37: 13:25480742-25480742
GRCh38: 13:24906604-24906604
11 CENPJ NM_018451.5(CENPJ):c.3268del (p.Glu1090fs) Deletion Pathogenic 1032803 GRCh37: 13:25463487-25463487
GRCh38: 13:24889349-24889349
12 CENPJ NM_018451.5(CENPJ):c.634G>T (p.Glu212Ter) SNV Pathogenic 620160 rs765113367 GRCh37: 13:25484159-25484159
GRCh38: 13:24910021-24910021
13 CENPJ , RNF17 NM_018451.5(CENPJ):c.3367-1G>A SNV Likely pathogenic 417856 rs763715733 GRCh37: 13:25459525-25459525
GRCh38: 13:24885387-24885387
14 CENPJ NM_018451.5(CENPJ):c.1586C>G (p.Ser529Ter) SNV Likely pathogenic 158194 rs202058504 GRCh37: 13:25480590-25480590
GRCh38: 13:24906452-24906452
15 CENPJ , RNF17 NM_018451.5(CENPJ):c.3495_3497dup (p.Lys1165dup) Duplication Likely pathogenic 210667 rs776528706 GRCh37: 13:25458581-25458582
GRCh38: 13:24884443-24884444
16 CENPJ NM_018451.5(CENPJ):c.1263G>C (p.Gln421His) SNV Likely pathogenic 210654 rs201088712 GRCh37: 13:25480913-25480913
GRCh38: 13:24906775-24906775
17 CENPJ , RNF17 NM_018451.5(CENPJ):c.3769C>A (p.Pro1257Thr) SNV Uncertain significance 311609 rs201774037 GRCh37: 13:25458156-25458156
GRCh38: 13:24884018-24884018
18 CENPJ NM_018451.5(CENPJ):c.1021T>G (p.Tyr341Asp) SNV Uncertain significance 210653 rs143258862 GRCh37: 13:25481285-25481285
GRCh38: 13:24907147-24907147
19 CENPJ , RNF17 NM_018451.5(CENPJ):c.*124G>A SNV Uncertain significance 311604 rs886050097 GRCh37: 13:25457191-25457191
GRCh38: 13:24883053-24883053
20 CENPJ NM_018451.5(CENPJ):c.1595C>T (p.Pro532Leu) SNV Uncertain significance 311622 rs371842504 GRCh37: 13:25480581-25480581
GRCh38: 13:24906443-24906443
21 CENPJ , RNF17 NM_018451.5(CENPJ):c.*779A>T SNV Uncertain significance 311586 rs183612636 GRCh37: 13:25456536-25456536
GRCh38: 13:24882398-24882398
22 CENPJ NM_018451.5(CENPJ):c.2150C>T (p.Ser717Leu) SNV Uncertain significance 311619 rs886050100 GRCh37: 13:25480026-25480026
GRCh38: 13:24905888-24905888
23 CENPJ NM_018451.5(CENPJ):c.3068G>A (p.Arg1023His) SNV Uncertain significance 311611 rs146950242 GRCh37: 13:25466929-25466929
GRCh38: 13:24892791-24892791
24 CENPJ NM_018451.5(CENPJ):c.195C>T (p.Phe65=) SNV Uncertain significance 311633 rs775969767 GRCh37: 13:25486969-25486969
GRCh38: 13:24912831-24912831
25 CENPJ , RNF17 NM_018451.5(CENPJ):c.*541T>C SNV Uncertain significance 311593 rs533142063 GRCh37: 13:25456774-25456774
GRCh38: 13:24882636-24882636
26 CENPJ NM_018451.5(CENPJ):c.659C>T (p.Ser220Leu) SNV Uncertain significance 311628 rs201219786 GRCh37: 13:25484134-25484134
GRCh38: 13:24909996-24909996
27 CENPJ NM_018451.5(CENPJ):c.1513G>A (p.Glu505Lys) SNV Uncertain significance 158193 rs145679691 GRCh37: 13:25480663-25480663
GRCh38: 13:24906525-24906525
28 CENPJ , RNF17 NM_018451.5(CENPJ):c.*292A>T SNV Uncertain significance 311602 rs886050095 GRCh37: 13:25457023-25457023
GRCh38: 13:24882885-24882885
29 CENPJ NM_018451.5(CENPJ):c.-148C>T SNV Uncertain significance 311635 rs376883999 GRCh37: 13:25496980-25496980
GRCh38: 13:24922842-24922842
30 CENPJ , RNF17 NM_018451.5(CENPJ):c.*303C>A SNV Uncertain significance 311600 rs886050094 GRCh37: 13:25457012-25457012
GRCh38: 13:24882874-24882874
