MCID: RHZ014
MIFTS: 45

Rhizomelic Chondrodysplasia Punctata, Type 2

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

Aliases & Classifications for Rhizomelic Chondrodysplasia Punctata, Type 2

MalaCards integrated aliases for Rhizomelic Chondrodysplasia Punctata, Type 2:

Name: Rhizomelic Chondrodysplasia Punctata, Type 2 57 75 73
Rhizomelic Chondrodysplasia Punctata Type 2 12 53 59 29 6 15
Dihydroxyacetonephosphate Acyltransferase Deficiency 57 12 53 75 55
Peroxisomal Dihydroxyacetonephosphate Acyltransferase Deficiency 57 12 53 75
Dhapat Deficiency 57 12 53 75
Rcdp2 57 12 53 75
Chondrodysplasia Punctata, Rhizomelic, Due to Dihydroxyacetonephosphate Acyltransferase Deficiency 57 12 75
Glyceronephosphate O-Acyltransferase Deficiency 57 12 75
Gnpat Deficiency 57 12 75
Chondrodysplasia Punctata, Rhizomelic, Type 2 13 40
Chondrodysplasia Punctata, Rhizomelic, Due to Dihydroxyacetonephosphate 53
Type 2 Rhizomelic Chondrodysplasia Punctata 53
Rhizomelic Chondrodysplasia Punctata 2 75
Glyceronephosphate O-Acyltransferase 13

Characteristics:

OMIM:

57
Inheritance:
autosomal recessive


HPO:

32
rhizomelic chondrodysplasia punctata, type 2:
Inheritance autosomal recessive inheritance


Classifications:



Summaries for Rhizomelic Chondrodysplasia Punctata, Type 2

OMIM : 57 Rhizomelic chondrodysplasia punctata (RCDP) is a peroxisomal disorder characterized by disproportionately short stature primarily affecting the proximal parts of the extremities, a typical facial appearance including a broad nasal bridge, epicanthus, high-arched palate, dysplastic external ears, and micrognathia, congenital contractures, characteristic ocular involvement, dwarfism, and severe mental retardation with spasticity. Biochemically, plasmalogen synthesis and phytanic acid alpha-oxidation are defective. Most patients die in the first decade of life. RCDP1 (215100) is the most frequent form of RCDP (summary by Wanders and Waterham, 2005). Whereas RCDP1 is a peroxisomal biogenesis disorder (PBD), RCDP2 is classified as a single peroxisome enzyme deficiency (Waterham and Ebberink, 2012). For a discussion of genetic heterogeneity of rhizomelic chondrodysplasia punctata, see 215100. (222765)

MalaCards based summary : Rhizomelic Chondrodysplasia Punctata, Type 2, also known as rhizomelic chondrodysplasia punctata type 2, is related to chondrodysplasia punctata syndrome and rhizomelic chondrodysplasia punctata. An important gene associated with Rhizomelic Chondrodysplasia Punctata, Type 2 is GNPAT (Glyceronephosphate O-Acyltransferase), and among its related pathways/superpathways are Peroxisome and Peroxisomal lipid metabolism. Affiliated tissues include bone and eye, and related phenotypes are high palate and osteopenia

Disease Ontology : 12 A rhizomelic chondrodysplasia punctata that has material basis in autosomal recessive inheritance of homozygous or compound heterozygous mutation in the GNPAT gene on chromosome 1q42.2.

UniProtKB/Swiss-Prot : 75 Rhizomelic chondrodysplasia punctata 2: A form of rhizomelic chondrodysplasia punctata, a disease characterized by severely disturbed endochondral bone formation, rhizomelic shortening of femur and humerus, vertebral disorders, dwarfism, cataract, cutaneous lesions, facial dysmorphism, and severe mental retardation with spasticity.

