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WARBM2
MCID: WRB003
MIFTS: 35

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 57 12 75 29 13 6 15 73
Micro Syndrome 2 57 12 75
Warbm2 57 12 75
Warburg Micro Syndrome, Type 2 40

Characteristics:

OMIM:

57
Inheritance:
autosomal recessive


HPO:

32
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: 33


Sources

Summaries for Warburg Micro Syndrome 2

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UniProtKB/Swiss-Prot : 75 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 eye, 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 9.8 RAB3GAP1 RAB3GAP2
2 rab18 deficiency 9.6 RAB18 RAB3GAP1 TBC1D20
3 warburg micro syndrome 9.5 RAB18 RAB3GAP1 RAB3GAP2 TBC1D20
4 warburg micro syndrome 1 9.5 RAB18 RAB3GAP1 RAB3GAP2 TBC1D20
5 warburg micro syndrome 4 9.4 RAB18 RAB3GAP1 RAB3GAP2 TBC1D20
6 spastic diplegia 9.4 RAB18 RAB3GAP1 RAB3GAP2 TBC1D20
7 microcephaly 9.4 RAB18 RAB3GAP1 RAB3GAP2 TBC1D20
8 martsolf syndrome 9.3 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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Symptoms via clinical synopsis from OMIM:

57
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

Human phenotypes related to Warburg Micro Syndrome 2:

32 (show all 27)
# Description HPO Frequency HPO Source Accession
1 macrotia 32 HP:0000400
2 short nose 32 HP:0003196
3 optic atrophy 32 HP:0000648
4 flexion contracture 32 HP:0001371
5 brachycephaly 32 HP:0000248
6 intellectual disability, severe 32 HP:0010864
7 severe global developmental delay 32 HP:0011344
8 absent speech 32 HP:0001344
9 cryptorchidism 32 HP:0000028
10 postnatal growth retardation 32 HP:0008897
11 prominent nasal bridge 32 HP:0000426
12 microphthalmia 32 HP:0000568
13 low anterior hairline 32 HP:0000294
14 microcornea 32 HP:0000482
15 polymicrogyria 32 HP:0002126
16 micropenis 32 HP:0000054
17 hypoplasia of the corpus callosum 32 HP:0002079
18 scrotal hypoplasia 32 HP:0000046
19 hypoplastic labia majora 32 HP:0000059
20 spastic diplegia 32 HP:0001264
21 postnatal microcephaly 32 HP:0005484
22 congenital cataract 32 HP:0000519
23 muscular hypotonia of the trunk 32 HP:0008936
24 overlapping toe 32 HP:0001845
25 global brain atrophy 32 HP:0002283
26 undetectable visual evoked potentials 32 HP:0007965
27 asymmetry of the ears 32 HP:0010722
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 29 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:

41
Brain, Eye
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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.499_507delTTCTACACT (p.Phe167_Thr169del) deletion Pathogenic GRCh37 Chromosome 1, 220384146: 220384154
2 RAB3GAP2 NM_012414.3(RAB3GAP2): c.499_507delTTCTACACT (p.Phe167_Thr169del) deletion Pathogenic GRCh38 Chromosome 1, 220210804: 220210812
3 RAB3GAP2 NM_012414.3(RAB3GAP2): c.1434G> A (p.Trp478Ter) single nucleotide variant Pathogenic rs587777168 GRCh37 Chromosome 1, 220364463: 220364463
4 RAB3GAP2 NM_012414.3(RAB3GAP2): c.1434G> A (p.Trp478Ter) single nucleotide variant Pathogenic rs587777168 GRCh38 Chromosome 1, 220191121: 220191121
5 RAB3GAP2 NM_012414.3(RAB3GAP2): c.3637C> T (p.Arg1213Ter) single nucleotide variant Pathogenic rs587777169 GRCh37 Chromosome 1, 220327318: 220327318
6 RAB3GAP2 NM_012414.3(RAB3GAP2): c.3637C> T (p.Arg1213Ter) single nucleotide variant Pathogenic rs587777169 GRCh38 Chromosome 1, 220153976: 220153976
7 RAB3GAP2 NM_012414.3(RAB3GAP2): c.3085G> T (p.Glu1029Ter) single nucleotide variant Pathogenic rs587777170 GRCh37 Chromosome 1, 220340637: 220340637
8 RAB3GAP2 NM_012414.3(RAB3GAP2): c.3085G> T (p.Glu1029Ter) single nucleotide variant Pathogenic rs587777170 GRCh38 Chromosome 1, 220167295: 220167295
9 RAB3GAP2 NM_012414.3(RAB3GAP2): c.774A> G (p.Leu258=) single nucleotide variant Conflicting interpretations of pathogenicity rs576411922 GRCh37 Chromosome 1, 220375655: 220375655
10 RAB3GAP2 NM_012414.3(RAB3GAP2): c.774A> G (p.Leu258=) single nucleotide variant Conflicting interpretations of pathogenicity rs576411922 GRCh38 Chromosome 1, 220202313: 220202313
11 RAB3GAP2 NM_012414.3(RAB3GAP2): c.2088A> G (p.Thr696=) single nucleotide variant Benign/Likely benign rs2577126 GRCh37 Chromosome 1, 220356184: 220356184
12 RAB3GAP2 NM_012414.3(RAB3GAP2): c.2088A> G (p.Thr696=) single nucleotide variant Benign/Likely benign rs2577126 GRCh38 Chromosome 1, 220182842: 220182842
13 RAB3GAP2 NM_012414.3(RAB3GAP2): c.2587A> G (p.Thr863Ala) single nucleotide variant Benign/Likely benign rs12045447 GRCh37 Chromosome 1, 220344453: 220344453
14 RAB3GAP2 NM_012414.3(RAB3GAP2): c.2587A> G (p.Thr863Ala) single nucleotide variant Benign/Likely benign rs12045447 GRCh38 Chromosome 1, 220171111: 220171111
15 RAB3GAP2 NM_012414.3(RAB3GAP2): c.713-2A> G single nucleotide variant Conflicting interpretations of pathogenicity rs797045103 GRCh37 Chromosome 1, 220375718: 220375718
16 RAB3GAP2 NM_012414.3(RAB3GAP2): c.713-2A> G single nucleotide variant Conflicting interpretations of pathogenicity rs797045103 GRCh38 Chromosome 1, 220202376: 220202376
17 RAB3GAP2 NM_012414.3(RAB3GAP2): c.4060A> G (p.Ile1354Val) single nucleotide variant Conflicting interpretations of pathogenicity rs59190330 GRCh37 Chromosome 1, 220324715: 220324715
18 RAB3GAP2 NM_012414.3(RAB3GAP2): c.4060A> G (p.Ile1354Val) single nucleotide variant Conflicting interpretations of pathogenicity rs59190330 GRCh38 Chromosome 1, 220151373: 220151373
19 RAB3GAP2 NM_012414.3(RAB3GAP2): c.3924G> C (p.Thr1308=) single nucleotide variant Benign rs73098539 GRCh37 Chromosome 1, 220325050: 220325050
20 RAB3GAP2 NM_012414.3(RAB3GAP2): c.3924G> C (p.Thr1308=) single nucleotide variant Benign rs73098539 GRCh38 Chromosome 1, 220151708: 220151708
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 GRCh37 Chromosome 1, 220338117: 220338117
26 RAB3GAP2 NM_012414.3(RAB3GAP2): c.3112A> G (p.Ile1038Val) single nucleotide variant Uncertain significance rs144779240 GRCh38 Chromosome 1, 220164775: 220164775
27 RAB3GAP2 NM_012414.3(RAB3GAP2): c.1215C> T (p.Phe405=) single nucleotide variant Benign/Likely benign rs762485949 GRCh37 Chromosome 1, 220366637: 220366637
28 RAB3GAP2 NM_012414.3(RAB3GAP2): c.1215C> T (p.Phe405=) single nucleotide variant Benign/Likely benign rs762485949 GRCh38 Chromosome 1, 220193295: 220193295
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 GRCh37 Chromosome 1, 220356065: 220356065
32 RAB3GAP2 NM_012414.3(RAB3GAP2): c.2207dup (p.Leu737Phefs) duplication Pathogenic GRCh38 Chromosome 1, 220182723: 220182723
33 RAB3GAP2 NM_012414.3(RAB3GAP2): c.310T> C (p.Trp104Arg) single nucleotide variant Uncertain significance GRCh37 Chromosome 1, 220386305: 220386305
34 RAB3GAP2 NM_012414.3(RAB3GAP2): c.310T> C (p.Trp104Arg) single nucleotide variant Uncertain significance GRCh38 Chromosome 1, 220212963: 220212963
35 RAB3GAP2 NM_012414.3(RAB3GAP2): c.3805G> A (p.Val1269Ile) single nucleotide variant Uncertain significance rs778851334 GRCh37 Chromosome 1, 220326589: 220326589
36 RAB3GAP2 NM_012414.3(RAB3GAP2): c.3805G> A (p.Val1269Ile) single nucleotide variant Uncertain significance rs778851334 GRCh38 Chromosome 1, 220153247: 220153247
37 RAB3GAP2 NM_012414.3(RAB3GAP2): c.1511T> C (p.Ile504Thr) single nucleotide variant Uncertain significance GRCh37 Chromosome 1, 220363839: 220363839
38 RAB3GAP2 NM_012414.3(RAB3GAP2): c.1511T> C (p.Ile504Thr) single nucleotide variant Uncertain significance 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 66
Show member pathways
 12.66 RAB18 RAB3GAP1 RAB3GAP2 TBC1D20
2
Golgi-to-ER retrograde transport 66
Show member pathways
 11.95 RAB18 RAB3GAP1 RAB3GAP2
3
RAB GEFs exchange GTP for GDP on RABs 66
11.09 RAB18 RAB3GAP1 RAB3GAP2
4
COPI-independent Golgi-to-ER retrograde traffic 66
10.25 RAB18 RAB3GAP1 RAB3GAP2
Sources

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 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
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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