MCPH3
MCID: MCR248
MIFTS: 39

Microcephaly 3, Primary, Autosomal Recessive (MCPH3)

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

Aliases & Classifications for Microcephaly 3, Primary, Autosomal Recessive

MalaCards integrated aliases for Microcephaly 3, Primary, Autosomal Recessive:

Name: Microcephaly 3, Primary, Autosomal Recessive 57 75 13
Primary Autosomal Recessive Microcephaly 3 12 29 6 15
Mcph3 57 12 75
Microcephaly, Primary Autosomal Recessive, 3 73

Characteristics:

OMIM:

57
Inheritance:
autosomal recessive


HPO:

32
microcephaly 3, primary, autosomal recessive:
Inheritance autosomal recessive inheritance


Classifications:



External Ids:

OMIM 57 604804
Disease Ontology 12 DOID:0070286
MedGen 42 C1858108
MeSH 44 D008831
UMLS 73 C1858108

Summaries for Microcephaly 3, Primary, Autosomal Recessive

UniProtKB/Swiss-Prot : 75 Microcephaly 3, primary, autosomal recessive: A disease defined as a head circumference more than 3 standard deviations below the age-related mean. Brain weight is markedly reduced and the cerebral cortex is disproportionately small. Despite this marked reduction in size, the gyral pattern is relatively well preserved, with no major abnormality in cortical architecture. Affected individuals are mentally retarded. Primary microcephaly is further defined by the absence of other syndromic features or significant neurological deficits due to degenerative brain disorder.

MalaCards based summary : Microcephaly 3, Primary, Autosomal Recessive, also known as primary autosomal recessive microcephaly 3, is related to microcephaly and primary microcephaly. An important gene associated with Microcephaly 3, Primary, Autosomal Recessive is CDK5RAP2 (CDK5 Regulatory Subunit Associated Protein 2), and among its related pathways/superpathways are Regulation of PLK1 Activity at G2/M Transition and Cell Cycle, Mitotic. Affiliated tissues include cortex, brain and eye, and related phenotypes are global developmental delay and microcephaly

Disease Ontology : 12 A primary autosomal recessive microcephaly that has material basis in homozygous or compound heterozygous mutation in the CDK5RAP2 gene on chromosome 9q33.

Description from OMIM: 604804

Related Diseases for Microcephaly 3, Primary, Autosomal Recessive

Diseases in the Microcephaly family:

Microcephaly, Autosomal Dominant Microcephaly 1, Primary, Autosomal Recessive
Microcephaly 4, Primary, Autosomal Recessive Microcephaly 3, Primary, Autosomal Recessive
Microcephaly 6, Primary, Autosomal Recessive Microcephaly 5, Primary, Autosomal Recessive
Microcephaly 7, Primary, Autosomal Recessive Microcephaly 8, Primary, Autosomal Recessive
Microcephaly 9, Primary, Autosomal Recessive Microcephaly 10, Primary, Autosomal Recessive
Microcephaly 11, Primary, Autosomal Recessive Microcephaly 13, Primary, Autosomal Recessive
Microcephaly 12, Primary, Autosomal Recessive Microcephaly 14, Primary, Autosomal Recessive
Microcephaly 15, Primary, Autosomal Recessive Microcephaly 16, Primary, Autosomal Recessive
Microcephaly 17, Primary, Autosomal Recessive Microcephaly 18, Primary, Autosomal Dominant
Microcephaly 19, Primary, Autosomal Recessive Microcephaly 20, Primary, Autosomal Recessive
Microcephaly 21, Primary, Autosomal Recessive Microcephaly 22, Primary, Autosomal Recessive
Microcephaly 23, Primary, Autosomal Recessive Primary Autosomal Recessive Microcephaly
Primary Microcephaly

Diseases related to Microcephaly 3, Primary, Autosomal Recessive via text searches within MalaCards or GeneCards Suite gene sharing:

