Kxd1 (KxDL motif containing 1) - Rat Genome Database

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Gene: Kxd1 (KxDL motif containing 1) Mus musculus
Analyze
Symbol: Kxd1
Name: KxDL motif containing 1
RGD ID: 1622240
MGI Page MGI
Description: Involved in vesicle-mediated transport. Part of BLOC-1 complex. Used to study Hermansky-Pudlak syndrome. Orthologous to human KXD1 (KxDL motif containing 1).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: 0610030B01Rik; 2810422J05Rik; C78305; hypothetical protein LOC75620; kxDL motif-containing protein 1; UPF0459 protein C19orf50 homolog
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39870,966,046 - 70,975,830 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl870,960,922 - 70,980,606 (-)EnsemblGRCm39 Ensembl
GRCm38870,513,396 - 70,523,180 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl870,508,272 - 70,527,956 (-)EnsemblGRCm38mm10GRCm38
MGSCv37873,037,295 - 73,047,079 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36873,442,375 - 73,452,456 (-)NCBIMGSCv36mm8
Celera873,069,814 - 73,079,598 (-)NCBICelera
Cytogenetic Map8B3.3NCBI
cM Map834.15NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

References - curated
# Reference Title Reference Citation
1. Mouse MP Annotation Import Pipeline RGD automated import pipeline
2. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:10349636   PMID:10725249   PMID:10922068   PMID:11042159   PMID:11076861   PMID:11217851   PMID:12466851   PMID:12477932   PMID:14610273   PMID:15782199   PMID:16141072   PMID:16141073  
PMID:17967808   PMID:18590716   PMID:18799693   PMID:21873635   PMID:22554196   PMID:25898167   PMID:27719760   PMID:31314175   PMID:33179593  