Related Diseases for Rhizomelic Chondrodysplasia Punctata, Type 2

Diseases in the Rhizomelic Chondrodysplasia Punctata family:

Rhizomelic Chondrodysplasia Punctata, Type 1 Rhizomelic Chondrodysplasia Punctata, Type 2
Rhizomelic Chondrodysplasia Punctata, Type 3 Rhizomelic Chondrodysplasia Punctata, Type 5

Diseases related to Rhizomelic Chondrodysplasia Punctata, Type 2 via text searches within MalaCards or GeneCards Suite gene sharing:

(show all 26)
# Related Disease Score Top Affiliating Genes
1 chondrodysplasia punctata syndrome 31.2 GNPAT PEX5 PEX7
2 rhizomelic chondrodysplasia punctata 30.3 AGPS GNPAT PEX5 PEX7 PHYH
3 familial porphyria cutanea tarda 30.1 HFE UROD
4 porphyria cutanea tarda 29.2 HAMP HFE UROD
5 mulibrey nanism 10.5 PEX5 PEX7
6 zellweger syndrome 10.4 AGPS GNPAT PEX5
7 porphyria 10.2
8 peroxisomal acyl-coa oxidase deficiency 10.1 CAT PEX5
9 d-bifunctional protein deficiency 10.0 CAT PEX5
10 neonatal adrenoleukodystrophy 9.9 CAT PEX5 PEX7
11 porphyria cutanea tarda, type i 9.9 HFE UROD
12 rhizomelic chondrodysplasia punctata, type 3 9.8 AGPS GNPAT PEX5 PEX7 UROD
13 acute porphyria 9.7 HFE UROD
14 hemochromatosis type 2 9.7 HAMP HFE
15 porphyria variegata 9.6 HFE UROD
16 peroxisomal biogenesis disorders 9.5 CAT PEX5 PEX7 PHEX
17 siderosis 9.4 HFE UROD
18 refsum disease, classic 9.4 CAT GNPAT PEX5 PEX7 PHYH
19 metal metabolism disorder 9.3 HAMP HFE
20 hemochromatosis, type 1 9.2 HAMP HFE UROD
21 peroxisomal disease 9.2 AGPS CAT GNPAT PEX5 PEX7 PHYH
22 hemosiderosis 9.0 HAMP HFE
23 peroxisome biogenesis disorder 1b 8.9 CAT GNPAT PEX5 PEX7 PHEX PHYH
24 deficiency anemia 8.9 CAT HAMP HFE
25 rhizomelic chondrodysplasia punctata, type 5 8.8 AGPS FAR1 GNPAT PEX5 PEX5L PEX7
26 rhizomelic chondrodysplasia punctata, type 1 7.7 AGPS FAR1 GNPAT PEX5 PEX5L PEX7

Graphical network of the top 20 diseases related to Rhizomelic Chondrodysplasia Punctata, Type 2:



Diseases related to Rhizomelic Chondrodysplasia Punctata, Type 2

Symptoms & Phenotypes for Rhizomelic Chondrodysplasia Punctata, Type 2

Symptoms via clinical synopsis from OMIM:

57
Skeletal:
osteopenia
contractures
calcific stippling

Skeletal Spine:
scoliosis
irregular vertebral endplates

Head And Neck Head:
microcephaly
large fontanelles

Head And Neck Nose:
broad nasal bridge
anteverted nostrils
low nasal bridge

Skeletal Limbs:
rhizomelic shortening
short humeri
short femora

Growth Height:
short stature, disproportionate

Laboratory Abnormalities:
decreased plasmalogens
normal phytanic acid
decreased dihydroxyacetonephosphate acyltransferase (dhap-at) activity

Growth Other:
failure to thrive

Head And Neck Eyes:
cataract

Head And Neck Face:
micrognathia
high forehead

Neurologic Central Nervous System:
hypotonia
mental retardation

Head And Neck Mouth:
high-arched palate

Skeletal Pelvis:
stippled calcification proximal humeral epiphyses


Clinical features from OMIM:

222765

Human phenotypes related to Rhizomelic Chondrodysplasia Punctata, Type 2:

