LOC122819150 (Sharpr-MPRA regulatory region 2128) - Rat Genome Database

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Gene: LOC122819150 (Sharpr-MPRA regulatory region 2128) Homo sapiens
Analyze
Symbol: LOC122819150
Name: Sharpr-MPRA regulatory region 2128
RGD ID: 150517568
Description: This genomic sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. A subregion was validated as a functional repressive element by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in HepG2 liver carcinoma cells (group: HepG2 Repressive DNase matched - State 4:PromP, inactive/poised promoter, highly conserved). This locus also includes two accessible chromatin subregions that were validated as silencers based on their ability to repress an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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
GRCh382127,107,002 - 127,107,387 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh372127,864,669 - 127,864,963 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map2qNCBI
T2T-CHM13v2.02127,541,393 - 127,541,778 (+)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:27701403   PMID:35858748  


Genomics

Variants

.
Variants in LOC122819150
14 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NM_139343.2(BIN1):c.-366C>A single nucleotide variant Myopathy, centronuclear, 2 [RCV000385865] Chr2:127107309 [GRCh38]
Chr2:127864885 [GRCh37]
Chr2:2q14.3		 uncertain significance
NM_139343.2(BIN1):c.-214T>G single nucleotide variant Myopathy, centronuclear, 2 [RCV000382584] Chr2:127107157 [GRCh38]
Chr2:127864733 [GRCh37]
Chr2:2q14.3		 uncertain significance
GRCh38/hg38 2q14.3(chr2:123169989-128460075)x1 copy number loss See cases [RCV000135455] Chr2:123169989..128460075 [GRCh38]
Chr2:123927565..129217649 [GRCh37]
Chr2:123644035..128934119 [NCBI36]
Chr2:2q14.3		 pathogenic
NC_000002.12:g.124348648_129410245del deletion See cases [RCV001568390] Chr2:124348648..129410245 [GRCh38]
Chr2:2q14.3-21.1		 not provided
NM_139343.3(BIN1):c.-177_-174dup duplication Myopathy, centronuclear, 2 [RCV000360110] Chr2:127107116..127107117 [GRCh38]
Chr2:127864692..127864693 [GRCh37]
Chr2:2q14.3		 uncertain significance
GRCh38/hg38 2q14.3-21.1(chr2:127063206-130527454)x3 copy number gain See cases [RCV000138369] Chr2:127063206..130527454 [GRCh38]
Chr2:127820782..131285027 [GRCh37]
Chr2:127537252..131001497 [NCBI36]
Chr2:2q14.3-21.1		 uncertain significance
GRCh38/hg38 2q14.3-21.1(chr2:122847356-129545581)x1 copy number loss See cases [RCV000137467] Chr2:122847356..129545581 [GRCh38]
Chr2:123604932..130303154 [GRCh37]
Chr2:123321402..130019624 [NCBI36]
Chr2:2q14.3-21.1		 likely pathogenic
NM_139343.3(BIN1):c.-192G>A single nucleotide variant Myopathy, centronuclear, 2 [RCV000267839] Chr2:127107135 [GRCh38]
Chr2:127864711 [GRCh37]
Chr2:2q14.3		 uncertain significance
GRCh38/hg38 2q14.3-22.1(chr2:123445762-140592538)x1 copy number loss See cases [RCV000136714] Chr2:123445762..140592538 [GRCh38]
Chr2:124203338..141350107 [GRCh37]
Chr2:123919808..141066577 [NCBI36]
Chr2:2q14.3-22.1		 pathogenic
NM_139343.2(BIN1):c.-314G>C single nucleotide variant Myopathy, centronuclear, 2 [RCV000329240] Chr2:127107257 [GRCh38]