Genomics

Comparative Map Data
Kxd1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39870,966,046 - 70,975,830 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl870,960,922 - 70,980,606 (-)EnsemblGRCm39 Ensembl
GRCm38870,513,396 - 70,523,180 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl870,508,272 - 70,527,956 (-)EnsemblGRCm38mm10GRCm38
MGSCv37873,037,295 - 73,047,079 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36873,442,375 - 73,452,456 (-)NCBIMGSCv36mm8
Celera873,069,814 - 73,079,598 (-)NCBICelera
Cytogenetic Map8B3.3NCBI
cM Map834.15NCBI
KXD1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381918,557,870 - 18,569,378 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1918,557,762 - 18,569,387 (+)EnsemblGRCh38hg38GRCh38
GRCh371918,668,680 - 18,680,188 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361918,529,604 - 18,541,188 (+)NCBINCBI36Build 36hg18NCBI36
Celera1918,570,781 - 18,582,406 (+)NCBICelera
Cytogenetic Map19p13.11NCBI
HuRef1918,231,216 - 18,242,793 (+)NCBIHuRef
CHM1_11918,668,755 - 18,680,395 (+)NCBICHM1_1
T2T-CHM13v2.01918,692,823 - 18,704,439 (+)NCBIT2T-CHM13v2.0
Kxd1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81618,929,316 - 18,950,239 (+)NCBIGRCr8
mRatBN7.21618,895,343 - 18,916,266 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1618,900,616 - 18,920,807 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1618,948,538 - 18,958,041 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01620,081,243 - 20,090,744 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01619,001,500 - 19,011,003 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01620,652,863 - 20,666,581 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1620,657,099 - 20,666,579 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01620,508,327 - 20,522,060 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41619,413,529 - 19,423,011 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1619,098,221 - 19,107,703 (+)NCBICelera
Cytogenetic Map16p14NCBI
Kxd1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555243,006,147 - 3,018,772 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555243,010,997 - 3,018,309 (-)NCBIChiLan1.0ChiLan1.0
KXD1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22023,416,612 - 23,428,315 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11922,425,093 - 22,436,806 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01918,034,887 - 18,046,603 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11919,005,136 - 19,016,552 (+)NCBIpanpan1.1PanPan1.1panPan2
KXD1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12044,480,634 - 44,489,287 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2044,481,557 - 44,489,188 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2044,395,324 - 44,403,971 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02044,966,831 - 44,975,480 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2044,966,833 - 44,975,457 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12044,204,193 - 44,212,842 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02044,614,149 - 44,622,792 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02044,889,594 - 44,898,242 (-)NCBIUU_Cfam_GSD_1.0
Kxd1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118203,162,194 - 203,170,726 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365962,706,994 - 2,719,846 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365962,711,326 - 2,719,839 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
KXD1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl259,242,310 - 59,247,713 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1259,242,301 - 59,250,893 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2259,051,909 - 59,060,504 (+)NCBISscrofa10.2Sscrofa10.2susScr3
KXD1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1617,028,785 - 17,037,871 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl617,028,819 - 17,037,867 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660742,300,533 - 2,309,641 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Kxd1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046249081,736,899 - 1,750,516 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046249081,737,166 - 1,744,918 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Kxd1
787 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1645
Count of miRNA genes:619
Interacting mature miRNAs:733
Transcripts:ENSMUST00000093456, ENSMUST00000117580, ENSMUST00000118850, ENSMUST00000121623, ENSMUST00000132867, ENSMUST00000137610, ENSMUST00000138260, ENSMUST00000138586, ENSMUST00000155677
Prediction methods:Miranda, Rnahybrid, Targetscan
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 (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1558870Eae36_mexperimental allergic encephalomyelitis susceptibility 36 (mouse)Not determined81477316071498244Mouse
10043992Hbnr11_mHeligmosomoides bakeri nematode resistance 11 (mouse)Not determined866326836100326976Mouse
4141437W10q14_mweight 10 weeks QTL 14 (mouse)Not determined3250657271740637Mouse
1301717Adip4_madiposity 4 (mouse)Not determined84809006482090180Mouse
1301013Capsq4_mcapsaicin sensitivity related QTL 4 (mouse)Not determined83663015493455280Mouse
1357715Alaa3_malopecia areata 3 (mouse)Not determined84924559183245673Mouse
11353828Gf7_mgonadal fat pad weight 7 (mouse)85892810792928107Mouse
14746987Manh64_mmandible shape 64 (mouse)85050595884505958Mouse
4141172W6q9_mweight 6 weeks QTL 9 (mouse)Not determined3250657271740637Mouse
1558875Eae31_mexperimental allergic encephalomyelitis susceptibility 31 (mouse)Not determined835109930115563747Mouse
1357787Vtbt5_mvertebral trabecular bone trait 5 (mouse)Not determined866084397100084549Mouse
1301506Aevm1_mautoimmune extremity vasculitis in MRL mice 1 (mouse)Not determined85474046188740637Mouse
10766453Char11_mP. chabaudi malaria resistance QTL 11 (mouse)84809006482090180Mouse
1301441Skull11_mskull morphology 11 (mouse)Not determined84819016882190288Mouse
1301952Im3_mimmunoregulatory 3 (mouse)Not determined85515925889159407Mouse
4140967Bmd39_mbone mineral density 39 (mouse)Not determined832506572117965439Mouse
4140966Egq12_mearly growth QTL 12 (mouse)Not determined3250657271740637Mouse
4141285Tgq18_mtriglyceride QTL 18 (mouse)Not determined6418673698186736Mouse
4141797Skmw16_mskeletal muscle weight 16 (mouse)Not determined86466617698666325Mouse
14747005Mancz7_mmandible centroid size 7 (mouse)85050595884505958Mouse
27226754Femd6_mfemur midshaft diameter 6, 10 week (mouse)837867154110326632Mouse
10043975Obq31_mobesity QTL 31 (mouse)Not determined85913640493136404Mouse
10412287Carg3_mCandida albicans resistance gene 3 (mouse)Not determined85629887290298872Mouse
10766466Char12_mP. chabaudi malaria resistance QTL 12 (mouse)86872247983326976Mouse
1357811Orq3_movulation rate QTL 3 (mouse)Not determined83250657271740637Mouse
11039503Ccc4_mcolitis susceptibility in the Collaborative Cross 4 (mouse)86517423778002730Mouse
1301688Orch6_mautoimmune orchitis resistance 6 (mouse)Not determined86151347995513605Mouse
12904744Carcdq1_mcardiac collagen deposition QTL 1 (mouse)84016229795416226Mouse
14700686Civq3_mcerebral infarct volume QTL 3 (mouse)85233484386334843Mouse
1301544Iba3_minduction of brown adipocytes 3 (mouse)Not determined84474791478748059Mouse