31 CENPJ , RNF17 NM_018451.5(CENPJ):c.*569A>G SNV Uncertain significance 311592 rs544072060 GRCh37: 13:25456746-25456746
GRCh38: 13:24882608-24882608
32 CENPJ NM_018451.5(CENPJ):c.2826-6T>C SNV Uncertain significance 311615 rs886050099 GRCh37: 13:25473728-25473728
GRCh38: 13:24899590-24899590
33 CENPJ NM_018451.5(CENPJ):c.-24A>G SNV Uncertain significance 311634 rs780644943 GRCh37: 13:25487187-25487187
GRCh38: 13:24913049-24913049
34 CENPJ , RNF17 NM_018451.5(CENPJ):c.3618+7T>C SNV Uncertain significance 311610 rs769845659 GRCh37: 13:25458454-25458454
GRCh38: 13:24884316-24884316
35 CENPJ NM_018451.5(CENPJ):c.777G>T (p.Ala259=) SNV Uncertain significance 311625 rs748696673 GRCh37: 13:25484016-25484016
GRCh38: 13:24909878-24909878
36 CENPJ , RNF17 NM_018451.5(CENPJ):c.3920C>T (p.Thr1307Ile) SNV Uncertain significance 158214 rs144251950 GRCh37: 13:25457412-25457412
GRCh38: 13:24883274-24883274
37 CENPJ NM_018451.5(CENPJ):c.2432T>A (p.Val811Asp) SNV Uncertain significance 444313 rs151299406 GRCh37: 13:25479744-25479744
GRCh38: 13:24905606-24905606
38 CENPJ NM_018451.5(CENPJ):c.600G>T (p.Gln200His) SNV Uncertain significance 158216 rs200061825 GRCh37: 13:25484193-25484193
GRCh38: 13:24910055-24910055
39 CENPJ NM_018451.5(CENPJ):c.444+3A>G SNV Uncertain significance 158215 rs587783411 GRCh37: 13:25486717-25486717
GRCh38: 13:24912579-24912579
40 CENPJ , RNF17 NM_018451.5(CENPJ):c.3943G>C (p.Glu1315Gln) SNV Uncertain significance 311607 rs761333511 GRCh37: 13:25457389-25457389
GRCh38: 13:24883251-24883251
41 CENPJ , RNF17 NM_018451.5(CENPJ):c.*464A>G SNV Uncertain significance 311595 rs886050093 GRCh37: 13:25456851-25456851
GRCh38: 13:24882713-24882713
42 CENPJ NM_018451.5(CENPJ):c.504A>G (p.Leu168=) SNV Uncertain significance 311630 rs886050101 GRCh37: 13:25486148-25486148
GRCh38: 13:24912010-24912010
43 CENPJ , RNF17 NM_018451.5(CENPJ):c.*783C>T SNV Uncertain significance 311585 rs886050092 GRCh37: 13:25456532-25456532
GRCh38: 13:24882394-24882394
44 CENPJ , RNF17 NM_018451.5(CENPJ):c.3922G>A (p.Val1308Ile) SNV Uncertain significance 194776 rs140564566 GRCh37: 13:25457410-25457410
GRCh38: 13:24883272-24883272
45 CENPJ NM_018451.5(CENPJ):c.739A>G (p.Thr247Ala) SNV Uncertain significance 311626 rs770285570 GRCh37: 13:25484054-25484054
GRCh38: 13:24909916-24909916
46 CENPJ NM_018451.5(CENPJ):c.1934G>A (p.Arg645His) SNV Uncertain significance 311621 rs773079639 GRCh37: 13:25480242-25480242
GRCh38: 13:24906104-24906104
47 CENPJ , RNF17 NM_018451.5(CENPJ):c.3619-12G>T SNV Uncertain significance 261032 rs527997591 GRCh37: 13:25458395-25458395
GRCh38: 13:24884257-24884257
48 CENPJ NM_018451.5(CENPJ):c.1960G>A (p.Ala654Thr) SNV Uncertain significance 158198 rs140927921 GRCh37: 13:25480216-25480216
GRCh38: 13:24906078-24906078
49 CENPJ NM_018451.5(CENPJ):c.2785A>G (p.Lys929Glu) SNV Uncertain significance 311616 rs141844033 GRCh37: 13:25478104-25478104
GRCh38: 13:24903966-24903966
50 CENPJ , RNF17 NM_018451.5(CENPJ):c.3960C>T (p.Ser1320=) SNV Uncertain significance 311606 rs113239817 GRCh37: 13:25457372-25457372
GRCh38: 13:24883234-24883234