32 (show all 22)
# Description HPO Frequency HPO Source Accession
1 high palate 32 HP:0000218
2 osteopenia 32 HP:0000938
3 intellectual disability 32 HP:0001249
4 muscular hypotonia 32 HP:0001252
5 failure to thrive 32 HP:0001508
6 scoliosis 32 HP:0002650
7 cataract 32 HP:0000518
8 depressed nasal bridge 32 HP:0005280
9 wide nasal bridge 32 HP:0000431
10 microcephaly 32 HP:0000252
11 anteverted nares 32 HP:0000463
12 flexion contracture 32 HP:0001371
13 micrognathia 32 HP:0000347
14 rhizomelia 32 HP:0008905
15 high forehead 32 HP:0000348
16 abnormality of pelvic girdle bone morphology 32 HP:0002644
17 large fontanelles 32 HP:0000239
18 generalized hypotonia 32 HP:0001290
19 short humerus 32 HP:0005792
20 irregular vertebral endplates 32 HP:0003301
21 calcific stippling 32 HP:0002832
22 stippled calcification proximal humeral epiphyses 32 HP:0008838

MGI Mouse Phenotypes related to Rhizomelic Chondrodysplasia Punctata, Type 2:

46
# Description MGI Source Accession Score Top Affiliating Genes
1 behavior/neurological MP:0005386 10.13 PEX5 PEX5L PEX7 PHEX PHYH PLP1
2 homeostasis/metabolism MP:0005376 10.13 AGPS C3 CAT CTSC GNPAT HFE
3 growth/size/body region MP:0005378 10.07 C3 CTSC GNPAT HFE NTS PEX5
4 cellular MP:0005384 10.06 C3 CAT CTSC GNPAT HFE PEX5
5 mortality/aging MP:0010768 9.85 AGPS C3 CAT GNPAT HFE PEX5
6 liver/biliary system MP:0005370 9.73 C3 HFE PEX5 PEX7 PHYH UROD
7 nervous system MP:0003631 9.7 C3 CTSC GNPAT HFE NTS PEX5
8 reproductive system MP:0005389 9.17 AGPS C3 GNPAT PEX5 PEX7 PHYH

Drugs & Therapeutics for Rhizomelic Chondrodysplasia Punctata, Type 2

Search Clinical Trials , NIH Clinical Center for Rhizomelic Chondrodysplasia Punctata, Type 2

Genetic Tests for Rhizomelic Chondrodysplasia Punctata, Type 2

Genetic tests related to Rhizomelic Chondrodysplasia Punctata, Type 2:

# Genetic test Affiliating Genes
1 Rhizomelic Chondrodysplasia Punctata Type 2 29 GNPAT

Anatomical Context for Rhizomelic Chondrodysplasia Punctata, Type 2

MalaCards organs/tissues related to Rhizomelic Chondrodysplasia Punctata, Type 2:

41
Bone, Eye

Publications for Rhizomelic Chondrodysplasia Punctata, Type 2

Articles related to Rhizomelic Chondrodysplasia Punctata, Type 2:

# Title Authors Year
1
Abnormal myelin formation in rhizomelic chondrodysplasia punctata type 2 (DHAPAT-deficiency). ( 10972423 )
2000
2
Acyl-CoA:dihydroxyacetonephosphate acyltransferase: cloning of the human cDNA and resolution of the molecular basis in rhizomelic chondrodysplasia punctata type 2. ( 9536089 )
1998

Variations for Rhizomelic Chondrodysplasia Punctata, Type 2

UniProtKB/Swiss-Prot genetic disease variations for Rhizomelic Chondrodysplasia Punctata, Type 2:

75
# Symbol AA change Variation ID SNP ID
1 GNPAT p.Arg211Cys VAR_006357 rs121434440
2 GNPAT p.Arg211His VAR_006358 rs121434439
3 GNPAT p.Asp519Gly VAR_025897 rs11558492

ClinVar genetic disease variations for Rhizomelic Chondrodysplasia Punctata, Type 2:

