WARBM2
MCID: WRB003
MIFTS: 41

Warburg Micro Syndrome 2 (WARBM2)

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

Aliases & Classifications for Warburg Micro Syndrome 2

MalaCards integrated aliases for Warburg Micro Syndrome 2:

Name: Warburg Micro Syndrome 2 56 12 73 29 13 6 15 71
Micro Syndrome 2 56 12 73
Warbm2 56 12 73
Warburg Micro Syndrome, Type 2 39

Characteristics:

OMIM:

56
Inheritance:
autosomal recessive


HPO:

31
warburg micro syndrome 2:
Inheritance autosomal recessive inheritance


Classifications:



Summaries for Warburg Micro Syndrome 2

UniProtKB/Swiss-Prot : 73 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 spastic cerebral palsy 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 Sertoli-Sertoli Cell Junction Dynamics. 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.

More information from OMIM: 614225 PS600118

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:

31 (show all 27)
# Description HPO Frequency HPO Source Accession
1 macrotia 31 HP:0000400
2 short nose 31 HP:0003196
3 optic atrophy 31 HP:0000648
4 flexion contracture 31 HP:0001371
5 brachycephaly 31 HP:0000248
6 intellectual disability, severe 31 HP:0010864
7 absent speech 31 HP:0001344
8 cryptorchidism 31 HP:0000028
9 postnatal growth retardation 31 HP:0008897
10 micropenis 31 HP:0000054
11 microphthalmia 31 HP:0000568
12 low anterior hairline 31 HP:0000294
13 prominent nasal bridge 31 HP:0000426
14 severe global developmental delay 31 HP:0011344
15 microcornea 31 HP:0000482
16 polymicrogyria 31 HP:0002126
17 scrotal hypoplasia 31 HP:0000046
18 hypoplastic labia majora 31 HP:0000059
19 hypoplasia of the corpus callosum 31 HP:0002079
20 postnatal microcephaly 31 HP:0005484
21 spastic diplegia 31 HP:0001264
22 muscular hypotonia of the trunk 31 HP:0008936
23 developmental cataract 31 HP:0000519
24 overlapping toe 31 HP:0001845
25 global brain atrophy 31 HP:0002283
26 asymmetry of the ears 31 HP:0010722
27 undetectable visual evoked potentials 31 HP:0007965

Symptoms via clinical synopsis from OMIM:

56
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 Eyes:
microphthalmia
microcornea
optic nerve atrophy
congenital cataracts, bilateral
atonic pupils
more
Skin Nails Hair Hair:
low anterior hairline

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

Genitourinary External Genitalia Male:
micropenis
scrotal hypoplasia

Head And Neck Face:
low anterior hairline

Skeletal Skull:
microcephaly, postnatal

Skeletal Feet:
overlapping toes

Genitourinary External Genitalia Female:
hypoplasia of labia majora

Clinical features from OMIM:

614225

MGI Mouse Phenotypes related to Warburg Micro Syndrome 2:

45
# Description MGI Source Accession Score Top Affiliating Genes
1 homeostasis/metabolism MP:0005376 9.36 EXO1 GSK3B HACD1 PRNP RAB2A RAB3A

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 29 RAB3GAP2

Anatomical Context for Warburg Micro Syndrome 2

MalaCards organs/tissues related to Warburg Micro Syndrome 2:

40
Brain

Publications for Warburg Micro Syndrome 2

Articles related to Warburg Micro Syndrome 2:

# Title Authors PMID Year
1
Mutation spectrum in RAB3GAP1, RAB3GAP2, and RAB18 and genotype-phenotype correlations in warburg micro syndrome and Martsolf syndrome. 6 56
23420520 2013
2
A homozygous RAB3GAP2 mutation causes Warburg Micro syndrome. 6 56
20967465 2011
3
RAB18 Deficiency 6
29300443 2018
4
Case report of four siblings in southeast Turkey with a novel RAB3GAP2 splice site mutation: Warburg micro syndrome or Martsolf syndrome? 61
29419336 2018

Variations for Warburg Micro Syndrome 2

ClinVar genetic disease variations for Warburg Micro Syndrome 2:

6 (show top 50) (show all 152) ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎
# Gene Name Type Significance ClinVarId dbSNP ID GRCh37 Pos GRCh38 Pos
1 RAB3GAP2 NM_012414.4(RAB3GAP2):c.2207dup (p.Leu737fs)duplication Pathogenic 436479 rs1553275687 1:220356064-220356065 1:220182722-220182723
2 RAB3GAP2 NM_012414.4(RAB3GAP2):c.1434G>A (p.Trp478Ter)SNV Pathogenic 100788 rs587777168 1:220364463-220364463 1:220191121-220191121
3 RAB3GAP2 NM_012414.4(RAB3GAP2):c.3637C>T (p.Arg1213Ter)SNV Pathogenic 100789 rs587777169 1:220327318-220327318 1:220153976-220153976
4 RAB3GAP2 NM_012414.4(RAB3GAP2):c.3085G>T (p.Glu1029Ter)SNV Pathogenic 100790 rs587777170 1:220340637-220340637 1:220167295-220167295
5 RAB3GAP2 NM_012414.4(RAB3GAP2):c.499_507del (p.Phe167_Thr169del)deletion Pathogenic 30782 rs1553278569 1:220384146-220384154 1:220210804-220210812
6 RAB3GAP2 NM_012414.4(RAB3GAP2):c.1276C>T (p.Arg426Cys)SNV Pathogenic/Likely pathogenic 100787 rs587777167 1:220364621-220364621 1:220191279-220191279
7 RAB3GAP2 NM_012414.4(RAB3GAP2):c.2008C>G (p.Leu670Val)SNV Conflicting interpretations of pathogenicity 211984 rs201613456 1:220356264-220356264 1:220182922-220182922
8 RAB3GAP2 NM_012414.4(RAB3GAP2):c.2290C>T (p.Leu764Phe)SNV Conflicting interpretations of pathogenicity 235683 rs139337049 1:220355619-220355619 1:220182277-220182277
9 RAB3GAP2 NM_012414.4(RAB3GAP2):c.3702C>T (p.Val1234=)SNV Conflicting interpretations of pathogenicity 286109 rs137897304 1:220326692-220326692 1:220153350-220153350
10 RAB3GAP2 NM_012414.4(RAB3GAP2):c.3842A>G (p.Tyr1281Cys)SNV Conflicting interpretations of pathogenicity 287196 rs34081806 1:220326552-220326552 1:220153210-220153210
11 RAB3GAP2 NM_012414.4(RAB3GAP2):c.713-2A>GSNV Conflicting interpretations of pathogenicity 208607 rs797045103 1:220375718-220375718 1:220202376-220202376
12 RAB3GAP2 NM_012414.4(RAB3GAP2):c.4060A>G (p.Ile1354Val)SNV Conflicting interpretations of pathogenicity 211989 rs59190330 1:220324715-220324715 1:220151373-220151373
13 RAB3GAP2 NM_012414.4(RAB3GAP2):c.2168T>A (p.Val723Glu)SNV Conflicting interpretations of pathogenicity 295652 rs150643803 1:220356104-220356104 1:220182762-220182762
14 RAB3GAP2 NM_012414.4(RAB3GAP2):c.3867+13C>TSNV Conflicting interpretations of pathogenicity 295640 rs200579008 1:220326514-220326514 1:220153172-220153172
15 RAB3GAP2 NM_012414.4(RAB3GAP2):c.3390G>A (p.Ala1130=)SNV Conflicting interpretations of pathogenicity 295642 rs140377995 1:220330777-220330777 1:220157435-220157435
16 RAB3GAP2 NM_012414.4(RAB3GAP2):c.774A>G (p.Leu258=)SNV Conflicting interpretations of pathogenicity 130073 rs576411922 1:220375655-220375655 1:220202313-220202313
17 RAB3GAP2 NM_012414.4(RAB3GAP2):c.3294T>C (p.Ser1098=)SNV Conflicting interpretations of pathogenicity 767430 1:220331186-220331186 1:220157844-220157844
18 RAB3GAP2 NM_012414.4(RAB3GAP2):c.*1340T>CSNV Uncertain significance 874117 1:220323253-220323253 1:220149911-220149911
19 RAB3GAP2 NM_012414.4(RAB3GAP2):c.*1087A>CSNV Uncertain significance 875049 1:220323506-220323506 1:220150164-220150164
20 RAB3GAP2 NM_012414.4(RAB3GAP2):c.*777T>CSNV Uncertain significance 875050 1:220323816-220323816 1:220150474-220150474
21 RAB3GAP2 NM_012414.4(RAB3GAP2):c.*509G>ASNV Uncertain significance 875978 1:220324084-220324084 1:220150742-220150742
22 RAB3GAP2 NM_012414.4(RAB3GAP2):c.*436A>GSNV Uncertain significance 876952 1:220324157-220324157 1:220150815-220150815
23 RAB3GAP2 NM_012414.4(RAB3GAP2):c.*417A>GSNV Uncertain significance 876953 1:220324176-220324176 1:220150834-220150834
24 RAB3GAP2 NM_012414.4(RAB3GAP2):c.*391C>TSNV Uncertain significance 876954 1:220324202-220324202 1:220150860-220150860
25 RAB3GAP2 NM_012414.4(RAB3GAP2):c.*104T>CSNV Uncertain significance 874166 1:220324489-220324489 1:220151147-220151147
26 RAB3GAP2 NM_012414.4(RAB3GAP2):c.*78G>ASNV Uncertain significance 874167 1:220324515-220324515 1:220151173-220151173
27 RAB3GAP2 NM_012414.4(RAB3GAP2):c.2922T>A (p.Gly974=)SNV Uncertain significance 874219 1:220340902-220340902 1:220167560-220167560
28 RAB3GAP2 NM_012414.4(RAB3GAP2):c.2340G>C (p.Lys780Asn)SNV Uncertain significance 876099 1:220346055-220346055 1:220172713-220172713
29 RAB3GAP2 NM_012414.4(RAB3GAP2):c.2059G>A (p.Glu687Lys)SNV Uncertain significance 877054 1:220356213-220356213 1:220182871-220182871
30 RAB3GAP2 NM_012414.4(RAB3GAP2):c.1608C>T (p.Asn536=)SNV Uncertain significance 875200 1:220363742-220363742 1:220190400-220190400
31 RAB3GAP2 NM_012414.4(RAB3GAP2):c.1593T>A (p.Ser531Arg)SNV Uncertain significance 875201 1:220363757-220363757 1:220190415-220190415
32 RAB3GAP2 NM_012414.4(RAB3GAP2):c.1589G>A (p.Gly530Glu)SNV Uncertain significance 875202 1:220363761-220363761 1:220190419-220190419
33 RAB3GAP2 NM_012414.4(RAB3GAP2):c.1580C>G (p.Pro527Arg)SNV Uncertain significance 876157 1:220363770-220363770 1:220190428-220190428
34 RAB3GAP2 NM_012414.4(RAB3GAP2):c.1516G>A (p.Gly506Ser)SNV Uncertain significance 876158 1:220363834-220363834 1:220190492-220190492
35 RAB3GAP2 NM_012414.4(RAB3GAP2):c.1328T>C (p.Val443Ala)SNV Uncertain significance 876299 1:220364569-220364569 1:220191227-220191227
36 RAB3GAP2 NM_012414.4(RAB3GAP2):c.1244G>A (p.Arg415Lys)SNV Uncertain significance 876300 1:220366608-220366608 1:220193266-220193266
37 RAB3GAP2 NM_012414.4(RAB3GAP2):c.695G>A (p.Arg232Gln)SNV Uncertain significance 875250 1:220379266-220379266 1:220205924-220205924
38 RAB3GAP2 NM_012414.4(RAB3GAP2):c.376G>A (p.Val126Ile)SNV Uncertain significance 876344 1:220386239-220386239 1:220212897-220212897
39 RAB3GAP2 NM_012414.4(RAB3GAP2):c.205A>G (p.Thr69Ala)SNV Uncertain significance 876345 1:220387297-220387297 1:220213955-220213955
40 RAB3GAP2 NM_012414.4(RAB3GAP2):c.86T>G (p.Ile29Ser)SNV Uncertain significance 874387 1:220445594-220445594 1:220272252-220272252
41 RAB3GAP2 NM_012414.4(RAB3GAP2):c.-20T>CSNV Uncertain significance 874388 1:220445699-220445699 1:220272357-220272357
42 RAB3GAP2 NM_012414.4(RAB3GAP2):c.-68C>TSNV Uncertain significance 875305 1:220445747-220445747 1:220272405-220272405
43 RAB3GAP2 NM_012414.4(RAB3GAP2):c.2981-7C>TSNV Uncertain significance 874218 1:220340748-220340748 1:220167406-220167406
44 RAB3GAP2 NM_012414.4(RAB3GAP2):c.960+13T>GSNV Uncertain significance 875249 1:220369579-220369579 1:220196237-220196237
45 RAB3GAP2 NM_012414.4(RAB3GAP2):c.613-14T>ASNV Uncertain significance 876216 1:220379362-220379362 1:220206020-220206020
46 RAB3GAP2 NM_012414.4(RAB3GAP2):c.1406C>T (p.Ala469Val)SNV Uncertain significance 436474 rs151225064 1:220364491-220364491 1:220191149-220191149
47 RAB3GAP2 NM_012414.4(RAB3GAP2):c.310T>C (p.Trp104Arg)SNV Uncertain significance 463030 rs1553278790 1:220386305-220386305 1:220212963-220212963
48 RAB3GAP2 NM_012414.4(RAB3GAP2):c.3805G>A (p.Val1269Ile)SNV Uncertain significance 463031 rs778851334 1:220326589-220326589 1:220153247-220153247
49 RAB3GAP2 NM_012414.4(RAB3GAP2):c.1511T>C (p.Ile504Thr)SNV Uncertain significance 463027 rs1553276414 1:220363839-220363839 1:220190497-220190497
50 RAB3GAP2 NM_012414.4(RAB3GAP2):c.1258C>T (p.Arg420Cys)SNV Uncertain significance 463026 rs188522997 1:220366594-220366594 1:220193252-220193252

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
12.97 TBC1D20 TBC1D1 RAB3GAP2 RAB3GAP1 RAB3A RAB18
2
Show member pathways
12.56 RAB3D RAB3A RAB2A RAB18 GSK3B
3 11.84 RAB3D RAB3A RAB2A RAB18
4 11.21 RAB3GAP2 RAB3GAP1 RAB3A RAB18
5 10.78 RAB3GAP2 RAB3GAP1 RAB18
6 10.74 RAB3D RAB3A RAB2A RAB18

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 postsynapse GO:0098794 9.43 RAB3GAP1 PRNP GSK3B
2 endomembrane system GO:0012505 9.26 RAB3D RAB3A RAB2A RAB18
3 endoplasmic reticulum membrane GO:0005789 9.17 TYRO3 TBC1D20 RAB3GAP2 RAB3GAP1 RAB2A RAB18
4 endoplasmic reticulum tubular network GO:0071782 9.16 RAB3GAP1 RAB18

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

(show all 13)
# Name GO ID Score Top Affiliating Genes
1 positive regulation of GTPase activity GO:0043547 9.72 TBC1D20 RAB3GAP2 RAB3GAP1 GSK3B AGFG1
2 vesicle docking involved in exocytosis GO:0006904 9.52 RAB3D RAB3A
3 negative regulation of calcineurin-NFAT signaling cascade GO:0070885 9.51 PRNP GSK3B
4 acrosome assembly GO:0001675 9.49 TBC1D20 AGFG1
5 regulation of short-term neuronal synaptic plasticity GO:0048172 9.48 RAB3GAP1 RAB3A
6 positive regulation of autophagosome assembly GO:2000786 9.46 RAB3GAP2 RAB3GAP1
7 positive regulation of regulated secretory pathway GO:1903307 9.43 RAB3D RAB3A
8 positive regulation of endoplasmic reticulum tubular network organization GO:1903373 9.4 RAB3GAP2 RAB3GAP1
9 positive regulation of protein lipidation GO:1903061 9.37 RAB3GAP2 RAB3GAP1
10 lipid droplet organization GO:0034389 9.33 TBC1D20 RAB3GAP1 RAB18
11 establishment of protein localization to endoplasmic reticulum membrane GO:0097051 9.26 RAB3GAP2 RAB3GAP1
12 Rab protein signal transduction GO:0032482 9.26 RAB3D RAB3A RAB2A RAB18
13 intracellular protein transport GO:0006886 9.1 TBC1D1 RAB3GAP2 RAB3D RAB3A RAB2A RAB18

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

# Name GO ID Score Top Affiliating Genes
1 nucleotide binding GO:0000166 9.87 TYRO3 STK38L RAB3D RAB3A RAB2A RAB18
2 GTP binding GO:0005525 9.67 RAB3D RAB3A RAB2A RAB18
3 GTPase activity GO:0003924 9.46 RAB3D RAB3A RAB2A RAB18
4 Rab guanyl-nucleotide exchange factor activity GO:0017112 9.43 RAB3GAP2 RAB3GAP1
5 GTP-dependent protein binding GO:0030742 9.4 RAB3D RAB3A
6 myosin V binding GO:0031489 9.26 RAB3D RAB3A
7 Rab GTPase binding GO:0017137 9.26 TBC1D20 TBC1D1 RAB3GAP2 RAB3GAP1
8 GTPase activator activity GO:0005096 9.02 TBC1D20 TBC1D1 RAB3GAP2 RAB3GAP1 AGFG1

Sources for Warburg Micro Syndrome 2

3 CDC
7 CNVD
9 Cosmic
10 dbSNP
11 DGIdb
17 EFO
18 ExPASy
19 FMA
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
43 MeSH
44 MESH via Orphanet
45 MGI
48 NCI
49 NCIt
50 NDF-RT
53 NINDS
54 Novoseek
56 OMIM
57 OMIM via Orphanet
61 PubMed
63 QIAGEN
68 SNOMED-CT via HPO
69 TGDB
70 Tocris
71 UMLS
72 UMLS via Orphanet
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