(show all 22)
# Related Disease Score Top Affiliating Genes
1 microcephaly 29.6 CDK5RAP2 CENPJ CEP152 CEP63 MCPH1 PNKP
2 primary microcephaly 29.6 CDK5RAP2 CENPJ CEP152 CEP63 MCPH1 PNKP
3 seckel syndrome 5 10.0 CENPJ CEP152
4 microcephaly 8, primary, autosomal recessive 10.0 CEP63 CNTLN
5 seckel syndrome 1 10.0 CENPJ CEP152
6 seckel syndrome 2 9.9 CENPJ CEP152
7 seckel syndrome 4 9.9 CENPJ CNTLN
8 meier-gorlin syndrome 1 9.9 CEP152 CEP63
9 corneal dystrophy, meesmann 9.9 CEP152 CNTLN
10 microcephalic osteodysplastic primordial dwarfism, type ii 9.8 CDK5RAP2 CENPJ CNTLN
11 physical disorder 9.8 CDK5RAP2 CENPJ CEP63 MCPH1
12 primary autosomal recessive microcephaly 9.8 CDK5RAP2 CENPJ CEP152 MCPH1
13 microcephaly 12, primary, autosomal recessive 9.7 CDK5RAP2 CENPJ CEP152 CEP63 MCPH1
14 microcephaly 18, primary, autosomal dominant 9.7 CDK5RAP2 CENPJ CEP152 CEP63 MCPH1
15 congenital nervous system abnormality 9.7 CDK5RAP2 CENPJ CEP152 CEP63 MCPH1
16 seckel syndrome 9.5 CENPJ CEP152 CEP63 CNTLN MCPH1
17 microcephaly 6, primary, autosomal recessive 9.5 CDK5RAP2 CENPJ CEP152 CEP63 CNTLN MCPH1
18 microcephaly 4, primary, autosomal recessive 9.4 CDK5RAP2 CENPJ CEP152 CEP63 CNTLN MCPH1
19 microcephaly 2, primary, autosomal recessive, with or without cortical malformations 9.4 CDK5RAP2 CENPJ CEP152 CEP63 CNTLN MCPH1
20 microcephaly 5, primary, autosomal recessive 9.4 CDK5RAP2 CENPJ CEP152 CEP63 CNTLN MCPH1
21 microcephaly 7, primary, autosomal recessive 9.4 CDK5RAP2 CENPJ CEP152 CEP63 CNTLN MCPH1
22 microcephaly 17, primary, autosomal recessive 9.2 CDK5 CDK5RAP2 CENPJ CEP152 CEP63 MCPH1

Graphical network of the top 20 diseases related to Microcephaly 3, Primary, Autosomal Recessive:



Diseases related to Microcephaly 3, Primary, Autosomal Recessive

Symptoms & Phenotypes for Microcephaly 3, Primary, Autosomal Recessive

Symptoms via clinical synopsis from OMIM:

57
Head And Neck Head:
sloping forehead
microcephaly, severe (-4 to -8 sds)

Head And Neck Ears:
hearing loss, sensorineural (in some patients)

Head And Neck Teeth:
conical-shaped teeth (in one patient)

Neurologic Central Nervous System:
developmental delay
mental retardation, mild to moderate
small but structurally normal cerebral cortex
simplified gyral pattern (in one patient)
small frontal lobes (in one patient)
more
Head And Neck Eyes:
prominent eyes (in one patient)


Clinical features from OMIM:

604804

Human phenotypes related to Microcephaly 3, Primary, Autosomal Recessive:

32 (show all 8)
# Description HPO Frequency HPO Source Accession
1 global developmental delay 32 HP:0001263
2 microcephaly 32 HP:0000252
3 sensorineural hearing impairment 32 occasional (7.5%) HP:0000407
4 intellectual disability, moderate 32 HP:0002342
5 proptosis 32 occasional (7.5%) HP:0000520
6 sloping forehead 32 HP:0000340
7 small cerebral cortex 32 HP:0002472
8 cortical gyral simplification 32 occasional (7.5%) HP:0009879

GenomeRNAi Phenotypes related to Microcephaly 3, Primary, Autosomal Recessive according to GeneCards Suite gene sharing:

26
# Description GenomeRNAi Source Accession Score Top Affiliating Genes
1 Decreased viability with poly (ADPa89ribose)a89polymerasea891 (PARP) inhibitor GR00114-A 8.62 CDK5 PNKP

