LOC107648851 (meiotic recombination hotspot TAP2) - Rat Genome Database

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Gene: LOC107648851 (meiotic recombination hotspot TAP2) Homo sapiens
Analyze
Symbol: LOC107648851
Name: meiotic recombination hotspot TAP2
RGD ID: 38604177
Description: This region is located within an intron of the transporter 2, ATP-binding cassette, sub-family B (MDR/TAP) (TAP2) gene within the class II region of the major histocompatibility complex (MHC) on the p arm of chromosome 6. This region has been identified as a meiotic recombination hotspot by sperm typing assays and linkage disequilibrium studies. Higher recombination frequencies in females relative to males has been reported in the MHC class II region. Meiotic hotspot activity can vary widely amongst individuals and can be influenced by both the nucleotide sequence at the meiotic recombination hotspot and the specific alleles present at the PR domain 9 (PRDM9) locus. [provided by RefSeq, Apr 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
GRCh38632,835,539 - 32,837,694 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37632,803,316 - 32,805,471 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map6p21.3NCBI
T2T-CHM13v2.0632,656,915 - 32,659,070 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

References
Additional References at PubMed
PMID:1360671   PMID:1727870   PMID:2711370   PMID:7762558   PMID:7795597   PMID:7868379   PMID:8106280   PMID:8267790   PMID:8428770   PMID:9012413   PMID:10749979   PMID:11586303  
PMID:15065666   PMID:15885980   PMID:20981099  