Markers in Region
BB157005  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38870,514,579 - 70,514,682UniSTSGRCm38
MGSCv37873,038,478 - 73,038,581UniSTSGRCm37
Celera873,070,997 - 73,071,100UniSTS
Cytogenetic Map8B3.3UniSTS
Whitehead/MRC_RH8743.1UniSTS
RH126344  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38870,513,406 - 70,513,604UniSTSGRCm38
MGSCv37873,037,305 - 73,037,503UniSTSGRCm37
Celera873,069,824 - 73,070,022UniSTS
Cytogenetic Map8B3.3UniSTS


Expression

RNA-SEQ Expression


Sequence


Ensembl Acc Id: ENSMUST00000093456   ⟹   ENSMUSP00000091165
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl870,966,046 - 70,975,830 (-)Ensembl
GRCm38.p6 Ensembl870,513,396 - 70,523,180 (-)Ensembl
Ensembl Acc Id: ENSMUST00000117580   ⟹   ENSMUSP00000112561
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl870,967,340 - 70,980,606 (-)Ensembl
GRCm38.p6 Ensembl870,514,690 - 70,527,956 (-)Ensembl
Ensembl Acc Id: ENSMUST00000118850   ⟹   ENSMUSP00000113816
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl870,966,254 - 70,975,929 (-)Ensembl
GRCm38.p6 Ensembl870,513,604 - 70,523,279 (-)Ensembl
Ensembl Acc Id: ENSMUST00000121623   ⟹   ENSMUSP00000113804
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl870,960,922 - 70,975,813 (-)Ensembl
GRCm38.p6 Ensembl870,508,272 - 70,523,163 (-)Ensembl
Ensembl Acc Id: ENSMUST00000132867   ⟹   ENSMUSP00000123679
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl870,971,061 - 70,980,433 (-)Ensembl
GRCm38.p6 Ensembl870,518,411 - 70,527,783 (-)Ensembl
Ensembl Acc Id: ENSMUST00000137610   ⟹   ENSMUSP00000121539
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl870,968,045 - 70,975,740 (-)Ensembl
GRCm38.p6 Ensembl870,515,395 - 70,523,090 (-)Ensembl
Ensembl Acc Id: ENSMUST00000138260   ⟹   ENSMUSP00000123438
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl870,961,100 - 70,980,606 (-)Ensembl
GRCm38.p6 Ensembl870,508,450 - 70,527,956 (-)Ensembl
Ensembl Acc Id: ENSMUST00000138586
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl870,971,721 - 70,975,754 (-)Ensembl
GRCm38.p6 Ensembl870,519,071 - 70,523,104 (-)Ensembl
Ensembl Acc Id: ENSMUST00000155677   ⟹   ENSMUSP00000123548
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl870,966,777 - 70,975,830 (-)Ensembl
GRCm38.p6 Ensembl870,514,127 - 70,523,180 (-)Ensembl
RefSeq Acc Id: NM_029366   ⟹   NP_083642
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39870,966,046 - 70,975,830 (-)NCBI
GRCm38870,513,396 - 70,523,180 (-)ENTREZGENE
MGSCv37873,037,295 - 73,047,079 (-)RGD
Celera873,069,814 - 73,079,598 (-)RGD
cM Map8 ENTREZGENE
Sequence:
RefSeq Acc Id: NP_083642   ⟸   NM_029366
- UniProtKB: Q80XH1 (UniProtKB/Swiss-Prot),   G3X9Z9 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSMUSP00000123438   ⟸   ENSMUST00000138260
Ensembl Acc Id: ENSMUSP00000113816   ⟸   ENSMUST00000118850
Ensembl Acc Id: ENSMUSP00000123679   ⟸   ENSMUST00000132867
Ensembl Acc Id: ENSMUSP00000091165   ⟸   ENSMUST00000093456
Ensembl Acc Id: ENSMUSP00000121539   ⟸   ENSMUST00000137610
Ensembl Acc Id: ENSMUSP00000112561   ⟸   ENSMUST00000117580
Ensembl Acc Id: ENSMUSP00000123548   ⟸   ENSMUST00000155677
Ensembl Acc Id: ENSMUSP00000113804   ⟸   ENSMUST00000121623
Protein Domains
KxDL   Ubiquitin-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q80XH1-F1-model_v2 AlphaFold Q80XH1 1-177 view protein structure

