WARBM2
MCID: WRB003
MIFTS: 34

Warburg Micro Syndrome 2 (WARBM2)

Categories: Eye diseases, Genetic diseases, Mental diseases, Neuronal diseases, Rare diseases

Aliases & Classifications for Warburg Micro Syndrome 2

Summaries for Warburg Micro Syndrome 2

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

Related Diseases for Warburg Micro Syndrome 2

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



Diseases related to Warburg Micro Syndrome 2

Symptoms & Phenotypes for Warburg Micro Syndrome 2

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

Drugs & Therapeutics for Warburg Micro Syndrome 2

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

Genetic Tests for Warburg Micro Syndrome 2

Genetic tests related to Warburg Micro Syndrome 2:

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

Anatomical Context for Warburg Micro Syndrome 2

MalaCards organs/tissues related to Warburg Micro Syndrome 2:

42
Brain

Publications for Warburg Micro Syndrome 2

Variations for Warburg Micro Syndrome 2

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

Expression for Warburg Micro Syndrome 2

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

Pathways for Warburg Micro Syndrome 2

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

# Super pathways Score Top Affiliating Genes
1
Show member pathways
12.66 RAB18 RAB3GAP1 RAB3GAP2 TBC1D20
2
Show member pathways
11.95 RAB18 RAB3GAP1 RAB3GAP2
3 11.09 RAB18 RAB3GAP1 RAB3GAP2
4 10.25 RAB18 RAB3GAP1 RAB3GAP2

GO Terms for Warburg Micro Syndrome 2

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 for Warburg Micro Syndrome 2

3 CDC
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10 dbSNP
11 DGIdb
17 EFO
18 ExPASy
20 FMA
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31 HGMD
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70 SNOMED-CT via HPO
71 SNOMED-CT via Orphanet
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75 UMLS via Orphanet
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