Genomics

Variants

.
Variants in LOC107648851
68 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NM_001290043.2(TAP2):c.526G>C (p.Val176Leu) single nucleotide variant Inborn genetic diseases [RCV003290113] Chr6:32837619 [GRCh38]
Chr6:32805396 [GRCh37]
Chr6:6p21.32		 uncertain significance
NM_001290043.2(TAP2):c.701T>A (p.Leu234Gln) single nucleotide variant MHC class I deficiency [RCV000696803]|not provided [RCV001551214] Chr6:32835681 [GRCh38]
Chr6:32803458 [GRCh37]
Chr6:6p21.32		 uncertain significance
NM_001290043.2(TAP2):c.703C>T (p.Arg235Cys) single nucleotide variant MHC class I deficiency [RCV000686750] Chr6:32835679 [GRCh38]
Chr6:32803456 [GRCh37]
Chr6:6p21.32		 uncertain significance
NM_001290043.2(TAP2):c.529A>T (p.Ile177Phe) single nucleotide variant MHC class I deficiency [RCV000690226] Chr6:32837616 [GRCh38]
Chr6:32805393 [GRCh37]
Chr6:6p21.32		 uncertain significance
NM_001290043.2(TAP2):c.739+12A>T single nucleotide variant MHC class I deficiency [RCV001512224]|not provided [RCV001692124]|not specified [RCV000454420] Chr6:32835631 [GRCh38]
Chr6:32803408 [GRCh37]
Chr6:6p21.32		 benign
NM_001290043.2(TAP2):c.727G>A (p.Glu243Lys) single nucleotide variant MHC class I deficiency [RCV000697707] Chr6:32835655 [GRCh38]
Chr6:32803432 [GRCh37]
Chr6:6p21.32		 uncertain significance
GRCh38/hg38 6p25.3-12.3(chr6:156974-46789291)x3 copy number gain See cases [RCV000143497] Chr6:156974..46789291 [GRCh38]
Chr6:156974..46757028 [GRCh37]
Chr6:101974..46864987 [NCBI36]
Chr6:6p25.3-12.3		 pathogenic
NM_001290043.2(TAP2):c.658C>A (p.Arg220=) single nucleotide variant MHC class I deficiency [RCV000534233]|TAP2-related condition [RCV003979988] Chr6:32835724 [GRCh38]
Chr6:32803501 [GRCh37]
Chr6:6p21.32		 benign
NM_001290043.2(TAP2):c.715G>A (p.Gly239Ser) single nucleotide variant MHC class I deficiency [RCV001071273] Chr6:32835667 [GRCh38]
Chr6:32803444 [GRCh37]
Chr6:6p21.32		 uncertain significance
NM_001290043.2(TAP2):c.661A>G (p.Ile221Val) single nucleotide variant MHC class I deficiency [RCV001038230] Chr6:32835721 [GRCh38]
Chr6:32803498 [GRCh37]
Chr6:6p21.32		 uncertain significance
NM_001290043.2(TAP2):c.676C>T (p.Arg226Trp) single nucleotide variant MHC class I deficiency [RCV001027847] Chr6:32835706 [GRCh38]
Chr6:32803483 [GRCh37]
Chr6:6p21.32		 uncertain significance
NM_001290043.2(TAP2):c.580T>G (p.Phe194Val) single nucleotide variant MHC class I deficiency [RCV001221752] Chr6:32837565 [GRCh38]
Chr6:32805342 [GRCh37]
Chr6:6p21.32		 uncertain significance
NM_001290043.2(TAP2):c.537C>T (p.Ile179=) single nucleotide variant MHC class I deficiency [RCV000899136] Chr6:32837608 [GRCh38]
Chr6:32805385 [GRCh37]
Chr6:6p21.32		 likely benign
NM_001290043.2(TAP2):c.656C>T (p.Ser219Phe) single nucleotide variant MHC class I deficiency [RCV000642363] Chr6:32835726 [GRCh38]
Chr6:32803503 [GRCh37]
Chr6:6p21.32		 uncertain significance
NM_001290043.2(TAP2):c.684G>A (p.Gln228=) single nucleotide variant MHC class I deficiency [RCV001434082] Chr6:32835698 [GRCh38]
Chr6:32803475 [GRCh37]
Chr6:6p21.32		 likely benign
NM_001290043.2(TAP2):c.515A>T (p.Tyr172Phe) single nucleotide variant MHC class I deficiency [RCV001323861] Chr6:32837630 [GRCh38]
Chr6:32805407 [GRCh37]
Chr6:6p21.32		 uncertain significance
NM_001290043.2(TAP2):c.524G>A (p.Arg175His) single nucleotide variant MHC class I deficiency [RCV001300694] Chr6:32837621 [GRCh38]
Chr6:32805398 [GRCh37]
Chr6:6p21.32		 uncertain significance
NM_001290043.2(TAP2):c.677G>A (p.Arg226Gln) single nucleotide variant MHC class I deficiency [RCV001366636] Chr6:32835705 [GRCh38]
Chr6:32803482 [GRCh37]
Chr6:6p21.32		 uncertain significance
NM_001290043.2(TAP2):c.608+7G>A single nucleotide variant MHC class I deficiency [RCV001520390]|not provided [RCV001824984] Chr6:32837530 [GRCh38]
Chr6:32805307 [GRCh37]
Chr6:6p21.32		 benign|not provided
NM_001290043.2(TAP2):c.714C>T (p.Leu238=) single nucleotide variant MHC class I deficiency [RCV001429181] Chr6:32835668 [GRCh38]
