LOC107303342 (3p25 TatD DNase domain containing 2 Alu-mediated recombination region) - Rat Genome Database

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Gene: LOC107303342 (3p25 TatD DNase domain containing 2 Alu-mediated recombination region) Homo sapiens
Analyze
Symbol: LOC107303342
Name: 3p25 TatD DNase domain containing 2 Alu-mediated recombination region
RGD ID: 38651351
Description: This biological region overlaps the TatD DNase domain containing 2 (TATDN2) gene and is known to undergo Alu-repeat-mediated non-allelic homologous recombination (NAHR) with the 3p25 FANCD2 Alu-mediated recombination region and the 3p25 BRK1 Alu-mediated recombination region, located about 175 kb and 115 kb centromere-distal of this region on the reference genome, respectively. Recombination between these regions can result in deletion of the intervening sequences, including the von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase (VHL) gene. Deletion of the VHL gene is one cause of Von Hippel-Lindau syndrome, which is inherited in autosomal dominant manner and predisposes individuals to multiple tumors. Deletions of various size have been reported, many of which are the result of Alu-mediated recombination. The severity of the disease is dependent on both the size and location of the deletion. This recombination region is composed of two NAHR sub-regions, representing different regions in which Alu-mediated recombination has been observed, and also contains meiotic recombination hotspots. Recombination events that result in the deletion of VHL have also been reported in regions overlapping the proline rich transmembrane protein 3 (PRRT3) gene, the von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase (VHL) gene, and the interleukin 1 receptor associated kinase 2 (IRAK2) gene. [provided by RefSeq, Oct 2016]
Type: biological-region
RefSeq Status: REVIEWED
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38310,253,583 - 10,272,080 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37310,295,267 - 10,313,764 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map3p25NCBI
T2T-CHM13v2.0310,246,883 - 10,265,377 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:9829911   PMID:10830910   PMID:12114495   PMID:14695531   PMID:15300849   PMID:15608663   PMID:15758713   PMID:16630138   PMID:16884328   PMID:17024664   PMID:17311301   PMID:17537157  
PMID:17661816   PMID:19014668   PMID:19280651   PMID:20981099   PMID:21750151   PMID:24555745   PMID:25395542  


