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WARBM2
MCID: WRB003
MIFTS: 34

Warburg Micro Syndrome 2 (WARBM2)

Categories: Eye diseases, Genetic diseases, Mental diseases, Neuronal diseases, Rare diseases
Genes Variations Tissues Related diseases Pathways Symptoms & Phenotypes
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Aliases & Classifications for Warburg Micro Syndrome 2

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MalaCards integrated aliases for Warburg Micro Syndrome 2:

Name: Warburg Micro Syndrome 2 58 12 76 30 13 6 15 74
Micro Syndrome 2 58 12 76
Warbm2 58 12 76
Warburg Micro Syndrome, Type 2 41

Characteristics:

OMIM:

58
Inheritance:
autosomal recessive


HPO:

33
warburg micro syndrome 2:
Inheritance autosomal recessive inheritance


Classifications:

MalaCards categories:
Global: Genetic diseases Rare diseases
Anatomical: Eye diseases Neuronal diseases Mental diseases
See all MalaCards categories (disease lists)
ICD10: 34


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Summaries for Warburg Micro Syndrome 2

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UniProtKB/Swiss-Prot : 76 Warburg micro syndrome 2: A rare syndrome characterized by microcephaly, microphthalmia, microcornia, congenital cataracts, optic atrophy, cortical dysplasia, in particular corpus callosum hypoplasia, severe mental retardation, spastic diplegia, and hypogonadism.

MalaCards based summary : Warburg Micro Syndrome 2, also known as micro syndrome 2, is related to steroid-induced glaucoma and rab18 deficiency. An important gene associated with Warburg Micro Syndrome 2 is RAB3GAP2 (RAB3 GTPase Activating Non-Catalytic Protein Subunit 2), and among its related pathways/superpathways are Vesicle-mediated transport and Golgi-to-ER retrograde transport. Affiliated tissues include brain, and related phenotypes are macrotia and short nose

Disease Ontology : 12 A Warburg micro syndrome that has material basis in autosomal recessive inheritance of homozygous or compound heterozygous mutation in the RAB3GAP2 gene on chromosome 1q41.

Description from OMIM: 614225
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Related Diseases for Warburg Micro Syndrome 2

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Diseases in the Warburg Micro Syndrome family:

Warburg Micro Syndrome 1 Warburg Micro Syndrome 3
Warburg Micro Syndrome 2 Warburg Micro Syndrome 4

Diseases related to Warburg Micro Syndrome 2 via text searches within MalaCards or GeneCards Suite gene sharing:

# Related Disease Score Top Affiliating Genes
1 steroid-induced glaucoma 9.7 RAB3GAP1 RAB3GAP2
2 rab18 deficiency 9.3 RAB18 RAB3GAP1 TBC1D20
3 warburg micro syndrome 9.2 RAB18 RAB3GAP1 RAB3GAP2 TBC1D20
4 warburg micro syndrome 1 9.2 RAB18 RAB3GAP1 RAB3GAP2 TBC1D20
5 warburg micro syndrome 4 9.1 RAB18 RAB3GAP1 RAB3GAP2 TBC1D20
6 spastic diplegia 9.1 RAB18 RAB3GAP1 RAB3GAP2 TBC1D20
7 microcephaly 9.0 RAB18 RAB3GAP1 RAB3GAP2 TBC1D20
8 martsolf syndrome 9.0 MIR664A RAB18 RAB3GAP1 RAB3GAP2 SNORA36B

Graphical network of the top 20 diseases related to Warburg Micro Syndrome 2:



Diseases related to Warburg Micro Syndrome 2
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Symptoms & Phenotypes for Warburg Micro Syndrome 2

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Human phenotypes related to Warburg Micro Syndrome 2:

33 (show all 27)
# Description HPO Frequency HPO Source Accession
1 macrotia 33 HP:0000400
2 short nose 33 HP:0003196
3 optic atrophy 33 HP:0000648
4 flexion contracture 33 HP:0001371
5 brachycephaly 33 HP:0000248
6 intellectual disability, severe 33 HP:0010864
7 severe global developmental delay 33 HP:0011344
8 absent speech 33 HP:0001344
9 cryptorchidism 33 HP:0000028
10 postnatal growth retardation 33 HP:0008897
11 prominent nasal bridge 33 HP:0000426
12 microphthalmia 33 HP:0000568
13 low anterior hairline 33 HP:0000294
14 microcornea 33 HP:0000482
15 polymicrogyria 33 HP:0002126
16 micropenis 33 HP:0000054
17 hypoplasia of the corpus callosum 33 HP:0002079
18 scrotal hypoplasia 33 HP:0000046
19 hypoplastic labia majora 33 HP:0000059
20 spastic diplegia 33 HP:0001264
21 postnatal microcephaly 33 HP:0005484
22 muscular hypotonia of the trunk 33 HP:0008936
23 global brain atrophy 33 HP:0002283
24 overlapping toe 33 HP:0001845
25 asymmetry of the ears 33 HP:0010722
26 developmental cataract 33 HP:0000519
27 undetectable visual evoked potentials 33 HP:0007965

Symptoms via clinical synopsis from OMIM:

58
Neurologic Central Nervous System:
global developmental delay
severe mental retardation
hypoplastic corpus callosum
axial hypotonia
generalized brain atrophy
more
Head And Neck Head:
brachycephaly
postnatal microcephaly

Growth Height:
postnatal growth retardation

Head And Neck Face:
low anterior hairline

Genitourinary External Genitalia Male:
micropenis
scrotal hypoplasia

Head And Neck Ears:
large ears
asymmetric ears

Skeletal Limbs:
contractures

Head And Neck Nose:
short nose
prominent nasal root

Genitourinary Internal Genitalia Male:
cryptorchidism

Head And Neck Eyes:
microphthalmia
microcornea
optic nerve atrophy
congenital cataracts, bilateral
atonic pupils
more
Skin Nails Hair Hair:
low anterior hairline

Skeletal Skull:
microcephaly, postnatal

Skeletal Feet:
overlapping toes

Genitourinary External Genitalia Female:
hypoplasia of labia majora

Clinical features from OMIM:

614225
Sources

Drugs & Therapeutics for Warburg Micro Syndrome 2

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Search Clinical Trials , NIH Clinical Center for Warburg Micro Syndrome 2

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Genetic Tests for Warburg Micro Syndrome 2

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Genetic tests related to Warburg Micro Syndrome 2:

# Genetic test Affiliating Genes
1 Warburg Micro Syndrome 2 30 RAB3GAP2
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Anatomical Context for Warburg Micro Syndrome 2

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MalaCards organs/tissues related to Warburg Micro Syndrome 2:

42
Brain
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Publications for Warburg Micro Syndrome 2

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Variations for Warburg Micro Syndrome 2

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ClinVar genetic disease variations for Warburg Micro Syndrome 2:

6 (show top 50) (show all 58)
# Gene Variation Type Significance SNP ID Assembly Location
1 RAB3GAP2 NM_012414.3(RAB3GAP2): c.713-2A> G single nucleotide variant Conflicting interpretations of pathogenicity rs797045103 GRCh37 Chromosome 1, 220375718: 220375718
2 RAB3GAP2 NM_012414.3(RAB3GAP2): c.713-2A> G single nucleotide variant Conflicting interpretations of pathogenicity rs797045103 GRCh38 Chromosome 1, 220202376: 220202376
3 RAB3GAP2 NM_012414.3(RAB3GAP2): c.4060A> G (p.Ile1354Val) single nucleotide variant Conflicting interpretations of pathogenicity rs59190330 GRCh37 Chromosome 1, 220324715: 220324715
4 RAB3GAP2 NM_012414.3(RAB3GAP2): c.4060A> G (p.Ile1354Val) single nucleotide variant Conflicting interpretations of pathogenicity rs59190330 GRCh38 Chromosome 1, 220151373: 220151373
5 RAB3GAP2 NM_012414.3(RAB3GAP2): c.3924G> C (p.Thr1308=) single nucleotide variant Benign rs73098539 GRCh37 Chromosome 1, 220325050: 220325050
6 RAB3GAP2 NM_012414.3(RAB3GAP2): c.3924G> C (p.Thr1308=) single nucleotide variant Benign rs73098539 GRCh38 Chromosome 1, 220151708: 220151708
7 RAB3GAP2 NM_012414.3(RAB3GAP2): c.499_507delTTCTACACT (p.Phe167_Thr169del) deletion Pathogenic rs1553278569 GRCh37 Chromosome 1, 220384146: 220384154
8 RAB3GAP2 NM_012414.3(RAB3GAP2): c.499_507delTTCTACACT (p.Phe167_Thr169del) deletion Pathogenic rs1553278569 GRCh38 Chromosome 1, 220210804: 220210812
9 RAB3GAP2 NM_012414.3(RAB3GAP2): c.1434G> A (p.Trp478Ter) single nucleotide variant Pathogenic rs587777168 GRCh37 Chromosome 1, 220364463: 220364463
10 RAB3GAP2 NM_012414.3(RAB3GAP2): c.1434G> A (p.Trp478Ter) single nucleotide variant Pathogenic rs587777168 GRCh38 Chromosome 1, 220191121: 220191121
11 RAB3GAP2 NM_012414.3(RAB3GAP2): c.3637C> T (p.Arg1213Ter) single nucleotide variant Pathogenic rs587777169 GRCh37 Chromosome 1, 220327318: 220327318
12 RAB3GAP2 NM_012414.3(RAB3GAP2): c.3637C> T (p.Arg1213Ter) single nucleotide variant Pathogenic rs587777169 GRCh38 Chromosome 1, 220153976: 220153976
13 RAB3GAP2 NM_012414.3(RAB3GAP2): c.3085G> T (p.Glu1029Ter) single nucleotide variant Pathogenic rs587777170 GRCh37 Chromosome 1, 220340637: 220340637
14 RAB3GAP2 NM_012414.3(RAB3GAP2): c.3085G> T (p.Glu1029Ter) single nucleotide variant Pathogenic rs587777170 GRCh38 Chromosome 1, 220167295: 220167295
15 RAB3GAP2 NM_012414.3(RAB3GAP2): c.774A> G (p.Leu258=) single nucleotide variant Conflicting interpretations of pathogenicity rs576411922 GRCh37 Chromosome 1, 220375655: 220375655
16 RAB3GAP2 NM_012414.3(RAB3GAP2): c.774A> G (p.Leu258=) single nucleotide variant Conflicting interpretations of pathogenicity rs576411922 GRCh38 Chromosome 1, 220202313: 220202313
17 RAB3GAP2 NM_012414.3(RAB3GAP2): c.2088A> G (p.Thr696=) single nucleotide variant Benign/Likely benign rs2577126 GRCh37 Chromosome 1, 220356184: 220356184
18 RAB3GAP2 NM_012414.3(RAB3GAP2): c.2088A> G (p.Thr696=) single nucleotide variant Benign/Likely benign rs2577126 GRCh38 Chromosome 1, 220182842: 220182842
19 RAB3GAP2 NM_012414.3(RAB3GAP2): c.2587A> G (p.Thr863Ala) single nucleotide variant Benign/Likely benign rs12045447 GRCh37 Chromosome 1, 220344453: 220344453
20 RAB3GAP2 NM_012414.3(RAB3GAP2): c.2587A> G (p.Thr863Ala) single nucleotide variant Benign/Likely benign rs12045447 GRCh38 Chromosome 1, 220171111: 220171111
21 RAB3GAP2 NM_012414.3(RAB3GAP2): c.2290C> T (p.Leu764Phe) single nucleotide variant Uncertain significance rs139337049 GRCh37 Chromosome 1, 220355619: 220355619
22 RAB3GAP2 NM_012414.3(RAB3GAP2): c.2290C> T (p.Leu764Phe) single nucleotide variant Uncertain significance rs139337049 GRCh38 Chromosome 1, 220182277: 220182277
23 RAB3GAP2 NM_012414.3(RAB3GAP2): c.2168T> A (p.Val723Glu) single nucleotide variant Conflicting interpretations of pathogenicity rs150643803 GRCh38 Chromosome 1, 220182762: 220182762
24 RAB3GAP2 NM_012414.3(RAB3GAP2): c.2168T> A (p.Val723Glu) single nucleotide variant Conflicting interpretations of pathogenicity rs150643803 GRCh37 Chromosome 1, 220356104: 220356104