Chr6:32803445 [GRCh37]
Chr6:6p21.32		 likely benign
NM_001290043.2(TAP2):c.739+9T>G single nucleotide variant MHC class I deficiency [RCV001503839] Chr6:32835634 [GRCh38]
Chr6:32803411 [GRCh37]
Chr6:6p21.32		 likely benign
NM_001290043.2(TAP2):c.494-11G>T single nucleotide variant MHC class I deficiency [RCV001518519] Chr6:32837662 [GRCh38]
Chr6:32805439 [GRCh37]
Chr6:6p21.32		 benign
NM_001290043.2(TAP2):c.576C>T (p.Ala192=) single nucleotide variant MHC class I deficiency [RCV001488591] Chr6:32837569 [GRCh38]
Chr6:32805346 [GRCh37]
Chr6:6p21.32		 likely benign
NM_001290043.2(TAP2):c.608+8G>A single nucleotide variant MHC class I deficiency [RCV001519355]|TAP2-related condition [RCV003980578] Chr6:32837529 [GRCh38]
Chr6:32805306 [GRCh37]
Chr6:6p21.32		 benign
NM_001290043.2(TAP2):c.672G>T (p.Arg224=) single nucleotide variant MHC class I deficiency [RCV002184935] Chr6:32835710 [GRCh38]
Chr6:32803487 [GRCh37]
Chr6:6p21.32		 likely benign
NM_001290043.2(TAP2):c.494-42G>C single nucleotide variant MHC class I deficiency [RCV001815644] Chr6:32837693 [GRCh38]
Chr6:32805470 [GRCh37]
Chr6:6p21.32		 benign
NM_001290043.2(TAP2):c.704G>A (p.Arg235His) single nucleotide variant MHC class I deficiency [RCV001892297] Chr6:32835678 [GRCh38]
Chr6:32803455 [GRCh37]
Chr6:6p21.32		 uncertain significance
NM_001290043.2(TAP2):c.494G>A (p.Gly165Asp) single nucleotide variant MHC class I deficiency [RCV001948834] Chr6:32837651 [GRCh38]
Chr6:32805428 [GRCh37]
Chr6:6p21.32		 uncertain significance
NM_001290043.2(TAP2):c.513C>G (p.His171Gln) single nucleotide variant MHC class I deficiency [RCV001894765] Chr6:32837632 [GRCh38]
Chr6:32805409 [GRCh37]
Chr6:6p21.32		 uncertain significance
NM_001290043.2(TAP2):c.665A>G (p.Asn222Ser) single nucleotide variant MHC class I deficiency [RCV002049687] Chr6:32835717 [GRCh38]
Chr6:32803494 [GRCh37]
Chr6:6p21.32		 uncertain significance
NM_001290043.2(TAP2):c.606C>T (p.Gly202=) single nucleotide variant MHC class I deficiency [RCV001961155] Chr6:32837539 [GRCh38]
Chr6:32805316 [GRCh37]
Chr6:6p21.32		 uncertain significance
NM_001290043.2(TAP2):c.561T>G (p.His187Gln) single nucleotide variant MHC class I deficiency [RCV002032994] Chr6:32837584 [GRCh38]
Chr6:32805361 [GRCh37]
Chr6:6p21.32		 uncertain significance
NM_001290043.2(TAP2):c.494-2A>G single nucleotide variant MHC class I deficiency [RCV002000304] Chr6:32837653 [GRCh38]
Chr6:32805430 [GRCh37]
Chr6:6p21.32		 likely pathogenic
NM_001290043.2(TAP2):c.609-19T>C single nucleotide variant MHC class I deficiency [RCV002153709] Chr6:32835792 [GRCh38]
Chr6:32803569 [GRCh37]
Chr6:6p21.32		 likely benign
NM_001290043.2(TAP2):c.739+10G>A single nucleotide variant MHC class I deficiency [RCV002080107] Chr6:32835633 [GRCh38]
Chr6:32803410 [GRCh37]
Chr6:6p21.32		 likely benign
NM_001290043.2(TAP2):c.739+19G>T single nucleotide variant MHC class I deficiency [RCV002125310] Chr6:32835624 [GRCh38]
Chr6:32803401 [GRCh37]
Chr6:6p21.32		 likely benign
NM_001290043.2(TAP2):c.494-13A>G single nucleotide variant MHC class I deficiency [RCV002177620] Chr6:32837664 [GRCh38]
Chr6:32805441 [GRCh37]
Chr6:6p21.32		 likely benign
NM_001290043.2(TAP2):c.608+15G>T single nucleotide variant MHC class I deficiency [RCV002103375] Chr6:32837522 [GRCh38]
Chr6:32805299 [GRCh37]
Chr6:6p21.32		 likely benign
NM_001290043.2(TAP2):c.515A>C (p.Tyr172Ser) single nucleotide variant Inborn genetic diseases [RCV002906022] Chr6:32837630 [GRCh38]
Chr6:32805407 [GRCh37]
Chr6:6p21.32		 uncertain significance
NM_001290043.2(TAP2):c.594C>G (p.Leu198=) single nucleotide variant MHC class I deficiency [RCV002861692] Chr6:32837551 [GRCh38]
Chr6:32805328 [GRCh37]
Chr6:6p21.32		 likely benign
NM_001290043.2(TAP2):c.728A>G (p.Glu243Gly) single nucleotide variant MHC class I deficiency [RCV002843821] Chr6:32835654 [GRCh38]
Chr6:32803431 [GRCh37]
Chr6:6p21.32		 uncertain significance
NM_001290043.2(TAP2):c.739+18G>C single nucleotide variant MHC class I deficiency [RCV002871461] Chr6:32835625 [GRCh38]