Promoters
RGD ID:8667319
Promoter ID:EPDNEW_M11690
Type:multiple initiation site
Name:Kxd1_1
Description:Mus musculus KxDL motif containing 1 , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38870,523,098 - 70,523,158EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1922870 AgrOrtholog
Ensembl Genes ENSMUSG00000055553 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000093456 ENTREZGENE
  ENSMUST00000093456.12 UniProtKB/Swiss-Prot
  ENSMUST00000117580.8 UniProtKB/TrEMBL
  ENSMUST00000118850.8 UniProtKB/TrEMBL
  ENSMUST00000121623 UniProtKB/TrEMBL
  ENSMUST00000132867.2 UniProtKB/TrEMBL
  ENSMUST00000137610.3 UniProtKB/TrEMBL
  ENSMUST00000138260.8 UniProtKB/TrEMBL
  ENSMUST00000155677.8 UniProtKB/TrEMBL
Gene3D-CATH 4.10.1060.50 UniProtKB/TrEMBL
InterPro KXD1-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  L40e_sf UniProtKB/TrEMBL
  Ribosomal_L40e UniProtKB/TrEMBL
  Ribosomal_zn-bd UniProtKB/TrEMBL
  Ubiquitin UniProtKB/TrEMBL
  Ubiquitin-rel_dom UniProtKB/TrEMBL
  Ubiquitin_CS UniProtKB/TrEMBL
  Ubiquitin_subgr UniProtKB/TrEMBL
  Uncharacterised_KxDL UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:75620 UniProtKB/Swiss-Prot
MGD MGI:1922870 ENTREZGENE
NCBI Gene 75620 ENTREZGENE
PANTHER KXDL MOTIF-CONTAINING PROTEIN 1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR13511 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam KxDL UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ribosomal_L40e UniProtKB/TrEMBL
  ubiquitin UniProtKB/TrEMBL
PhenoGen Kxd1 PhenoGen
PRINTS UBIQUITIN UniProtKB/TrEMBL
PROSITE UBIQUITIN_1 UniProtKB/TrEMBL
  UBIQUITIN_2 UniProtKB/TrEMBL
SMART Ribosomal_L40e UniProtKB/TrEMBL
  UBQ UniProtKB/TrEMBL
Superfamily-SCOP SSF54236 UniProtKB/TrEMBL
  SSF57829 UniProtKB/TrEMBL
UniProt D3YWA5_MOUSE UniProtKB/TrEMBL
  D3YXX6_MOUSE UniProtKB/TrEMBL
  D3Z2M8_MOUSE UniProtKB/TrEMBL
  E9Q4P0_MOUSE UniProtKB/TrEMBL
  E9QNP0_MOUSE UniProtKB/TrEMBL
  G3X9Z9 ENTREZGENE, UniProtKB/TrEMBL
  KXDL1_MOUSE UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-11-20 Kxd1  KxDL motif containing 1  2810422J05Rik  RIKEN cDNA 2810422J05 gene  Symbol and/or name change 5135510 APPROVED