Genomics

Variants

.
Variants in LOC107303342
26 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NM_014760.4(TATDN2):c.1487T>C (p.Ile496Thr) single nucleotide variant not specified [RCV004313666] Chr3:10270669 [GRCh38]
Chr3:10312353 [GRCh37]
Chr3:3p25.3		 uncertain significance
NM_014760.4(TATDN2):c.430A>G (p.Ser144Gly) single nucleotide variant not specified [RCV004306016] Chr3:10260152 [GRCh38]
Chr3:10301836 [GRCh37]
Chr3:3p25.3		 uncertain significance
NM_014760.4(TATDN2):c.784A>G (p.Lys262Glu) single nucleotide variant not specified [RCV004308819] Chr3:10260506 [GRCh38]
Chr3:10302190 [GRCh37]
Chr3:3p25.3		 uncertain significance
GRCh38/hg38 3p26.3-25.3(chr3:32241-11379835)x1 copy number loss See cases [RCV000138376] Chr3:32241..11379835 [GRCh38]
Chr3:73914..11421309 [GRCh37]
Chr3:48914..11396309 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic|likely benign
GRCh38/hg38 3p26.3-25.3(chr3:52266-11089569)x1 copy number loss See cases [RCV000051447] Chr3:52266..11089569 [GRCh38]
Chr3:93949..11131255 [GRCh37]
Chr3:68949..11106255 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic
GRCh38/hg38 3p26.1-25.1(chr3:7356110-14360442)x3 copy number gain See cases [RCV000143766] Chr3:7356110..14360442 [GRCh38]
Chr3:7397797..14401942 [GRCh37]
Chr3:7372797..14376946 [NCBI36]
Chr3:3p26.1-25.1		 pathogenic
GRCh38/hg38 3p26.3-22.2(chr3:52266-37148076)x3 copy number gain See cases [RCV000051097] Chr3:52266..37148076 [GRCh38]
Chr3:93949..37189567 [GRCh37]
Chr3:68949..37164571 [NCBI36]
Chr3:3p26.3-22.2		 pathogenic
GRCh38/hg38 3p25.3-25.2(chr3:9394874-11690612)x1 copy number loss See cases [RCV000137433] Chr3:9394874..11690612 [GRCh38]
Chr3:9436558..11732086 [GRCh37]
Chr3:9411558..11707086 [NCBI36]
Chr3:3p25.3-25.2		 pathogenic
GRCh38/hg38 3p25.3(chr3:10220962-11165449)x1 copy number loss See cases [RCV000143098] Chr3:10220962..11165449 [GRCh38]
Chr3:10262646..11207135 [GRCh37]
Chr3:10237646..11182135 [NCBI36]
Chr3:3p25.3		 uncertain significance
GRCh38/hg38 3p25.3(chr3:9875909-10572677)x1 copy number loss See cases [RCV000137755] Chr3:9875909..10572677 [GRCh38]
Chr3:9917593..10614361 [GRCh37]
Chr3:9892593..10589361 [NCBI36]
Chr3:3p25.3		 pathogenic
GRCh38/hg38 3p26.3-24.1(chr3:32241-30064208)x3 copy number gain See cases [RCV000138004] Chr3:32241..30064208 [GRCh38]
Chr3:73914..30105699 [GRCh37]
Chr3:48914..30080703 [NCBI36]
Chr3:3p26.3-24.1		 pathogenic
GRCh38/hg38 3p26.1-25.2(chr3:7975734-12636917)x3 copy number gain See cases [RCV000137309] Chr3:7975734..12636917 [GRCh38]
Chr3:8017421..12678416 [GRCh37]
Chr3:7992421..12653416 [NCBI36]
Chr3:3p26.1-25.2		 likely pathogenic
GRCh38/hg38 3p26.3-25.1(chr3:32241-13613818)x3 copy number gain See cases [RCV000138946] Chr3:32241..13613818 [GRCh38]
Chr3:73914..13655318 [GRCh37]
Chr3:48914..13630319 [NCBI36]
Chr3:3p26.3-25.1		 pathogenic
GRCh38/hg38 3p26.3-25.2(chr3:32241-12681483)x1 copy number loss See cases [RCV000138143] Chr3:32241..12681483 [GRCh38]
Chr3:73914..12722982 [GRCh37]
Chr3:48914..12697982 [NCBI36]
Chr3:3p26.3-25.2		 pathogenic
GRCh38/hg38 3p26.3-24.3(chr3:32241-20334387)x3 copy number gain See cases [RCV000137941] Chr3:32241..20334387 [GRCh38]
Chr3:73914..20375879 [GRCh37]
Chr3:48914..20350883 [NCBI36]
Chr3:3p26.3-24.3		 pathogenic
GRCh38/hg38 3p26.3-22.1(chr3:53308-41381521)x3 copy number gain See cases [RCV000141810] Chr3:53308..41381521 [GRCh38]
Chr3:94991..41423012 [GRCh37]
Chr3:69991..41398016 [NCBI36]
Chr3:3p26.3-22.1		 pathogenic
GRCh38/hg38 3p26.1-25.3(chr3:8038727-11240931)x4 copy number gain See cases [RCV000135641] Chr3:8038727..11240931 [GRCh38]
Chr3:8080414..11282617 [GRCh37]
Chr3:8055414..11257617 [NCBI36]
Chr3:3p26.1-25.3		 likely pathogenic
GRCh38/hg38 3p26.3-25.3(chr3:32241-10631310)x1 copy number loss See cases [RCV000143173] Chr3:32241..10631310 [GRCh38]
Chr3:73914..10672995 [GRCh37]
Chr3:48914..10647995 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic
GRCh38/hg38 3p26.3-25.3(chr3:688897-11051142)x1 copy number loss See cases [RCV000143706] Chr3:688897..11051142 [GRCh38]
Chr3:730581..11092828 [GRCh37]
Chr3:705581..11067828 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic
GRCh38/hg38 3p26.3-25.3(chr3:32241-10323124)x1 copy number loss See cases [RCV000143325] Chr3:32241..10323124 [GRCh38]
Chr3:73914..10364808 [GRCh37]
Chr3:48914..10339808 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic
GRCh38/hg38 3p26.3-24.3(chr3:52066-20280127)x3 copy number gain See cases [RCV000051690] Chr3:52066..20280127 [GRCh38]
Chr3:93749..20321619 [GRCh37]
