MCID: RHZ014
MIFTS: 47

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 53 71 69
Dihydroxyacetonephosphate Acyltransferase Deficiency 53 12 49 71 51
Rhizomelic Chondrodysplasia Punctata Type 2 12 49 55 28 14
Peroxisomal Dihydroxyacetonephosphate Acyltransferase Deficiency 53 12 49 71
Dhapat Deficiency 53 12 49 71
Rcdp2 53 12 49 71
Chondrodysplasia Punctata, Rhizomelic, Due to Dihydroxyacetonephosphate Acyltransferase Deficiency 53 12 71
Glyceronephosphate O-Acyltransferase Deficiency 53 12 71
Gnpat Deficiency 53 12 71
Chondrodysplasia Punctata, Rhizomelic, Due to Dihydroxyacetonephosphate 49
Chondrodysplasia Punctata, Rhizomelic, Type 2 13
Type 2 Rhizomelic Chondrodysplasia Punctata 49
Rhizomelic Chondrodysplasia Punctata 2 71
Glyceronephosphate O-Acyltransferase 13

Characteristics:

OMIM:

53
Inheritance:
autosomal recessive


HPO:

31
rhizomelic chondrodysplasia punctata, type 2:
Inheritance autosomal recessive inheritance


Classifications:



Summaries for Rhizomelic Chondrodysplasia Punctata, Type 2

OMIM : 53 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 dihydroxyacetonephosphate acyltransferase deficiency, is related to chondrodysplasia punctata syndrome and rhizomelic chondrodysplasia punctata, and has symptoms including high palate, osteopenia and intellectual disability. 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 behavior/neurological and homeostasis/metabolism

UniProtKB/Swiss-Prot : 71 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.

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.

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 25)
# Related Disease Score Top Affiliating Genes
1 chondrodysplasia punctata syndrome 30.9 GNPAT PEX5 PEX7
2 rhizomelic chondrodysplasia punctata 30.4 AGPS GNPAT PEX5 PEX7 PHYH
3 familial porphyria cutanea tarda 30.1 HFE UROD
4 porphyria cutanea tarda 29.6 HAMP HFE UROD
5 mulibrey nanism 10.3 PEX5 PEX7
6 zellweger syndrome 10.2 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 10.0 CAT PEX5 PEX7
11 rhizomelic chondrodysplasia punctata, type 3 9.9 AGPS GNPAT PEX5 PEX7 UROD
12 acute porphyria 9.8 HFE UROD
13 hemochromatosis type 2 9.8 HAMP HFE
14 porphyria variegata 9.8 HFE UROD
15 peroxisomal biogenesis disorders 9.7 CAT PEX5 PEX7 PHEX
16 siderosis 9.6 HFE UROD
17 refsum disease, classic 9.6 CAT GNPAT PEX5 PEX7 PHYH
18 metal metabolism disorder 9.6 HAMP HFE
19 hemochromatosis, type 1 9.5 HAMP HFE UROD
20 peroxisomal disease 9.5 AGPS CAT GNPAT PEX5 PEX7 PHYH
21 hemosiderosis 9.4 HAMP HFE
22 peroxisome biogenesis disorder 1b 9.3 CAT GNPAT PEX5 PEX7 PHEX PHYH
23 deficiency anemia 9.3 CAT HAMP HFE
24 rhizomelic chondrodysplasia punctata, type 5 9.2 AGPS FAR1 GNPAT PEX5 PEX5L PEX7
25 rhizomelic chondrodysplasia punctata, type 1 8.6 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:

53
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:

31 (show all 21)
# Description HPO Frequency HPO Source Accession
1 high palate 31 HP:0000218
2 osteopenia 31 HP:0000938
3 intellectual disability 31 HP:0001249
4 failure to thrive 31 HP:0001508
5 scoliosis 31 HP:0002650
6 cataract 31 HP:0000518
7 depressed nasal bridge 31 HP:0005280
8 wide nasal bridge 31 HP:0000431
9 microcephaly 31 HP:0000252
10 anteverted nares 31 HP:0000463
11 flexion contracture 31 HP:0001371
12 micrognathia 31 HP:0000347
13 rhizomelia 31 HP:0008905
14 high forehead 31 HP:0000348
15 abnormality of pelvic girdle bone morphology 31 HP:0002644
16 large fontanelles 31 HP:0000239
17 generalized hypotonia 31 HP:0001290
18 short humerus 31 HP:0005792
19 irregular vertebral endplates 31 HP:0003301
20 calcific stippling 31 HP:0002832
21 stippled calcification proximal humeral epiphyses 31 HP:0008838