MGI Mouse Phenotypes related to Microcephaly 3, Primary, Autosomal Recessive:

46
# Description MGI Source Accession Score Top Affiliating Genes
1 cellular MP:0005384 9.5 BIRC5 CDK5RAP2 CENPJ CEP152 CEP63 MCPH1
2 nervous system MP:0003631 9.17 CDK5 CDK5RAP2 CENPJ CEP152 CEP63 MCPH1

Drugs & Therapeutics for Microcephaly 3, Primary, Autosomal Recessive

Search Clinical Trials , NIH Clinical Center for Microcephaly 3, Primary, Autosomal Recessive

Genetic Tests for Microcephaly 3, Primary, Autosomal Recessive

Genetic tests related to Microcephaly 3, Primary, Autosomal Recessive:

# Genetic test Affiliating Genes
1 Primary Autosomal Recessive Microcephaly 3 29 CDK5RAP2

Anatomical Context for Microcephaly 3, Primary, Autosomal Recessive

MalaCards organs/tissues related to Microcephaly 3, Primary, Autosomal Recessive:

41
Cortex, Brain, Eye

Publications for Microcephaly 3, Primary, Autosomal Recessive

Variations for Microcephaly 3, Primary, Autosomal Recessive

ClinVar genetic disease variations for Microcephaly 3, Primary, Autosomal Recessive:

6 (show top 50) (show all 124)
# Gene Variation Type Significance SNP ID Assembly Location
1 CDK5RAP2 NM_018249.5(CDK5RAP2): c.246T> A (p.Tyr82Ter) single nucleotide variant Pathogenic rs199422126 GRCh37 Chromosome 9, 123313130: 123313130
2 CDK5RAP2 NM_018249.5(CDK5RAP2): c.246T> A (p.Tyr82Ter) single nucleotide variant Pathogenic rs199422126 GRCh38 Chromosome 9, 120550852: 120550852
3 CDK5RAP2 NM_018249.5(CDK5RAP2): c.4005-15A> G single nucleotide variant Pathogenic rs387906274 GRCh37 Chromosome 9, 123182253: 123182253
4 CDK5RAP2 NM_018249.5(CDK5RAP2): c.4005-15A> G single nucleotide variant Pathogenic rs387906274 GRCh38 Chromosome 9, 120419975: 120419975
5 CDK5RAP2 NM_018249.5(CDK5RAP2): c.1712T> C (p.Leu571Pro) single nucleotide variant Benign rs41296081 GRCh37 Chromosome 9, 123239643: 123239643
6 CDK5RAP2 NM_018249.5(CDK5RAP2): c.1712T> C (p.Leu571Pro) single nucleotide variant Benign rs41296081 GRCh38 Chromosome 9, 120477365: 120477365
7 CDK5RAP2 NM_018249.5(CDK5RAP2): c.2599G> A (p.Gly867Arg) single nucleotide variant Benign rs10984919 GRCh37 Chromosome 9, 123215928: 123215928
8 CDK5RAP2 NM_018249.5(CDK5RAP2): c.2599G> A (p.Gly867Arg) single nucleotide variant Benign rs10984919 GRCh38 Chromosome 9, 120453650: 120453650
9 CDK5RAP2 NM_018249.5(CDK5RAP2): c.3065G> A (p.Gly1022Glu) single nucleotide variant Benign rs34523498 GRCh37 Chromosome 9, 123205981: 123205981
10 CDK5RAP2 NM_018249.5(CDK5RAP2): c.3065G> A (p.Gly1022Glu) single nucleotide variant Benign rs34523498 GRCh38 Chromosome 9, 120443703: 120443703
11 CDK5RAP2 NM_018249.5(CDK5RAP2): c.3134G> C (p.Arg1045Thr) single nucleotide variant Benign/Likely benign rs3780679 GRCh37 Chromosome 9, 123205912: 123205912
12 CDK5RAP2 NM_018249.5(CDK5RAP2): c.3134G> C (p.Arg1045Thr) single nucleotide variant Benign/Likely benign rs3780679 GRCh38 Chromosome 9, 120443634: 120443634
13 CDK5RAP2 NM_018249.5(CDK5RAP2): c.3989A> T (p.Asn1330Ile) single nucleotide variant Benign rs7875294 GRCh37 Chromosome 9, 123184986: 123184986
14 CDK5RAP2 NM_018249.5(CDK5RAP2): c.3989A> T (p.Asn1330Ile) single nucleotide variant Benign rs7875294 GRCh38 Chromosome 9, 120422708: 120422708
15 CDK5RAP2 NM_018249.5(CDK5RAP2): c.409G> T (p.Ala137Ser) single nucleotide variant Benign rs41302645 GRCh37 Chromosome 9, 123301417: 123301417
16 CDK5RAP2 NM_018249.5(CDK5RAP2): c.409G> T (p.Ala137Ser) single nucleotide variant Benign rs41302645 GRCh38 Chromosome 9, 120539139: 120539139
17 CDK5RAP2 NM_018249.5(CDK5RAP2): c.4103C> T (p.Ser1368Phe) single nucleotide variant Benign rs41309342 GRCh37 Chromosome 9, 123182140: 123182140
18 CDK5RAP2 NM_018249.5(CDK5RAP2): c.4103C> T (p.Ser1368Phe) single nucleotide variant Benign rs41309342 GRCh38 Chromosome 9, 120419862: 120419862
19 CDK5RAP2 NM_018249.5(CDK5RAP2): c.4547A> G (p.Glu1516Gly) single nucleotide variant Benign rs3210500 GRCh37 Chromosome 9, 123171462: 123171462
20 CDK5RAP2 NM_018249.5(CDK5RAP2): c.4547A> G (p.Glu1516Gly) single nucleotide variant Benign rs3210500 GRCh38 Chromosome 9, 120409184: 120409184
21 CDK5RAP2 NM_018249.5(CDK5RAP2): c.4618G> C (p.Val1540Leu) single nucleotide variant Benign rs4837768 GRCh37 Chromosome 9, 123170733: 123170733
22 CDK5RAP2 NM_018249.5(CDK5RAP2): c.4618G> C (p.Val1540Leu) single nucleotide variant Benign rs4837768 GRCh38 Chromosome 9, 120408455: 120408455
23 CDK5RAP2 NM_018249.5(CDK5RAP2): c.4665G> T (p.Gln1555His) single nucleotide variant Benign/Likely benign rs35909061 GRCh37 Chromosome 9, 123170686: 123170686
24 CDK5RAP2 NM_018249.5(CDK5RAP2): c.4665G> T (p.Gln1555His) single nucleotide variant Benign/Likely benign rs35909061 GRCh38 Chromosome 9, 120408408: 120408408
25 CDK5RAP2 NM_018249.5(CDK5RAP2): c.546T> G (p.Phe182Leu) single nucleotide variant Benign rs13287599 GRCh37 Chromosome 9, 123298766: 123298766
