MCID: RHZ004
MIFTS: 38

Rhizomelic Chondrodysplasia Punctata, Type 3

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

Aliases & Classifications for Rhizomelic Chondrodysplasia Punctata, Type 3

MalaCards integrated aliases for Rhizomelic Chondrodysplasia Punctata, Type 3:

Name: Rhizomelic Chondrodysplasia Punctata, Type 3 57 53 75 13 73
Rhizomelic Chondrodysplasia Punctata Type 3 12 53 59 29 6 15
Alkyldihydroxyacetonephosphate Synthase Deficiency 57 12 53 75
Agps Deficiency 57 12 53 75
Rcdp3 57 12 53 75
Alkylglycerone-Phosphate Synthase Deficiency 57 12 75
Chondrodysplasia Punctata, Rhizomelic, Type 3 40
Alkyglycerone-Phosphate Synthase Deficiency 53
Rhizomelic Chondrodysplasia Punctata 3 75
Alkylglycerone-Phosphate Synthase 13

Characteristics:

OMIM:

57
Inheritance:
autosomal recessive


HPO:

32
rhizomelic chondrodysplasia punctata, type 3:
Inheritance autosomal recessive inheritance


Classifications:



External Ids:

OMIM 57 600121
Disease Ontology 12 DOID:0110853
ICD10 33 Q77.3
Orphanet 59 ORPHA309803
ICD10 via Orphanet 34 Q77.3
UMLS via Orphanet 74 C1838612
MedGen 42 C1838612
MeSH 44 D018902
UMLS 73 C1838612

Summaries for Rhizomelic Chondrodysplasia Punctata, Type 3

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 is the most frequent form of RCDP (summary by Wanders and Waterham, 2005). Whereas RCDP1 is a peroxisomal biogenesis disorder (PBD), RCDP3 is classified as a single peroxisome enzyme deficiency (Waterham and Ebberink, 2012). For a discussion of genetic heterogeneity of rhizomelic chondrodysplasia punctata, see 215100. (600121)

MalaCards based summary : Rhizomelic Chondrodysplasia Punctata, Type 3, also known as rhizomelic chondrodysplasia punctata type 3, is related to rhizomelic chondrodysplasia punctata and peroxisomal disease. An important gene associated with Rhizomelic Chondrodysplasia Punctata, Type 3 is AGPS (Alkylglycerone Phosphate Synthase), and among its related pathways/superpathways are Acyl chain remodelling of PE and triacylglycerol biosynthesis. Affiliated tissues include bone and eye, and related phenotypes are failure to thrive and short femur

Disease Ontology : 12 A rhizomelic chondrodysplasia punctata that has material basis in autosomal recessive inheritance of homozygous or compound heterozygous mutation in the AGPS gene on chromosome 2q31.2.

UniProtKB/Swiss-Prot : 75 Rhizomelic chondrodysplasia punctata 3: 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 3

Graphical network of the top 20 diseases related to Rhizomelic Chondrodysplasia Punctata, Type 3:



Diseases related to Rhizomelic Chondrodysplasia Punctata, Type 3

Symptoms & Phenotypes for Rhizomelic Chondrodysplasia Punctata, Type 3

Symptoms via clinical synopsis from OMIM:

57
Growth Height:
short stature, disproportionate short limb

Skeletal Limbs:
rhizomelic limb shortening
severely shortened humeri
severely shorted femora
stippled epiphyses

Growth Other:
failure to thrive

Laboratory Abnormalities:
absent alkyl-dhap synthase activity
normal plasma phytanic acid
decreased erythrocyte plasmalogen


Clinical features from OMIM:

600121

Human phenotypes related to Rhizomelic Chondrodysplasia Punctata, Type 3:

32
# Description HPO Frequency HPO Source Accession
1 failure to thrive 32 HP:0001508
2 short femur 32 HP:0003097
3 short humerus 32 HP:0005792
4 rhizomelia 32 HP:0008905
5 epiphyseal stippling 32 HP:0010655

GenomeRNAi Phenotypes related to Rhizomelic Chondrodysplasia Punctata, Type 3 according to GeneCards Suite gene sharing:

26 (show all 11)
# Description GenomeRNAi Source Accession Score Top Affiliating Genes
1 Increased shRNA abundance (Z-score > 2) GR00366-A-100 9.4 UROD
2 Increased shRNA abundance (Z-score > 2) GR00366-A-105 9.4 AGPS
3 Increased shRNA abundance (Z-score > 2) GR00366-A-122 9.4 AGPS
4 Increased shRNA abundance (Z-score > 2) GR00366-A-125 9.4 UROD
5 Increased shRNA abundance (Z-score > 2) GR00366-A-13 9.4 AGPS
6 Increased shRNA abundance (Z-score > 2) GR00366-A-159 9.4 UROD
7 Increased shRNA abundance (Z-score > 2) GR00366-A-36 9.4 AGPS UROD
8 Increased shRNA abundance (Z-score > 2) GR00366-A-39 9.4 UROD
9 Increased shRNA abundance (Z-score > 2) GR00366-A-73 9.4 UROD
10 Increased shRNA abundance (Z-score > 2) GR00366-A-85 9.4 UROD
11 Increased shRNA abundance (Z-score > 2) GR00366-A-93 9.4 AGPS

MGI Mouse Phenotypes related to Rhizomelic Chondrodysplasia Punctata, Type 3:

46
# Description MGI Source Accession Score Top Affiliating Genes
1 endocrine/exocrine gland MP:0005379 9.56 AGPS GNPAT PEX5 PEX7
2 homeostasis/metabolism MP:0005376 9.55 AGPS GNPAT PEX5 PEX7 UROD
3 mortality/aging MP:0010768 9.35 AGPS GNPAT PEX5 PEX7 UROD
4 reproductive system MP:0005389 8.92 AGPS GNPAT PEX5 PEX7

Drugs & Therapeutics for Rhizomelic Chondrodysplasia Punctata, Type 3

Search Clinical Trials , NIH Clinical Center for Rhizomelic Chondrodysplasia Punctata, Type 3

Genetic Tests for Rhizomelic Chondrodysplasia Punctata, Type 3

Genetic tests related to Rhizomelic Chondrodysplasia Punctata, Type 3:

# Genetic test Affiliating Genes
1 Rhizomelic Chondrodysplasia Punctata Type 3 29 AGPS

Anatomical Context for Rhizomelic Chondrodysplasia Punctata, Type 3

MalaCards organs/tissues related to Rhizomelic Chondrodysplasia Punctata, Type 3:

41
Bone, Eye

Publications for Rhizomelic Chondrodysplasia Punctata, Type 3

Articles related to Rhizomelic Chondrodysplasia Punctata, Type 3:

# Title Authors Year
1
Human alkyldihydroxyacetonephosphate synthase deficiency: a new peroxisomal disorder. ( 7807941 )
1994

Variations for Rhizomelic Chondrodysplasia Punctata, Type 3

UniProtKB/Swiss-Prot genetic disease variations for Rhizomelic Chondrodysplasia Punctata, Type 3:

75
# Symbol AA change Variation ID SNP ID
1 AGPS p.Arg419His VAR_005002 rs121434411
2 AGPS p.Thr309Ile VAR_025895 rs121434412
3 AGPS p.Leu469Pro VAR_025896 rs121434413
4 AGPS p.Arg182Gln VAR_066929
5 AGPS p.Glu471Lys VAR_066930
6 AGPS p.Thr568Met VAR_066931 rs387907214

ClinVar genetic disease variations for Rhizomelic Chondrodysplasia Punctata, Type 3:

6
# Gene Variation Type Significance SNP ID Assembly Location
1 AGPS NM_003659.3(AGPS): c.1256G> A (p.Arg419His) single nucleotide variant Pathogenic rs121434411 GRCh37 Chromosome 2, 178357898: 178357898
2 AGPS NM_003659.3(AGPS): c.1256G> A (p.Arg419His) single nucleotide variant Pathogenic rs121434411 GRCh38 Chromosome 2, 177493170: 177493170
3 AGPS NM_003659.3(AGPS): c.926C> T (p.Thr309Ile) single nucleotide variant Pathogenic rs121434412 GRCh37 Chromosome 2, 178326676: 178326676
4 AGPS NM_003659.3(AGPS): c.926C> T (p.Thr309Ile) single nucleotide variant Pathogenic rs121434412 GRCh38 Chromosome 2, 177461948: 177461948
5 AGPS NM_003659.3(AGPS): c.1406T> C (p.Leu469Pro) single nucleotide variant Pathogenic rs121434413 GRCh37 Chromosome 2, 178364389: 178364389
6 AGPS NM_003659.3(AGPS): c.1406T> C (p.Leu469Pro) single nucleotide variant Pathogenic rs121434413 GRCh38 Chromosome 2, 177499661: 177499661
7 AGPS NM_003659.3(AGPS): c.1703C> T (p.Thr568Met) single nucleotide variant Pathogenic rs387907214 GRCh37 Chromosome 2, 178386002: 178386002
8 AGPS NM_003659.3(AGPS): c.1703C> T (p.Thr568Met) single nucleotide variant Pathogenic rs387907214 GRCh38 Chromosome 2, 177521274: 177521274

Expression for Rhizomelic Chondrodysplasia Punctata, Type 3

Search GEO for disease gene expression data for Rhizomelic Chondrodysplasia Punctata, Type 3.

Pathways for Rhizomelic Chondrodysplasia Punctata, Type 3

Pathways related to Rhizomelic Chondrodysplasia Punctata, Type 3 according to GeneCards Suite gene sharing:

# Super pathways Score Top Affiliating Genes
1
Show member pathways
11.52 AGPS GNPAT
2
Show member pathways
11.1 AGPS GNPAT
3
Show member pathways
10.88 AGPS GNPAT
4 10.84 AGPS GNPAT PEX5 PEX7
5
Show member pathways
10.32 AGPS GNPAT

GO Terms for Rhizomelic Chondrodysplasia Punctata, Type 3

Cellular components related to Rhizomelic Chondrodysplasia Punctata, Type 3 according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 peroxisomal membrane GO:0005778 9.33 AGPS GNPAT PEX5
2 peroxisomal matrix GO:0005782 9.13 AGPS GNPAT PEX7
3 peroxisome GO:0005777 8.92 AGPS GNPAT PEX5 PEX7

Biological processes related to Rhizomelic Chondrodysplasia Punctata, Type 3 according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 neuron migration GO:0001764 9.37 PEX5 PEX7
2 fatty acid beta-oxidation GO:0006635 9.32 PEX5 PEX7
3 peroxisome organization GO:0007031 9.26 PEX5 PEX7
4 cellular lipid metabolic process GO:0044255 9.16 GNPAT PEX5
5 protein import into peroxisome matrix GO:0016558 8.96 PEX5 PEX7
6 ether lipid biosynthetic process GO:0008611 8.8 AGPS GNPAT PEX7

Sources for Rhizomelic Chondrodysplasia Punctata, Type 3

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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