Chr3:68749..20296623 [NCBI36]
Chr3:3p26.3-24.3		 pathogenic
GRCh38/hg38 3p26.3-24.3(chr3:63843-19510600)x3 copy number gain See cases [RCV000051719] Chr3:63843..19510600 [GRCh38]
Chr3:105526..19552092 [GRCh37]
Chr3:80526..19527096 [NCBI36]
Chr3:3p26.3-24.3		 pathogenic
GRCh38/hg38 3p26.3-25.3(chr3:20213-11221602)x1 copy number loss See cases [RCV000141731] Chr3:20213..11221602 [GRCh38]
Chr3:61891..11263288 [GRCh37]
Chr3:36891..11238288 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic
GRCh38/hg38 3p25.3-25.2(chr3:10019780-12251358)x1 copy number loss See cases [RCV000051506] Chr3:10019780..12251358 [GRCh38]
Chr3:10061464..12292857 [GRCh37]
Chr3:10036464..12267857 [NCBI36]
Chr3:3p25.3-25.2		 pathogenic
NM_014760.4(TATDN2):c.1255T>C (p.Tyr419His) single nucleotide variant not specified [RCV004207157] Chr3:10270437 [GRCh38]
Chr3:10312121 [GRCh37]
Chr3:3p25.3		 uncertain significance
NM_014760.4(TATDN2):c.1310C>T (p.Ser437Leu) single nucleotide variant not specified [RCV004242855] Chr3:10270492 [GRCh38]
Chr3:10312176 [GRCh37]
Chr3:3p25.3		 uncertain significance
NM_014760.4(TATDN2):c.1292C>T (p.Ser431Phe) single nucleotide variant not specified [RCV004207949] Chr3:10270474 [GRCh38]
Chr3:10312158 [GRCh37]
Chr3:3p25.3		 uncertain significance
NM_014760.4(TATDN2):c.676A>G (p.Arg226Gly) single nucleotide variant not specified [RCV004132008] Chr3:10260398 [GRCh38]
Chr3:10302082 [GRCh37]
Chr3:3p25.3		 uncertain significance
NM_014760.4(TATDN2):c.1309T>G (p.Ser437Ala) single nucleotide variant not specified [RCV004242854] Chr3:10270491 [GRCh38]
Chr3:10312175 [GRCh37]
Chr3:3p25.3		 likely benign
NM_014760.4(TATDN2):c.1174C>T (p.Pro392Ser) single nucleotide variant not specified [RCV004233888] Chr3:10270356 [GRCh38]
Chr3:10312040 [GRCh37]
Chr3:3p25.3		 uncertain significance
NM_014760.4(TATDN2):c.1034C>G (p.Ser345Cys) single nucleotide variant not specified [RCV004069172] Chr3:10270216 [GRCh38]
Chr3:10311900 [GRCh37]
Chr3:3p25.3		 uncertain significance
NM_014760.4(TATDN2):c.1445T>C (p.Leu482Pro) single nucleotide variant not specified [RCV004102044] Chr3:10270627 [GRCh38]
Chr3:10312311 [GRCh37]
Chr3:3p25.3		 uncertain significance
NM_014760.4(TATDN2):c.593C>T (p.Ser198Leu) single nucleotide variant not specified [RCV004130961] Chr3:10260315 [GRCh38]
Chr3:10301999 [GRCh37]
Chr3:3p25.3		 uncertain significance
NM_014760.4(TATDN2):c.1705C>T (p.Arg569Cys) single nucleotide variant not specified [RCV004212148] Chr3:10270887 [GRCh38]
Chr3:10312571 [GRCh37]
Chr3:3p25.3		 uncertain significance
NM_014760.4(TATDN2):c.1315G>A (p.Glu439Lys) single nucleotide variant not specified [RCV004331889] Chr3:10270497 [GRCh38]
Chr3:10312181 [GRCh37]
Chr3:3p25.3		 uncertain significance
NM_014760.4(TATDN2):c.1193C>T (p.Thr398Ile) single nucleotide variant not specified [RCV004268921] Chr3:10270375 [GRCh38]
Chr3:10312059 [GRCh37]
Chr3:3p25.3		 uncertain significance
NM_014760.4(TATDN2):c.1186C>T (p.Pro396Ser) single nucleotide variant not specified [RCV004363314] Chr3:10270368 [GRCh38]
Chr3:10312052 [GRCh37]
Chr3:3p25.3		 uncertain significance
NM_014760.4(TATDN2):c.1209C>T (p.Asn403=) single nucleotide variant not provided [RCV003433424] Chr3:10270391 [GRCh38]
Chr3:10312075 [GRCh37]
Chr3:3p25.3		 likely benign
NM_014760.4(TATDN2):c.1767G>A (p.Val589=) single nucleotide variant not provided [RCV003433425] Chr3:10270949 [GRCh38]
Chr3:10312633 [GRCh37]
Chr3:3p25.3		 likely benign
NM_014760.4(TATDN2):c.427G>A (p.Asp143Asn) single nucleotide variant not specified [RCV004471686] Chr3:10260149 [GRCh38]
Chr3:10301833 [GRCh37]
Chr3:3p25.3		 uncertain significance
NM_014760.4(TATDN2):c.812A>G (p.Tyr271Cys) single nucleotide variant not specified [RCV004471688] Chr3:10260534 [GRCh38]
Chr3:10302218 [GRCh37]
Chr3:3p25.3		 likely benign
NM_014760.4(TATDN2):c.1114C>G (p.Pro372Ala) single nucleotide variant not specified [RCV004471682] Chr3:10270296 [GRCh38]
Chr3:10311980 [GRCh37]
Chr3:3p25.3		 likely benign
NM_014760.4(TATDN2):c.932A>G (p.His311Arg) single nucleotide variant not specified [RCV004471690] Chr3:10260654 [GRCh38]
Chr3:10302338 [GRCh37]
Chr3:3p25.3		 uncertain significance
NM_014760.4(TATDN2):c.1271C>T (p.Thr424Ile) single nucleotide variant not specified [RCV004673319] Chr3:10270453 [GRCh38]
Chr3:10312137 [GRCh37]
Chr3:3p25.3		 uncertain significance
NM_014760.4(TATDN2):c.1414C>T (p.Arg472Cys) single nucleotide variant not specified [RCV004336511] Chr3:10270596 [GRCh38]
Chr3:10312280 [GRCh37]
Chr3:3p25.3		 uncertain significance