25 RAB3GAP2 NM_012414.3(RAB3GAP2): c.3112A> G (p.Ile1038Val) single nucleotide variant Uncertain significance rs144779240 GRCh38 Chromosome 1, 220164775: 220164775
26 RAB3GAP2 NM_012414.3(RAB3GAP2): c.3112A> G (p.Ile1038Val) single nucleotide variant Uncertain significance rs144779240 GRCh37 Chromosome 1, 220338117: 220338117
27 RAB3GAP2 NM_012414.3(RAB3GAP2): c.1215C> T (p.Phe405=) single nucleotide variant Benign/Likely benign rs762485949 GRCh38 Chromosome 1, 220193295: 220193295
28 RAB3GAP2 NM_012414.3(RAB3GAP2): c.1215C> T (p.Phe405=) single nucleotide variant Benign/Likely benign rs762485949 GRCh37 Chromosome 1, 220366637: 220366637
29 RAB3GAP2 NM_012414.3(RAB3GAP2): c.3171G> A (p.Met1057Ile) single nucleotide variant Uncertain significance rs368434757 GRCh37 Chromosome 1, 220335594: 220335594
30 RAB3GAP2 NM_012414.3(RAB3GAP2): c.3171G> A (p.Met1057Ile) single nucleotide variant Uncertain significance rs368434757 GRCh38 Chromosome 1, 220162252: 220162252
31 RAB3GAP2 NM_012414.3(RAB3GAP2): c.2207dup (p.Leu737Phefs) duplication Pathogenic rs1553275687 GRCh38 Chromosome 1, 220182723: 220182723
32 RAB3GAP2 NM_012414.3(RAB3GAP2): c.2207dup (p.Leu737Phefs) duplication Pathogenic rs1553275687 GRCh37 Chromosome 1, 220356065: 220356065
33 RAB3GAP2 NM_012414.3(RAB3GAP2): c.310T> C (p.Trp104Arg) single nucleotide variant Uncertain significance rs1553278790 GRCh37 Chromosome 1, 220386305: 220386305
34 RAB3GAP2 NM_012414.3(RAB3GAP2): c.310T> C (p.Trp104Arg) single nucleotide variant Uncertain significance rs1553278790 GRCh38 Chromosome 1, 220212963: 220212963
35 RAB3GAP2 NM_012414.3(RAB3GAP2): c.3805G> A (p.Val1269Ile) single nucleotide variant Uncertain significance rs778851334 GRCh38 Chromosome 1, 220153247: 220153247
36 RAB3GAP2 NM_012414.3(RAB3GAP2): c.3805G> A (p.Val1269Ile) single nucleotide variant Uncertain significance rs778851334 GRCh37 Chromosome 1, 220326589: 220326589
37 RAB3GAP2 NM_012414.3(RAB3GAP2): c.1511T> C (p.Ile504Thr) single nucleotide variant Uncertain significance rs1553276414 GRCh37 Chromosome 1, 220363839: 220363839
38 RAB3GAP2 NM_012414.3(RAB3GAP2): c.1511T> C (p.Ile504Thr) single nucleotide variant Uncertain significance rs1553276414 GRCh38 Chromosome 1, 220190497: 220190497
39 RAB3GAP2 NM_012414.3(RAB3GAP2): c.2417-7C> T single nucleotide variant Likely benign rs973067244 GRCh37 Chromosome 1, 220345398: 220345398
40 RAB3GAP2 NM_012414.3(RAB3GAP2): c.2417-7C> T single nucleotide variant Likely benign rs973067244 GRCh38 Chromosome 1, 220172056: 220172056
41 RAB3GAP2 NM_012414.3(RAB3GAP2): c.1258C> T (p.Arg420Cys) single nucleotide variant Uncertain significance rs188522997 GRCh37 Chromosome 1, 220366594: 220366594
42 RAB3GAP2 NM_012414.3(RAB3GAP2): c.1258C> T (p.Arg420Cys) single nucleotide variant Uncertain significance rs188522997 GRCh38 Chromosome 1, 220193252: 220193252
43 RAB3GAP2 NM_012414.3(RAB3GAP2): c.812-6T> A single nucleotide variant Likely benign rs575925720 GRCh37 Chromosome 1, 220369746: 220369746
44 RAB3GAP2 NM_012414.3(RAB3GAP2): c.812-6T> A single nucleotide variant Likely benign rs575925720 GRCh38 Chromosome 1, 220196404: 220196404
45 RAB3GAP2 NM_012414.3(RAB3GAP2): c.180T> A (p.Pro60=) single nucleotide variant Uncertain significance rs138809681 GRCh37 Chromosome 1, 220406141: 220406141
46 RAB3GAP2 NM_012414.3(RAB3GAP2): c.180T> A (p.Pro60=) single nucleotide variant Uncertain significance rs138809681 GRCh38 Chromosome 1, 220232799: 220232799
47 RAB3GAP2 NM_012414.3(RAB3GAP2): c.2667T> G (p.Leu889=) single nucleotide variant Likely benign rs145550355 GRCh37 Chromosome 1, 220344373: 220344373
48 RAB3GAP2 NM_012414.3(RAB3GAP2): c.2667T> G (p.Leu889=) single nucleotide variant Likely benign rs145550355 GRCh38 Chromosome 1, 220171031: 220171031
49 RAB3GAP2 NM_012414.3(RAB3GAP2): c.4161C> T (p.Ala1387=) single nucleotide variant Likely benign rs772430156 GRCh37 Chromosome 1, 220324614: 220324614
50 RAB3GAP2 NM_012414.3(RAB3GAP2): c.4161C> T (p.Ala1387=) single nucleotide variant Likely benign rs772430156 GRCh38 Chromosome 1, 220151272: 220151272
Sources