Chr6:32803402 [GRCh37]
Chr6:6p21.32		 likely benign
NM_001290043.2(TAP2):c.724C>T (p.Gln242Ter) single nucleotide variant MHC class I deficiency [RCV002885234] Chr6:32835658 [GRCh38]
Chr6:32803435 [GRCh37]
Chr6:6p21.32		 pathogenic
NM_001290043.2(TAP2):c.526G>A (p.Val176Met) single nucleotide variant MHC class I deficiency [RCV002923206] Chr6:32837619 [GRCh38]
Chr6:32805396 [GRCh37]
Chr6:6p21.32		 uncertain significance
NM_001290043.2(TAP2):c.620C>T (p.Ala207Val) single nucleotide variant MHC class I deficiency [RCV002622659] Chr6:32835762 [GRCh38]
Chr6:32803539 [GRCh37]
Chr6:6p21.32		 uncertain significance
NM_001290043.2(TAP2):c.739+20T>A single nucleotide variant MHC class I deficiency [RCV003008041] Chr6:32835623 [GRCh38]
Chr6:32803400 [GRCh37]
Chr6:6p21.32		 likely benign
NM_001290043.2(TAP2):c.552T>C (p.Phe184=) single nucleotide variant MHC class I deficiency [RCV002580848] Chr6:32837593 [GRCh38]
Chr6:32805370 [GRCh37]
Chr6:6p21.32		 likely benign
NM_001290043.2(TAP2):c.659G>A (p.Arg220Gln) single nucleotide variant MHC class I deficiency [RCV003092046] Chr6:32835723 [GRCh38]
Chr6:32803500 [GRCh37]
Chr6:6p21.32		 uncertain significance
NM_001290043.2(TAP2):c.658C>T (p.Arg220Ter) single nucleotide variant MHC class I deficiency [RCV003060033] Chr6:32835724 [GRCh38]
Chr6:32803501 [GRCh37]
Chr6:6p21.32		 pathogenic
NM_001290043.2(TAP2):c.609-7C>G single nucleotide variant MHC class I deficiency [RCV002628408] Chr6:32835780 [GRCh38]
Chr6:32803557 [GRCh37]
Chr6:6p21.32		 uncertain significance
NM_001290043.2(TAP2):c.730A>G (p.Thr244Ala) single nucleotide variant MHC class I deficiency [RCV003010032] Chr6:32835652 [GRCh38]
Chr6:32803429 [GRCh37]
Chr6:6p21.32		 uncertain significance
NM_001290043.2(TAP2):c.670C>T (p.Arg224Trp) single nucleotide variant MHC class I deficiency [RCV002943517] Chr6:32835712 [GRCh38]
Chr6:32803489 [GRCh37]
Chr6:6p21.32		 uncertain significance
NM_001290043.2(TAP2):c.736A>G (p.Thr246Ala) single nucleotide variant MHC class I deficiency [RCV002814836] Chr6:32835646 [GRCh38]
Chr6:32803423 [GRCh37]
Chr6:6p21.32		 uncertain significance
NM_001290043.2(TAP2):c.494-10C>T single nucleotide variant MHC class I deficiency [RCV002611765] Chr6:32837661 [GRCh38]
Chr6:32805438 [GRCh37]
Chr6:6p21.32		 likely benign
NM_001290043.2(TAP2):c.629G>A (p.Arg210Gln) single nucleotide variant MHC class I deficiency [RCV003323338] Chr6:32835753 [GRCh38]
Chr6:32803530 [GRCh37]
Chr6:6p21.32		 uncertain significance
NM_001290043.2(TAP2):c.690C>T (p.Phe230=) single nucleotide variant MHC class I deficiency [RCV003507706] Chr6:32835692 [GRCh38]
Chr6:32803469 [GRCh37]
Chr6:6p21.32		 likely benign
NM_001290043.2(TAP2):c.667T>C (p.Leu223=) single nucleotide variant MHC class I deficiency [RCV003506764] Chr6:32835715 [GRCh38]
Chr6:32803492 [GRCh37]
Chr6:6p21.32		 likely benign
NM_001290043.2(TAP2):c.609-16T>C single nucleotide variant MHC class I deficiency [RCV003507833] Chr6:32835789 [GRCh38]
Chr6:32803566 [GRCh37]
Chr6:6p21.32		 likely benign
NM_001290043.2(TAP2):c.591C>T (p.Cys197=) single nucleotide variant MHC class I deficiency [RCV003508814] Chr6:32837554 [GRCh38]
Chr6:32805331 [GRCh37]
Chr6:6p21.32		 likely benign
NM_001290043.2(TAP2):c.687T>G (p.Leu229=) single nucleotide variant MHC class I deficiency [RCV003830227] Chr6:32835695 [GRCh38]
Chr6:32803472 [GRCh37]
Chr6:6p21.32		 likely benign
NM_001290043.2(TAP2):c.609-7C>T single nucleotide variant MHC class I deficiency [RCV003507179] Chr6:32835780 [GRCh38]
Chr6:32803557 [GRCh37]
Chr6:6p21.32		 likely benign
NM_001290043.2(TAP2):c.609-14C>T single nucleotide variant MHC class I deficiency [RCV003620675] Chr6:32835787 [GRCh38]
Chr6:32803564 [GRCh37]
Chr6:6p21.32		 likely benign

Expression


Sequence



Additional Information

Database Acc Id Source(s)
COSMIC LOC107648851 COSMIC
GTEx LOC107648851 GTEx
Human Proteome Map LOC107648851 Human Proteome Map
NCBI Gene LOC107648851 ENTREZGENE