QTLs in Region (GRCh38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
407363222GWAS1012198_Hghrelin measurement QTL GWAS1012198 (human)3e-17ghrelin measurement31026708810267089Human
407216983GWAS865959_Hgastric carcinoma QTL GWAS865959 (human)0.000005gastric carcinoma31026524710265248Human
407318706GWAS967682_Hcysteine-rich with EGF-like domain protein 1 measurement QTL GWAS967682 (human)9e-13cysteine-rich with EGF-like domain protein 1 measurement31025419910254200Human
407363234GWAS1012210_Hghrelin measurement QTL GWAS1012210 (human)2e-13ghrelin measurement31025419910254200Human
407362960GWAS1011936_Hghrelin measurement QTL GWAS1011936 (human)1e-24ghrelin measurement31027008910270090Human
2316345GLUCO224_HGlucose level QTL 224 (human)1.270.008Glucose level3121543441Human
406953310GWAS602286_Hliver fat measurement QTL GWAS602286 (human)0.000006liver lipid amount (VT:0010764)liver fat morphological measurement (CMO:0002187)31027042910270430Human


Expression

RNA-SEQ Expression


Sequence



Additional Information

Database Acc Id Source(s)
COSMIC LOC107303342 COSMIC
GTEx LOC107303342 GTEx
Human Proteome Map LOC107303342 Human Proteome Map
NCBI Gene LOC107303342 ENTREZGENE