6
# Gene Variation Type Significance SNP ID Assembly Location
1 GNPAT NM_014236.3(GNPAT): c.632G> A (p.Arg211His) single nucleotide variant Pathogenic rs121434439 GRCh37 Chromosome 1, 231401102: 231401102
2 GNPAT NM_014236.3(GNPAT): c.632G> A (p.Arg211His) single nucleotide variant Pathogenic rs121434439 GRCh38 Chromosome 1, 231265356: 231265356
3 GNPAT NM_014236.3(GNPAT): c.631C> T (p.Arg211Cys) single nucleotide variant Pathogenic rs121434440 GRCh37 Chromosome 1, 231401101: 231401101
4 GNPAT NM_014236.3(GNPAT): c.631C> T (p.Arg211Cys) single nucleotide variant Pathogenic rs121434440 GRCh38 Chromosome 1, 231265355: 231265355
5 GNPAT GNPAT, 2-BP INS, 848TT insertion Pathogenic
6 GNPAT GNPAT, 1-BP DEL, NT780 deletion Pathogenic
7 GNPAT GNPAT, 1-BP DEL, NT1575 deletion Pathogenic
8 GNPAT GNPAT, IVS9AS, T-G, -3 single nucleotide variant Pathogenic
9 GNPAT GNPAT, 2-BP DEL, 1429AT deletion Pathogenic
10 GNPAT GNPAT, IVS14DS, G-A, +5 single nucleotide variant Pathogenic

Expression for Rhizomelic Chondrodysplasia Punctata, Type 2

Search GEO for disease gene expression data for Rhizomelic Chondrodysplasia Punctata, Type 2.

Pathways for Rhizomelic Chondrodysplasia Punctata, Type 2

Pathways related to Rhizomelic Chondrodysplasia Punctata, Type 2 according to GeneCards Suite gene sharing:

# Super pathways Score Top Affiliating Genes
1 11.14 AGPS CAT FAR1 GNPAT PEX5 PEX5L
2
Show member pathways
10.86 AGPS GNPAT PHYH
3
Show member pathways
10.62 AGPS GNPAT
4 10 HAMP HFE

GO Terms for Rhizomelic Chondrodysplasia Punctata, Type 2

Cellular components related to Rhizomelic Chondrodysplasia Punctata, Type 2 according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 peroxisomal membrane GO:0005778 9.63 AGPS CAT FAR1 GNPAT PEX5 PEX5L
2 peroxisome GO:0005777 9.5 AGPS CAT FAR1 GNPAT PEX5 PEX7
3 peroxisomal matrix GO:0005782 9.1 AGPS CAT FAR1 GNPAT PEX7 PHYH

Biological processes related to Rhizomelic Chondrodysplasia Punctata, Type 2 according to GeneCards Suite gene sharing:

(show all 14)
# Name GO ID Score Top Affiliating Genes
1 aging GO:0007568 9.69 CAT CTSC HAMP
2 fatty acid metabolic process GO:0006631 9.67 C3 GNPAT PHYH
3 acute-phase response GO:0006953 9.54 HAMP HFE
4 liver regeneration GO:0097421 9.52 HAMP HFE
5 peroxisome organization GO:0007031 9.48 PEX5 PEX7
6 response to vitamin A GO:0033189 9.46 CAT HAMP
7 cellular lipid metabolic process GO:0044255 9.43 GNPAT PEX5
8 response to iron ion GO:0010039 9.4 HAMP HFE
9 response to fatty acid GO:0070542 9.37 CAT GNPAT
10 protein import into peroxisome matrix GO:0016558 9.32 PEX5 PEX7
11 multicellular organismal iron ion homeostasis GO:0060586 9.26 HAMP HFE
12 protein import into peroxisome matrix, docking GO:0016560 9.16 PEX5 PEX5L
13 response to iron ion starvation GO:1990641 8.96 HAMP HFE
14 ether lipid biosynthetic process GO:0008611 8.92 AGPS FAR1 GNPAT PEX7

Molecular functions related to Rhizomelic Chondrodysplasia Punctata, Type 2 according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 signaling receptor binding GO:0005102 9.46 C3 CAT GNPAT HFE
2 peroxisome targeting sequence binding GO:0000268 8.96 PEX5 PEX5L
3 peroxisome matrix targeting signal-1 binding GO:0005052 8.62 PEX5 PEX5L

Sources for Rhizomelic Chondrodysplasia Punctata, Type 2

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
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42 MedGen
44 MeSH
45 MESH via Orphanet
46 MGI
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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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