26 CDK5RAP2 NM_018249.5(CDK5RAP2): c.546T> G (p.Phe182Leu) single nucleotide variant Benign rs13287599 GRCh38 Chromosome 9, 120536488: 120536488
27 CDK5RAP2 NM_018249.5(CDK5RAP2): c.547G> C (p.Ala183Pro) single nucleotide variant Uncertain significance rs13287734 GRCh37 Chromosome 9, 123298765: 123298765
28 CDK5RAP2 NM_018249.5(CDK5RAP2): c.547G> C (p.Ala183Pro) single nucleotide variant Uncertain significance rs13287734 GRCh38 Chromosome 9, 120536487: 120536487
29 CDK5RAP2 NM_018249.5(CDK5RAP2): c.569C> T (p.Ala190Val) single nucleotide variant Benign rs13287876 GRCh37 Chromosome 9, 123298743: 123298743
30 CDK5RAP2 NM_018249.5(CDK5RAP2): c.569C> T (p.Ala190Val) single nucleotide variant Benign rs13287876 GRCh38 Chromosome 9, 120536465: 120536465
31 CDK5RAP2 NM_018249.5(CDK5RAP2): c.764C> T (p.Ser255Leu) single nucleotide variant Uncertain significance rs35199933 GRCh37 Chromosome 9, 123292317: 123292317
32 CDK5RAP2 NM_018249.5(CDK5RAP2): c.764C> T (p.Ser255Leu) single nucleotide variant Uncertain significance rs35199933 GRCh38 Chromosome 9, 120530039: 120530039
33 CDK5RAP2 NM_018249.5(CDK5RAP2): c.865G> C (p.Glu289Gln) single nucleotide variant Benign rs4836822 GRCh37 Chromosome 9, 123291036: 123291036
34 CDK5RAP2 NM_018249.5(CDK5RAP2): c.865G> C (p.Glu289Gln) single nucleotide variant Benign rs4836822 GRCh38 Chromosome 9, 120528758: 120528758
35 CDK5RAP2 NM_018249.5(CDK5RAP2): c.91G> A (p.Asp31Asn) single nucleotide variant Benign rs58961732 GRCh37 Chromosome 9, 123334288: 123334288
36 CDK5RAP2 NM_018249.5(CDK5RAP2): c.91G> A (p.Asp31Asn) single nucleotide variant Benign rs58961732 GRCh38 Chromosome 9, 120572010: 120572010
37 CDK5RAP2 NM_018249.5(CDK5RAP2): c.700G> T (p.Glu234Ter) single nucleotide variant Pathogenic rs398122971 GRCh37 Chromosome 9, 123292381: 123292381
38 CDK5RAP2 NM_018249.5(CDK5RAP2): c.700G> T (p.Glu234Ter) single nucleotide variant Pathogenic rs398122971 GRCh38 Chromosome 9, 120530103: 120530103
39 CDK5RAP2 NM_018249.5(CDK5RAP2): c.4546G> T (p.Glu1516Ter) single nucleotide variant Pathogenic rs374351172 GRCh37 Chromosome 9, 123171463: 123171463
40 CDK5RAP2 NM_018249.5(CDK5RAP2): c.4546G> T (p.Glu1516Ter) single nucleotide variant Pathogenic rs374351172 GRCh38 Chromosome 9, 120409185: 120409185
41 CDK5RAP2 NM_018249.5(CDK5RAP2): c.4672C> T (p.Arg1558Ter) single nucleotide variant Pathogenic rs373278668 GRCh37 Chromosome 9, 123170679: 123170679
42 CDK5RAP2 NM_018249.5(CDK5RAP2): c.4672C> T (p.Arg1558Ter) single nucleotide variant Pathogenic rs373278668 GRCh38 Chromosome 9, 120408401: 120408401
43 CDK5RAP2 NM_018249.5(CDK5RAP2): c.-19T> C single nucleotide variant Benign rs932974 GRCh37 Chromosome 9, 123342275: 123342275
44 CDK5RAP2 NM_018249.5(CDK5RAP2): c.-19T> C single nucleotide variant Benign rs932974 GRCh38 Chromosome 9, 120579997: 120579997
45 CDK5RAP2 NM_018249.5(CDK5RAP2): c.-3G> T single nucleotide variant Benign rs932975 GRCh37 Chromosome 9, 123342259: 123342259
46 CDK5RAP2 NM_018249.5(CDK5RAP2): c.-3G> T single nucleotide variant Benign rs932975 GRCh38 Chromosome 9, 120579981: 120579981
47 CDK5RAP2 NM_018249.5(CDK5RAP2): c.524_528delAGGCA (p.Gln175Argfs) deletion Pathogenic rs587783393 GRCh37 Chromosome 9, 123298784: 123298788
48 CDK5RAP2 NM_018249.5(CDK5RAP2): c.524_528delAGGCA (p.Gln175Argfs) deletion Pathogenic rs587783393 GRCh38 Chromosome 9, 120536506: 120536510
49 CDK5RAP2 NM_018249.5(CDK5RAP2): c.2274T> C (p.Asp758=) single nucleotide variant Benign/Likely benign rs2501727 GRCh37 Chromosome 9, 123220829: 123220829
50 CDK5RAP2 NM_018249.5(CDK5RAP2): c.2274T> C (p.Asp758=) single nucleotide variant Benign/Likely benign rs2501727 GRCh38 Chromosome 9, 120458551: 120458551