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

43
# Description MGI Source Accession Score Top Affiliating Genes
1 behavior/neurological MP:0005386 10.13 C3 CTSC HFE NTS PEX5 PEX5L
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 PLP1 UROD AGPS C3 CAT GNPAT
6 liver/biliary system MP:0005370 9.73 PEX5 PEX7 PHYH UROD C3 HFE
7 nervous system MP:0003631 9.7 PEX5 PEX5L PEX7 PHEX PHYH PLP1
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 28 GNPAT

Anatomical Context for Rhizomelic Chondrodysplasia Punctata, Type 2

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

38
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
3
Abnormal myelination in peroxisomal isolated dihydroxyacetonephosphate acyltransferase deficiency. ( 9165515 )
1997
4
Isolated dihydroxyacetonephosphate acyltransferase deficiency presenting with developmental delay. ( 7530787 )
1994

Variations for Rhizomelic Chondrodysplasia Punctata, Type 2

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

71
# 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 GNPAT, IVS9AS, T-G, -3 single nucleotide variant Pathogenic
2 GNPAT GNPAT, 2-BP DEL, 1429AT deletion Pathogenic
3 GNPAT GNPAT, IVS14DS, G-A, +5 single nucleotide variant Pathogenic
4 GNPAT NM_014236.3(GNPAT): c.632G> A (p.Arg211His) single nucleotide variant Pathogenic rs121434439 GRCh37 Chromosome 1, 231401102: 231401102
5 GNPAT NM_014236.3(GNPAT): c.631C> T (p.Arg211Cys) single nucleotide variant Pathogenic rs121434440 GRCh37 Chromosome 1, 231401101: 231401101
6 GNPAT GNPAT, 2-BP INS, 848TT insertion Pathogenic
7 GNPAT GNPAT, 1-BP DEL, NT780 deletion Pathogenic
8 GNPAT GNPAT, 1-BP DEL, NT1575 deletion 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 13)
# Name GO ID Score Top Affiliating Genes
1 aging GO:0007568 9.67 CAT CTSC HAMP
2 acute-phase response GO:0006953 9.52 HAMP HFE
3 liver regeneration GO:0097421 9.51 HAMP HFE
4 peroxisome organization GO:0007031 9.48 PEX5 PEX7
5 response to iron ion GO:0010039 9.46 HAMP HFE
6 response to vitamin A GO:0033189 9.43 CAT HAMP
7 response to fatty acid GO:0070542 9.4 CAT GNPAT
8 cellular lipid metabolic process GO:0044255 9.37 GNPAT PEX5
9 multicellular organismal iron ion homeostasis GO:0060586 9.32 HAMP HFE
10 protein import into peroxisome matrix GO:0016558 9.26 PEX5 PEX7
11 protein import into peroxisome matrix, docking GO:0016560 9.16 PEX5 PEX5L
12 response to iron ion starvation GO:1990641 8.96 HAMP HFE
13 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 receptor binding GO:0005102 9.56 C3 CAT GNPAT HFE
2 small GTPase binding GO:0031267 9.16 PEX5 PEX5L
3 peroxisome targeting sequence binding GO:0000268 8.96 PEX5 PEX5L
4 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
16 ExPASy
18 FMA
27 GO
28 GTR
29 HGMD
30 HMDB
31 HPO
32 ICD10
33 ICD10 via Orphanet
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35 IUPHAR
36 KEGG
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41 MeSH
42 MESH via Orphanet
43 MGI
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50 NINDS
51 Novoseek
53 OMIM
54 OMIM via Orphanet
58 PubMed
60 QIAGEN
65 SNOMED-CT via HPO
66 SNOMED-CT via Orphanet
67 TGDB
68 Tocris
69 UMLS
70 UMLS via Orphanet
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