Chr2:127864833 [GRCh37]
Chr2:2q14.3		 uncertain significance
GRCh38/hg38 2q14.3(chr2:121824798-128870804)x1 copy number loss See cases [RCV000054059] Chr2:121824798..128870804 [GRCh38]
Chr2:122582374..129628378 [GRCh37]
Chr2:122298844..129344848 [NCBI36]
Chr2:2q14.3		 pathogenic
GRCh38/hg38 2q14.3(chr2:122324343-128371704)x1 copy number loss See cases [RCV000054060] Chr2:122324343..128371704 [GRCh38]
Chr2:123081919..129129278 [GRCh37]
Chr2:122798389..128845748 [NCBI36]
Chr2:2q14.3		 pathogenic
NM_139343.2(BIN1):c.-272G>A single nucleotide variant Myopathy, centronuclear, 2 [RCV000271831] Chr2:127107215 [GRCh38]
Chr2:127864791 [GRCh37]
Chr2:2q14.3		 uncertain significance
NM_139343.3(BIN1):c.-163T>C single nucleotide variant Myopathy, centronuclear, 2 [RCV000303136] Chr2:127107106 [GRCh38]
Chr2:127864682 [GRCh37]
Chr2:2q14.3		 uncertain significance
NM_139343.2(BIN1):c.-403C>G single nucleotide variant not provided [RCV000839562] Chr2:127107346 [GRCh38]
Chr2:127864922 [GRCh37]
Chr2:2q14.3		 benign
NM_139343.2(BIN1):c.-402G>C single nucleotide variant not provided [RCV000839563] Chr2:127107345 [GRCh38]
Chr2:127864921 [GRCh37]
Chr2:2q14.3		 benign
GRCh38/hg38 2q14.1-14.3(chr2:115302067-129071130)x1 copy number loss See cases [RCV000141584] Chr2:115302067..129071130 [GRCh38]
Chr2:116059643..129828703 [GRCh37]
Chr2:115776113..129545173 [NCBI36]
Chr2:2q14.1-14.3		 pathogenic
NM_139343.3(BIN1):c.-197C>A single nucleotide variant Myopathy, centronuclear, 2 [RCV000325664] Chr2:127107140 [GRCh38]
Chr2:127864716 [GRCh37]
Chr2:2q14.3		 uncertain significance
NM_139343.2(BIN1):c.-389T>A single nucleotide variant Myopathy, centronuclear, 2 [RCV000336665]|not provided [RCV001618681] Chr2:127107332 [GRCh38]
Chr2:127864908 [GRCh37]
Chr2:2q14.3		 benign|likely benign
GRCh38/hg38 2q14.1-21.3(chr2:118086324-134964738)x1 copy number loss See cases [RCV000054058] Chr2:118086324..134964738 [GRCh38]
Chr2:118843900..135722308 [GRCh37]
Chr2:118560370..135438778 [NCBI36]
Chr2:2q14.1-21.3		 pathogenic
NM_139343.3(BIN1):c.-105G>T single nucleotide variant Myopathy, centronuclear, 2 [RCV001136348] Chr2:127107048 [GRCh38]
Chr2:127864624 [GRCh37]
Chr2:2q14.3		 uncertain significance
NM_139343.3(BIN1):c.-105G>C single nucleotide variant Myopathy, centronuclear, 2 [RCV001136349] Chr2:127107048 [GRCh38]
Chr2:127864624 [GRCh37]
Chr2:2q14.3		 uncertain significance
NM_139343.3(BIN1):c.-146C>G single nucleotide variant Myopathy, centronuclear, 2 [RCV001136350] Chr2:127107089 [GRCh38]
Chr2:127864665 [GRCh37]
Chr2:2q14.3		 uncertain significance
NM_139343.3(BIN1):c.-62G>A single nucleotide variant Myopathy, centronuclear, 2 [RCV000356829] Chr2:127107005 [GRCh38]
Chr2:127864581 [GRCh37]
Chr2:2q14.3		 uncertain significance
NM_139343.3(BIN1):c.-114del deletion Myopathy, centronuclear, 2 [RCV000264305] Chr2:127107057 [GRCh38]
Chr2:127864633 [GRCh37]
Chr2:2q14.3		 uncertain significance

Expression


Sequence



Additional Information

Database Acc Id Source(s)
COSMIC LOC122819150 COSMIC
GTEx LOC122819150 GTEx
Human Proteome Map LOC122819150 Human Proteome Map
NCBI Gene LOC122819150 ENTREZGENE