Expression for Microcephaly 3, Primary, Autosomal Recessive

Search GEO for disease gene expression data for Microcephaly 3, Primary, Autosomal Recessive.

Pathways for Microcephaly 3, Primary, Autosomal Recessive

GO Terms for Microcephaly 3, Primary, Autosomal Recessive

Cellular components related to Microcephaly 3, Primary, Autosomal Recessive according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 nucleoplasm GO:0005654 9.91 BIRC5 CDK5 CENPJ CEP152 CNTLN MCPH1
2 centrosome GO:0005813 9.65 CDK5RAP2 CENPJ CEP152 CEP63 CNTLN
3 microtubule GO:0005874 9.62 BIRC5 CDK5 CDK5RAP2 CENPJ
4 microtubule organizing center GO:0005815 9.55 CDK5RAP2 CENPJ CEP152 CEP63 MCPH1
5 pericentriolar material GO:0000242 9.4 CDK5RAP2 CEP152
6 centriole GO:0005814 9.26 CENPJ CEP152 CEP63 CNTLN
7 cytoskeleton GO:0005856 9.23 BIRC5 CDK5 CDK5RAP2 CENPJ CEP152 CEP63
8 cytoplasm GO:0005737 10.03 BIRC5 CDK5 CDK5RAP2 CENPJ CEP152 CEP63
9 cytosol GO:0005829 10 BIRC5 CDK5 CDK5RAP2 CENPJ CEP152 CEP63

Biological processes related to Microcephaly 3, Primary, Autosomal Recessive according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 cell division GO:0051301 9.67 BIRC5 CDK5 CENPJ CEP63
2 G2/M transition of mitotic cell cycle GO:0000086 9.56 CDK5RAP2 CENPJ CEP152 CEP63
3 chromosome segregation GO:0007059 9.48 BIRC5 CDK5RAP2
4 cerebral cortex development GO:0021987 9.46 CDK5 MCPH1
5 ciliary basal body-plasma membrane docking GO:0097711 9.46 CDK5RAP2 CENPJ CEP152 CEP63
6 establishment of mitotic spindle orientation GO:0000132 9.43 CDK5RAP2 MCPH1
7 centrosome duplication GO:0051298 9.4 CENPJ CEP152
8 de novo centriole assembly involved in multi-ciliated epithelial cell differentiation GO:0098535 9.32 CEP152 CEP63
9 regulation of G2/M transition of mitotic cell cycle GO:0010389 9.26 CDK5RAP2 CENPJ CEP152 CEP63
10 centriole replication GO:0007099 8.92 CDK5RAP2 CENPJ CEP152 CEP63

Molecular functions related to Microcephaly 3, Primary, Autosomal Recessive according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 tubulin binding GO:0015631 9.16 CDK5RAP2 CENPJ
2 microtubule binding GO:0008017 9.13 BIRC5 CDK5 CDK5RAP2
3 protein kinase binding GO:0019901 9.02 CDK5 CDK5RAP2 CENPJ CEP152 CNTLN

Sources for Microcephaly 3, Primary, Autosomal Recessive

3 CDC
7 CNVD
9 Cosmic
10 dbSNP
11 DGIdb
17 ExPASy
19 FMA
28 GO
29 GTR
30 HGMD
31 HMDB
32 HPO
33 ICD10
34 ICD10 via Orphanet
35 ICD9CM
36 IUPHAR
37 KEGG
38 LifeMap
40 LOVD
42 MedGen
44 MeSH
45 MESH via Orphanet
46 MGI
49 NCI
50 NCIt
51 NDF-RT
54 NINDS
55 Novoseek
57 OMIM
58 OMIM via Orphanet
62 PubMed
64 QIAGEN
69 SNOMED-CT via HPO
70 SNOMED-CT via Orphanet
71 TGDB
72 Tocris
73 UMLS
74 UMLS via Orphanet
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