Gdap1 (ganglioside-induced differentiation-associated-protein 1) - Rat Genome Database

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Pathways
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Gene: Gdap1 (ganglioside-induced differentiation-associated-protein 1) Rattus norvegicus
Analyze
Symbol: Gdap1
Name: ganglioside-induced differentiation-associated-protein 1
RGD ID: 1309005
Description: Involved in cellular response to vitamin D. Predicted to be located in cytosol and mitochondrial outer membrane. Human ortholog(s) of this gene implicated in Charcot-Marie-Tooth disease; Charcot-Marie-Tooth disease axonal type 2C; Charcot-Marie-Tooth disease axonal type 2K; Charcot-Marie-Tooth disease recessive intermediate A; and Charcot-Marie-Tooth disease type 4A. Orthologous to human GDAP1 (ganglioside induced differentiation associated protein 1); PARTICIPATES IN mitochondria fission pathway; INTERACTS WITH 6-propyl-2-thiouracil; amitrole; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: ganglioside-induced differentiation-associated protein 1; LOC312890
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr856,715,935 - 6,735,013 (-)NCBIGRCr8
mRatBN7.251,932,613 - 1,951,691 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl51,932,613 - 2,030,061 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx54,048,988 - 4,068,071 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.055,687,862 - 5,706,945 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.055,381,543 - 5,400,606 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.051,328,963 - 1,347,946 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl51,328,913 - 1,347,921 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.051,323,590 - 1,342,573 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.451,006,203 - 1,025,281 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.151,008,936 - 1,025,382 (-)NCBI
Celera51,574,343 - 1,593,421 (-)NCBICelera
Cytogenetic Map5q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytosol  (IEA,ISO)
mitochondrial outer membrane  (IBA,ISO,ISS)
mitochondrion  (ISO)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Ganglioside-induced differentiation-associated protein-1 is mutant in Charcot-Marie-Tooth disease type 4A/8q21. Baxter RV, etal., Nat Genet. 2002 Jan;30(1):21-2. Epub 2001 Dec 17.
2. The gene encoding ganglioside-induced differentiation-associated protein 1 is mutated in axonal Charcot-Marie-Tooth type 4A disease. Cuesta A, etal., Nat Genet. 2002 Jan;30(1):22-5. Epub 2001 Dec 17.
3. Mitochondria dynamism: of shape, transport and cell migration. da Silva AF, etal., Cell Mol Life Sci. 2014 Jun;71(12):2313-24. doi: 10.1007/s00018-014-1557-8. Epub 2014 Jan 18.
4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
5. L239F founder mutation in GDAP1 is associated with a mild Charcot-Marie-Tooth type 4C4 (CMT4C4) phenotype. Kabzinska D, etal., Neurogenetics. 2010 Jul;11(3):357-66. doi: 10.1007/s10048-010-0237-6. Epub 2010 Mar 16.
6. A new missense GDAP1 mutation disturbing targeting to the mitochondrial membrane causes a severe form of AR-CMT2C disease. Kabzinska D, etal., Neurogenetics. 2011 May;12(2):145-53. doi: 10.1007/s10048-011-0276-7. Epub 2011 Mar 2.
7. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
8. Mutations in GDAP1: autosomal recessive CMT with demyelination and axonopathy. Nelis E, etal., Neurology 2002 Dec 24;59(12):1865-72.
9. The Gdap1 knockout mouse mechanistically links redox control to Charcot-Marie-Tooth disease. Niemann A, etal., Brain. 2014 Mar;137(Pt 3):668-82. doi: 10.1093/brain/awt371. Epub 2014 Jan 29.
10. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
11. The regulation of mitochondrial morphology: intricate mechanisms and dynamic machinery. Palmer CS, etal., Cell Signal. 2011 Oct;23(10):1534-45. doi: 10.1016/j.cellsig.2011.05.021. Epub 2011 Jun 13.
12. Cell expression of GDAP1 in the nervous system and pathogenesis of Charcot-Marie-Tooth type 4A disease. Pedrola L, etal., J Cell Mol Med. 2008 Apr;12(2):679-89. Epub 2007 Nov 16.
13. Discovery of novel vitamin D-regulated proteins in INS-1 cells: a proteomic approach. Pepaj M, etal., Diabetes Metab Res Rev. 2015 Jul;31(5):481-91. doi: 10.1002/dmrr.2629. Epub 2015 Feb 6.
14. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
15. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
16. Comprehensive gene review and curation RGD comprehensive gene curation
17. A novel mutation in the GDAP1 gene is associated with autosomal recessive Charcot-Marie-Tooth disease in an Amish family. Xin B, etal., Clin Genet. 2008 Sep;74(3):274-8. doi: 10.1111/j.1399-0004.2008.01018.x. Epub 2008 May 19.
Additional References at PubMed
PMID:10217254   PMID:15772096   PMID:19946888   PMID:21630459   PMID:21753178   PMID:22871113  