Expression for Seckel Syndrome 4

Search GEO for disease gene expression data for Seckel Syndrome 4.

Pathways for Seckel Syndrome 4

Pathways related to Seckel Syndrome 4 according to GeneCards Suite gene sharing:

# Super pathways Score Top Affiliating Genes
1
Show member pathways
12.39 RFC2 RBBP8 PCNT NUP85 MCPH1 CEP152
2
Show member pathways
11.98 PCNT CEP152 CENPJ CDK5RAP2

GO Terms for Seckel Syndrome 4

Cellular components related to Seckel Syndrome 4 according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 nucleoplasm GO:0005654 10.06 TTBK1 RFC2 RBBP8 NUP85 MCPH1 IRF4
2 microtubule organizing center GO:0005815 9.65 PCNT MCPH1 CEP152 CENPJ CDK5RAP2
3 microtubule GO:0005874 9.62 PCNT CENPJ CDK5RAP2 ASPM
4 cytoskeleton GO:0005856 9.56 PCNT NUP85 MCPH1 CNTLN CEP152 CENPJ
5 centriole GO:0005814 9.46 PCNT CNTLN CEP152 CENPJ
6 mitotic spindle pole GO:0097431 9.43 CDK5RAP2 ASPM
7 pericentriolar material GO:0000242 9.37 CEP152 CDK5RAP2
8 centrosome GO:0005813 9.1 PCNT CNTLN CEP152 CENPJ CDK5RAP2 ASPM

Biological processes related to Seckel Syndrome 4 according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 G2/M transition of mitotic cell cycle GO:0000086 9.56 PCNT CEP152 CENPJ CDK5RAP2
2 GPI anchor biosynthetic process GO:0006506 9.4 PGAP2 CWH43
3 establishment of mitotic spindle orientation GO:0000132 9.37 MCPH1 CDK5RAP2
4 centriole replication GO:0007099 9.33 CEP152 CENPJ CDK5RAP2
5 neuronal stem cell population maintenance GO:0097150 9.32 MCPH1 ASPM
6 ciliary basal body-plasma membrane docking GO:0097711 9.26 PCNT CEP152 CENPJ CDK5RAP2
7 regulation of G2/M transition of mitotic cell cycle GO:0010389 8.92 PCNT CEP152 CENPJ CDK5RAP2

Molecular functions related to Seckel Syndrome 4 according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 calmodulin binding GO:0005516 9.33 PCNT CDK5RAP2 ASPM
2 protein kinase binding GO:0019901 9.26 CNTLN CEP152 CENPJ CDK5RAP2
3 gamma-tubulin binding GO:0043015 8.62 CENPJ CDK5RAP2

Sources for Seckel Syndrome 4

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 20-May-2021)
61 PubMed
63 QIAGEN
68 SNOMED-CT via HPO
69 Tocris
70 UMLS
71 UMLS via Orphanet
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