RCDP3
MCID: RHZ004
MIFTS: 42

Rhizomelic Chondrodysplasia Punctata, Type 3 (RCDP3)

Categories: Bone diseases, Eye diseases, Fetal diseases, Genetic diseases, Mental diseases, Metabolic diseases, Neuronal diseases, Rare 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 20 72 13 70
Rhizomelic Chondrodysplasia Punctata Type 3 12 20 58 29 6 15
Alkyldihydroxyacetonephosphate Synthase Deficiency 57 12 20 72
Agps Deficiency 57 12 20 72
Rcdp3 57 12 20 72
Alkylglycerone-Phosphate Synthase Deficiency 57 12 72
Chondrodysplasia Punctata, Rhizomelic, Type 3 39
Alkyglycerone-Phosphate Synthase Deficiency 20
Rhizomelic Chondrodysplasia Punctata 3 72

Characteristics:

OMIM®:

57 (Updated 05-Apr-2021)
Inheritance:
autosomal recessive


HPO:

31
rhizomelic chondrodysplasia punctata, type 3:
Inheritance autosomal recessive inheritance


Classifications:

Orphanet: 58  
Rare neurological diseases
Rare eye diseases
Rare bone diseases
Inborn errors of metabolism
Developmental anomalies during embryogenesis


External Ids:

Disease Ontology 12 DOID:0110853
OMIM® 57 600121
OMIM Phenotypic Series 57 PS215100
MeSH 44 D018902
ICD10 32 Q77.3
ICD10 via Orphanet 33 Q77.3
UMLS via Orphanet 71 C1838612
Orphanet 58 ORPHA309803
MedGen 41 C1838612
UMLS 70 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) (Updated 05-Apr-2021)

MalaCards based summary : Rhizomelic Chondrodysplasia Punctata, Type 3, also known as rhizomelic chondrodysplasia punctata type 3, is related to rhizomelic chondrodysplasia punctata and cataract. An important gene associated with Rhizomelic Chondrodysplasia Punctata, Type 3 is AGPS (Alkylglycerone Phosphate Synthase), and among its related pathways/superpathways are triacylglycerol biosynthesis and Peroxisome. Affiliated tissues include eye, and related phenotypes are failure to thrive and epiphyseal stippling

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 : 72 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

Human phenotypes related to Rhizomelic Chondrodysplasia Punctata, Type 3:

31
# Description HPO Frequency HPO Source Accession
1 failure to thrive 31 HP:0001508
2 epiphyseal stippling 31 HP:0010655
3 rhizomelia 31 HP:0008905
4 short humerus 31 HP:0005792
5 short femur 31 HP:0003097

Symptoms via clinical synopsis from OMIM®:

57 (Updated 05-Apr-2021)
Growth Other:
failure to thrive

Growth Height:
short stature, disproportionate short limb

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

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

Clinical features from OMIM®:

600121 (Updated 05-Apr-2021)

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

46
# Description MGI Source Accession Score Top Affiliating Genes
1 behavior/neurological MP:0005386 9.56 GNPAT PDE11A PEX5 PEX5L PEX7 PHYH
2 reproductive system MP:0005389 9.1 AGPS GNPAT PDE11A PEX5 PEX7 PHYH

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:

40
Eye

Publications for Rhizomelic Chondrodysplasia Punctata, Type 3

Articles related to Rhizomelic Chondrodysplasia Punctata, Type 3:

(show all 11)
# Title Authors PMID Year
1
Functional characterization of novel mutations in GNPAT and AGPS, causing rhizomelic chondrodysplasia punctata (RCDP) types 2 and 3. 6 57
21990100 2012
2
Alkyl-dihydroxyacetonephosphate synthase. Fate in peroxisome biogenesis disorders and identification of the point mutation underlying a single enzyme deficiency. 57 6
9553082 1998
3
Human alkyldihydroxyacetonephosphate synthase deficiency: a new peroxisomal disorder. 57 6
7807941 1994
4
Genetics and molecular basis of human peroxisome biogenesis disorders. 57
22871920 2012
5
Peroxisomal disorders I: biochemistry and genetics of peroxisome biogenesis disorders. 57
15679822 2005
6
Impaired membrane traffic in defective ether lipid biosynthesis. 6
11152660 2001
7
Prenatal diagnosis of rhizomelic chondrodysplasia punctata due to isolated alkyldihydroacetonephosphate acyltransferase synthase deficiency. 57
10327148 1999
8
Non-rhizomelic and rhizomelic chondrodysplasia punctata within a single complementation group. 57
8611652 1996
9
Blind sterile 2 (bs2), a hypomorphic mutation in Agps, results in cataracts and male sterility in mice. 61
21353609 2011
10
Identifying a recombinant alkyldihydroxyacetonephosphate synthase suited for crystallographic studies. 61
17601746 2007
11
The crucial step in ether phospholipid biosynthesis: structural basis of a noncanonical reaction associated with a peroxisomal disorder. 61
17562315 2007

Variations for Rhizomelic Chondrodysplasia Punctata, Type 3

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

6 (show top 50) (show all 139)
# Gene Name Type Significance ClinVarId dbSNP ID Position
1 AGPS NM_003659.4(AGPS):c.1256G>A (p.Arg419His) SNV Pathogenic 6645 rs121434411 GRCh37: 2:178357898-178357898
GRCh38: 2:177493170-177493170
2 AGPS NM_003659.4(AGPS):c.926C>T (p.Thr309Ile) SNV Pathogenic 6646 rs121434412 GRCh37: 2:178326676-178326676
GRCh38: 2:177461948-177461948
3 AGPS NM_003659.4(AGPS):c.1406T>C (p.Leu469Pro) SNV Pathogenic 6647 rs121434413 GRCh37: 2:178364389-178364389
GRCh38: 2:177499661-177499661
4 AGPS NM_003659.4(AGPS):c.1703C>T (p.Thr568Met) SNV Pathogenic 35469 rs387907214 GRCh37: 2:178386002-178386002
GRCh38: 2:177521274-177521274
5 AGPS NM_003659.4(AGPS):c.1273C>T (p.Gln425Ter) SNV Pathogenic 1032144 GRCh37: 2:178357915-178357915
GRCh38: 2:177493187-177493187
6 AGPS NM_003659.4(AGPS):c.1380A>C (p.Pro460=) SNV Conflicting interpretations of pathogenicity 289429 rs148418568 GRCh37: 2:178364363-178364363
GRCh38: 2:177499635-177499635
7 AGPS NM_003659.4(AGPS):c.148C>T (p.Arg50Trp) SNV Uncertain significance 790910 rs778087162 GRCh37: 2:178257665-178257665
GRCh38: 2:177392937-177392937
8 AGPS NM_003659.4(AGPS):c.1244C>T (p.Pro415Leu) SNV Uncertain significance 892844 GRCh37: 2:178357886-178357886
GRCh38: 2:177493158-177493158
9 AGPS NM_003659.4(AGPS):c.1475+12A>G SNV Uncertain significance 892845 GRCh37: 2:178364470-178364470
GRCh38: 2:177499742-177499742
10 AGPS NM_003659.4(AGPS):c.1519C>T (p.Leu507=) SNV Uncertain significance 763969 rs761831871 GRCh37: 2:178370277-178370277
GRCh38: 2:177505549-177505549
11 AGPS NM_003659.4(AGPS):c.1569A>G (p.Val523=) SNV Uncertain significance 747115 rs150977180 GRCh37: 2:178372721-178372721
GRCh38: 2:177507993-177507993
12 AGPS NM_003659.4(AGPS):c.*1073T>C SNV Uncertain significance 892882 GRCh37: 2:178403996-178403996
GRCh38: 2:177539268-177539268
13 AGPS NM_003659.4(AGPS):c.*1238T>C SNV Uncertain significance 892883 GRCh37: 2:178404161-178404161
GRCh38: 2:177539433-177539433
14 AGPS NM_003659.4(AGPS):c.*1312T>C SNV Uncertain significance 892884 GRCh37: 2:178404235-178404235
GRCh38: 2:177539507-177539507
15 AGPS NM_003659.4(AGPS):c.*2833G>T SNV Uncertain significance 892922 GRCh37: 2:178405756-178405756
GRCh38: 2:177541028-177541028
16 AGPS NM_003659.4(AGPS):c.*4780G>A SNV Uncertain significance 892959 GRCh37: 2:178407703-178407703
GRCh38: 2:177542975-177542975
17 AGPS NM_003659.4(AGPS):c.*4788G>T SNV Uncertain significance 892960 GRCh37: 2:178407711-178407711
GRCh38: 2:177542983-177542983
18 AGPS NM_003659.4(AGPS):c.14C>T (p.Ala5Val) SNV Uncertain significance 893624 GRCh37: 2:178257531-178257531
GRCh38: 2:177392803-177392803
19 AGPS NM_003659.4(AGPS):c.1665G>A (p.Lys555=) SNV Uncertain significance 893658 GRCh37: 2:178378604-178378604
GRCh38: 2:177513876-177513876
20 AGPS NM_003659.4(AGPS):c.1908T>C (p.Phe636=) SNV Uncertain significance 799563 rs765895661 GRCh37: 2:178402854-178402854
GRCh38: 2:177538126-177538126
21 AGPS NM_003659.4(AGPS):c.*1424G>A SNV Uncertain significance 893694 GRCh37: 2:178404347-178404347
GRCh38: 2:177539619-177539619
22 AGPS NM_003659.4(AGPS):c.*1469T>G SNV Uncertain significance 893695 GRCh37: 2:178404392-178404392
GRCh38: 2:177539664-177539664
23 AGPS NM_003659.4(AGPS):c.*1865C>T SNV Uncertain significance 893964 GRCh37: 2:178404788-178404788
GRCh38: 2:177540060-177540060
24 AGPS NM_003659.4(AGPS):c.*1869T>C SNV Uncertain significance 893965 GRCh37: 2:178404792-178404792
GRCh38: 2:177540064-177540064
25 AGPS NM_003659.4(AGPS):c.*1880A>G SNV Uncertain significance 893966 GRCh37: 2:178404803-178404803
GRCh38: 2:177540075-177540075
26 AGPS NM_003659.4(AGPS):c.*1882A>G SNV Uncertain significance 893967 GRCh37: 2:178404805-178404805
GRCh38: 2:177540077-177540077
27 AGPS NM_003659.4(AGPS):c.*3931A>G SNV Uncertain significance 893996 GRCh37: 2:178406854-178406854
GRCh38: 2:177542126-177542126
28 AGPS NM_003659.4(AGPS):c.*3971A>G SNV Uncertain significance 893997 GRCh37: 2:178406894-178406894
GRCh38: 2:177542166-177542166
29 AGPS NM_003659.4(AGPS):c.*4056T>C SNV Uncertain significance 893998 GRCh37: 2:178406979-178406979
GRCh38: 2:177542251-177542251
30 AGPS NM_003659.4(AGPS):c.*4100A>G SNV Uncertain significance 893999 GRCh37: 2:178407023-178407023
GRCh38: 2:177542295-177542295
31 AGPS NM_003659.4(AGPS):c.774G>A (p.Leu258=) SNV Uncertain significance 894305 GRCh37: 2:178307199-178307199
GRCh38: 2:177442471-177442471
32 AGPS NM_003659.4(AGPS):c.*731A>G SNV Uncertain significance 894329 GRCh37: 2:178403654-178403654
GRCh38: 2:177538926-177538926
33 AGPS NM_003659.4(AGPS):c.*794C>T SNV Uncertain significance 894330 GRCh37: 2:178403717-178403717
GRCh38: 2:177538989-177538989
34 AGPS NM_003659.4(AGPS):c.*823T>A SNV Uncertain significance 894331 GRCh37: 2:178403746-178403746
GRCh38: 2:177539018-177539018
35 AGPS NM_003659.4(AGPS):c.*2311G>A SNV Uncertain significance 894364 GRCh37: 2:178405234-178405234
GRCh38: 2:177540506-177540506
36 AGPS NM_003659.4(AGPS):c.*2318A>G SNV Uncertain significance 894365 GRCh37: 2:178405241-178405241
GRCh38: 2:177540513-177540513
37 AGPS NM_003659.4(AGPS):c.*4228A>C SNV Uncertain significance 894405 GRCh37: 2:178407151-178407151
GRCh38: 2:177542423-177542423
38 AGPS NM_003659.4(AGPS):c.214A>G (p.Thr72Ala) SNV Uncertain significance 218623 rs560217758 GRCh37: 2:178257731-178257731
GRCh38: 2:177393003-177393003
39 AGPS NM_003659.4(AGPS):c.64G>A (p.Ala22Thr) SNV Uncertain significance 893911 GRCh37: 2:178257581-178257581
GRCh38: 2:177392853-177392853
40 AGPS NM_003659.4(AGPS):c.*361C>T SNV Uncertain significance 893938 GRCh37: 2:178403284-178403284
GRCh38: 2:177538556-177538556
41 AGPS NM_003659.4(AGPS):c.637+13C>T SNV Uncertain significance 332515 rs182602770 GRCh37: 2:178301795-178301795
GRCh38: 2:177437067-177437067
42 AGPS NM_003659.4(AGPS):c.*1628C>G SNV Uncertain significance 332545 rs535440679 GRCh37: 2:178404551-178404551
GRCh38: 2:177539823-177539823
43 AGPS NM_003659.4(AGPS):c.*2088T>G SNV Uncertain significance 332567 rs529240564 GRCh37: 2:178405011-178405011
GRCh38: 2:177540283-177540283
44 AGPS NM_003659.4(AGPS):c.*4132A>G SNV Uncertain significance 332590 rs544412431 GRCh37: 2:178407055-178407055
GRCh38: 2:177542327-177542327
45 AGPS NM_003659.4(AGPS):c.*2455C>T SNV Uncertain significance 332570 rs376557428 GRCh37: 2:178405378-178405378
GRCh38: 2:177540650-177540650
46 AGPS NM_003659.4(AGPS):c.1135A>G (p.Ile379Val) SNV Uncertain significance 811158 rs867493363 GRCh37: 2:178346816-178346816
GRCh38: 2:177482088-177482088
47 AGPS NM_003659.4(AGPS):c.*1744A>G SNV Uncertain significance 893697 GRCh37: 2:178404667-178404667
GRCh38: 2:177539939-177539939
48 AGPS NM_003659.4(AGPS):c.*1858A>G SNV Uncertain significance 893698 GRCh37: 2:178404781-178404781
GRCh38: 2:177540053-177540053
49 AGPS NM_003659.4(AGPS):c.*1860G>A SNV Uncertain significance 893699 GRCh37: 2:178404783-178404783
GRCh38: 2:177540055-177540055
50 AGPS NM_003659.4(AGPS):c.*3524T>C SNV Uncertain significance 893730 GRCh37: 2:178406447-178406447
GRCh38: 2:177541719-177541719

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

72
# 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

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

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 cytosol GO:0005829 10 SLC22A16 SCP2 PLEKHA3 PHYH PEX7 PEX5L
2 mitochondrion GO:0005739 9.72 SCP2 PHYH PEX5 GNPAT AGPS
3 peroxisomal membrane GO:0005778 9.55 PEX7 PEX5L PEX5 GNPAT AGPS
4 peroxisome GO:0005777 9.43 SCP2 PHYH PEX7 PEX5 GNPAT AGPS
5 peroxisomal matrix GO:0005782 9.1 SCP2 PHYH PEX7 PEX5 GNPAT AGPS

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

# Name GO ID Score Top Affiliating Genes
1 intermembrane lipid transfer GO:0120009 9.48 SCP2 PLEKHA3
2 bile acid biosynthetic process GO:0006699 9.46 SCP2 OSBPL6
3 cellular lipid metabolic process GO:0044255 9.43 PEX5 GNPAT
4 fatty acid beta-oxidation GO:0006635 9.43 SCP2 PEX7 PEX5
5 sterol transport GO:0015918 9.4 SCP2 OSBPL6
6 protein import into peroxisome matrix GO:0016558 9.37 PEX7 PEX5
7 peroxisome organization GO:0007031 9.33 SCP2 PEX7 PEX5
8 protein import into peroxisome matrix, docking GO:0016560 9.32 PEX5L PEX5
9 ether lipid biosynthetic process GO:0008611 9.13 PEX7 GNPAT AGPS
10 protein targeting to peroxisome GO:0006625 9.1 SCP2 PHYH PEX7 PEX5 GNPAT AGPS

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

# Name GO ID Score Top Affiliating Genes
1 catalytic activity GO:0003824 9.55 SCP2 PHYH PDE11A GNPAT AGPS
2 lipid binding GO:0008289 9.54 SCP2 PLEKHA3 OSBPL6
3 cholesterol binding GO:0015485 9.32 SCP2 OSBPL6
4 sterol binding GO:0032934 9.26 SCP2 OSBPL6
5 peroxisome targeting sequence binding GO:0000268 8.96 PEX5L PEX5
6 peroxisome matrix targeting signal-1 binding GO:0005052 8.62 PEX5L PEX5

Sources for Rhizomelic Chondrodysplasia Punctata, Type 3

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