Expression for Warburg Micro Syndrome 2

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Search GEO for disease gene expression data for Warburg Micro Syndrome 2.
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Pathways for Warburg Micro Syndrome 2

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Pathways related to Warburg Micro Syndrome 2 according to GeneCards Suite gene sharing:

# Super pathways Score Top Affiliating Genes
1
Vesicle-mediated transport 67
Show member pathways
 12.66 RAB18 RAB3GAP1 RAB3GAP2 TBC1D20
2
Golgi-to-ER retrograde transport 67
Show member pathways
 11.95 RAB18 RAB3GAP1 RAB3GAP2
3
RAB GEFs exchange GTP for GDP on RABs 67
11.09 RAB18 RAB3GAP1 RAB3GAP2
4
COPI-independent Golgi-to-ER retrograde traffic 67
10.25 RAB18 RAB3GAP1 RAB3GAP2
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GO Terms for Warburg Micro Syndrome 2

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Cellular components related to Warburg Micro Syndrome 2 according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 endoplasmic reticulum membrane GO:0005789 9.26 RAB18 RAB3GAP1 RAB3GAP2 TBC1D20
2 endoplasmic reticulum tubular network GO:0071782 8.62 RAB18 RAB3GAP1

Biological processes related to Warburg Micro Syndrome 2 according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 positive regulation of GTPase activity GO:0043547 9.54 RAB3GAP1 RAB3GAP2 TBC1D20
2 regulation of GTPase activity GO:0043087 9.43 RAB3GAP1 RAB3GAP2
3 camera-type eye development GO:0043010 9.4 RAB3GAP1 TBC1D20
4 positive regulation of autophagosome assembly GO:2000786 9.32 RAB3GAP1 RAB3GAP2
5 positive regulation of endoplasmic reticulum tubular network organization GO:1903373 9.26 RAB3GAP1 RAB3GAP2
6 positive regulation of protein lipidation GO:1903061 9.16 RAB3GAP1 RAB3GAP2
7 establishment of protein localization to endoplasmic reticulum membrane GO:0097051 8.96 RAB3GAP1 RAB3GAP2
8 lipid droplet organization GO:0034389 8.8 RAB18 RAB3GAP1 TBC1D20

Molecular functions related to Warburg Micro Syndrome 2 according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 Rab guanyl-nucleotide exchange factor activity GO:0017112 9.16 RAB3GAP1 RAB3GAP2
2 GTPase activator activity GO:0005096 9.13 RAB3GAP1 RAB3GAP2 TBC1D20
3 Rab GTPase binding GO:0017137 8.8 RAB3GAP1 RAB3GAP2 TBC1D20
Sources

Sources for Warburg Micro Syndrome 2

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3 CDC
7 CNVD
9 Cosmic
10 dbSNP
11 DGIdb
17 EFO
18 ExPASy
20 FMA
29 GO
30 GTR
31 HGMD
32 HMDB
33 HPO
34 ICD10
35 ICD10 via Orphanet
36 ICD9CM
37 IUPHAR
38 KEGG
39 LifeMap
41 LOVD
43 MedGen
45 MeSH
46 MESH via Orphanet
47 MGI
50 NCI
51 NCIt
52 NDF-RT
55 NINDS
56 Novoseek
58 OMIM
59 OMIM via Orphanet
63 PubMed
65 QIAGEN
70 SNOMED-CT via HPO
71 SNOMED-CT via Orphanet
72 TGDB
73 Tocris
74 UMLS
75 UMLS via Orphanet
The MalaCards human disease database index: 1-9 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
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