Genomics

Comparative Map Data
Gdap1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr856,715,935 - 6,735,013 (-)NCBIGRCr8
mRatBN7.251,932,613 - 1,951,691 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl51,932,613 - 2,030,061 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx54,048,988 - 4,068,071 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.055,687,862 - 5,706,945 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.055,381,543 - 5,400,606 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.051,328,963 - 1,347,946 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl51,328,913 - 1,347,921 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.051,323,590 - 1,342,573 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.451,006,203 - 1,025,281 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.151,008,936 - 1,025,382 (-)NCBI
Celera51,574,343 - 1,593,421 (-)NCBICelera
Cytogenetic Map5q11NCBI
GDAP1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38874,350,403 - 74,488,872 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl874,320,613 - 74,518,007 (+)EnsemblGRCh38hg38GRCh38
GRCh37875,262,638 - 75,401,107 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36875,425,173 - 75,441,900 (+)NCBINCBI36Build 36hg18NCBI36
Build 34875,425,251 - 75,439,157NCBI
Celera871,260,475 - 71,277,203 (+)NCBICelera
Cytogenetic Map8q21.11NCBI
HuRef870,753,599 - 70,770,326 (+)NCBIHuRef
CHM1_1875,314,604 - 75,331,330 (+)NCBICHM1_1
T2T-CHM13v2.0874,779,703 - 74,918,431 (+)NCBIT2T-CHM13v2.0
Gdap1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39117,202,028 - 17,234,513 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl117,215,586 - 17,234,495 (+)EnsemblGRCm39 Ensembl
GRCm38117,145,373 - 17,164,271 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl117,145,362 - 17,164,271 (+)EnsemblGRCm38mm10GRCm38
MGSCv37117,135,454 - 17,154,352 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36117,130,611 - 17,149,485 (+)NCBIMGSCv36mm8
Celera117,069,144 - 17,087,736 (+)NCBICelera
Cytogenetic Map1A3NCBI
cM Map15.21NCBI
Gdap1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554446,051,301 - 6,069,765 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554446,053,422 - 6,069,741 (-)NCBIChiLan1.0ChiLan1.0
GDAP1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2790,064,000 - 90,109,634 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1865,691,783 - 65,820,188 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0870,854,665 - 70,900,532 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1872,528,869 - 72,545,354 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl872,528,869 - 72,545,346 (+)Ensemblpanpan1.1panPan2
GDAP1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12922,805,468 - 22,835,909 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2922,804,965 - 22,833,069 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2923,070,273 - 23,100,798 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02922,916,906 - 22,947,452 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2922,928,645 - 23,031,398 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12922,976,040 - 23,006,559 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02923,010,785 - 23,041,610 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02923,361,889 - 23,392,422 (+)NCBIUU_Cfam_GSD_1.0
Gdap1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440530356,448,982 - 56,466,822 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366482,981,546 - 3,014,430 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366482,981,802 - 2,999,161 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
GDAP1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl461,577,112 - 61,596,049 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1461,577,413 - 61,596,106 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2467,190,455 - 67,209,140 (-)NCBISscrofa10.2Sscrofa10.2susScr3
GDAP1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1869,948,800 - 69,965,168 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl869,949,052 - 69,966,421 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603971,407,858 - 71,452,631 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Gdap1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474416,859,700 - 16,879,057 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474416,859,946 - 16,878,723 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Gdap1
34 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:232
Count of miRNA genes:161
Interacting mature miRNAs:189
Transcripts:ENSRNOT00000007994
Prediction methods:Miranda
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5190450412Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51131345958Rat
1331771Rf35Renal function QTL 354.36965kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)572947086724018Rat


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 68 1
Low 2 9 14 4 6 4 8 10 6 18 33 11 8
Below cutoff 1 34 24 18 13 18 1 17 5

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000007994   ⟹   ENSRNOP00000007994
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl51,932,613 - 2,030,061 (-)Ensembl
Rnor_6.0 Ensembl51,328,913 - 1,347,921 (-)Ensembl
RefSeq Acc Id: NM_001107897   ⟹   NP_001101367
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr856,715,935 - 6,735,013 (-)NCBI
mRatBN7.251,932,613 - 1,951,691 (-)NCBI
Rnor_6.051,328,963 - 1,347,946 (-)NCBI
Rnor_5.051,323,590 - 1,342,573 (-)NCBI
RGSC_v3.451,006,203 - 1,025,281 (-)RGD
Celera51,574,343 - 1,593,421 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001101367 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM11488 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000007994
  ENSRNOP00000007994.5
Reference Protein Sequences
RefSeq Acc Id: NP_001101367   ⟸   NM_001107897
- UniProtKB: D4A5X7 (UniProtKB/TrEMBL),   A6JF92 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000007994   ⟸   ENSRNOT00000007994
Protein Domains
GST C-terminal   GST N-terminal

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A5X7-F1-model_v2 AlphaFold D4A5X7 1-358 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309005 AgrOrtholog
BioCyc Gene G2FUF-42324 BioCyc
Ensembl Genes ENSRNOG00000005850 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000007994 ENTREZGENE
  ENSRNOT00000007994.7 UniProtKB/TrEMBL
Gene3D-CATH 1.20.1050.10 UniProtKB/TrEMBL
  Glutaredoxin UniProtKB/TrEMBL
InterPro GDAP1 UniProtKB/TrEMBL
  Glutathione-S-Trfase_C-like UniProtKB/TrEMBL
  Glutathione-S-Trfase_C_sf UniProtKB/TrEMBL
  Glutathione_S-Trfase UniProtKB/TrEMBL
  Glutathione_S-Trfase_N UniProtKB/TrEMBL
  Thioredoxin-like_sf UniProtKB/TrEMBL
KEGG Report rno:312890 UniProtKB/TrEMBL
NCBI Gene 312890 ENTREZGENE
PANTHER GDAP1, ISOFORM A UniProtKB/TrEMBL
  PTHR44188:SF3 UniProtKB/TrEMBL
Pfam GST_C_2 UniProtKB/TrEMBL
  GST_N_3 UniProtKB/TrEMBL
PhenoGen Gdap1 PhenoGen
PROSITE GST_CTER UniProtKB/TrEMBL
  GST_NTER UniProtKB/TrEMBL
RatGTEx ENSRNOG00000005850 RatGTEx
Superfamily-SCOP GST_C_like UniProtKB/TrEMBL
  Thiordxn-like_fd UniProtKB/TrEMBL
UniProt A6JF92 ENTREZGENE, UniProtKB/TrEMBL
  D4A5X7 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Gdap1  ganglioside-induced differentiation-associated-protein 1   Gdap1_predicted  ganglioside-induced differentiation-associated-protein 1 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Gdap1_predicted  ganglioside-induced differentiation-associated-protein 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED