LOC122056818 (Sharpr-MPRA regulatory region 8387) - Rat Genome Database

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Gene: LOC122056818 (Sharpr-MPRA regulatory region 8387) Homo sapiens
Analyze
Symbol: LOC122056818
Name: Sharpr-MPRA regulatory region 8387
RGD ID: 149735785
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. The major subregion was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay in naive human embryonic stem cells, where it is marked by the H3K27ac and H3K4me1 histone modifications. Another subregion was validated as a repressive element by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 7:EnhWF, candidate poised/weak enhancer, flanking open chromatin of candidate enhancers). [provided by RefSeq, Jan 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
GRCh38129,324,962 - 29,325,991 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37129,652,209 - 29,652,503 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map1pNCBI
T2T-CHM13v2.0129,167,616 - 29,168,645 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
Dwarfism  (IAGP)
genetic disease  (IAGP)

Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
Short stature  (IAGP)
References
Additional References at PubMed
PMID:27701403   PMID:30033119  


Genomics

Variants

.
Variants in LOC122056818
4 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 1p36.11-35.2(chr1:26963045-32279045)x3 copy number gain See cases [RCV000051801] Chr1:26963045..32279045 [GRCh38]
Chr1:27289536..32744646 [GRCh37]
Chr1:27162123..32517233 [NCBI36]
Chr1:1p36.11-35.2		 pathogenic
GRCh38/hg38 1p35.3(chr1:29260983-29831866)x1 copy number loss See cases [RCV000142785] Chr1:29260983..29831866 [GRCh38]
Chr1:29587495..30304713 [GRCh37]
Chr1:29460082..30077300 [NCBI36]
Chr1:1p35.3		 uncertain significance
GRCh38/hg38 1p36.11-34.2(chr1:24381206-41401517)x3 copy number gain See cases [RCV000138891] Chr1:24381206..41401517 [GRCh38]
Chr1:24707696..41886350 [GRCh37]
Chr1:24580283..41658937 [NCBI36]
Chr1:1p36.11-34.2		 pathogenic
GRCh38/hg38 1p35.3-35.2(chr1:29274476-31126076)x1 copy number loss See cases [RCV000142463] Chr1:29274476..31126076 [GRCh38]
Chr1:29600988..31598923 [GRCh37]
Chr1:29473575..31371510 [NCBI36]
Chr1:1p35.3-35.2		 pathogenic
GRCh38/hg38 1p35.3-35.1(chr1:28424867-33122854)x1 copy number loss See cases [RCV000135447] Chr1:28424867..33122854 [GRCh38]
Chr1:28751378..33588455 [GRCh37]
Chr1:28623965..33361042 [NCBI36]
Chr1:1p35.3-35.1		 pathogenic
GRCh38/hg38 1p35.3-35.2(chr1:29015141-30983083)x3 copy number gain See cases [RCV000134933] Chr1:29015141..30983083 [GRCh38]
Chr1:29341653..31455930 [GRCh37]
Chr1:29214240..31228517 [NCBI36]
Chr1:1p35.3-35.2		 uncertain significance
NM_133178.4(PTPRU):c.4165A>C (p.Met1389Leu) single nucleotide variant Short stature [RCV000736222] Chr1:29325243 [GRCh38]
Chr1:29651755 [GRCh37]
Chr1:1p35.3		 likely pathogenic
NM_133178.4(PTPRU):c.4144G>A (p.Ala1382Thr) single nucleotide variant Inborn genetic diseases [RCV002802720] Chr1:29325222 [GRCh38]
Chr1:29651734 [GRCh37]
Chr1:1p35.3		 uncertain significance
NM_133178.4(PTPRU):c.4150G>A (p.Ala1384Thr) single nucleotide variant Inborn genetic diseases [RCV002997609] Chr1:29325228 [GRCh38]
Chr1:29651740 [GRCh37]
Chr1:1p35.3		 uncertain significance
GRCh38/hg38 1p36.33-35.1(chr1:99125-34026935)x3 copy number gain Trisomy 12p [RCV003447845] Chr1:99125..34026935 [GRCh38]
Chr1:1p36.33-35.1		 pathogenic
NM_133178.4(PTPRU):c.4149C>T (p.Cys1383=) single nucleotide variant PTPRU-related condition [RCV003966340]|not provided [RCV003413014] Chr1:29325227 [GRCh38]
Chr1:29651739 [GRCh37]
Chr1:1p35.3		 likely benign
NM_133178.4(PTPRU):c.4248+5_4248+6insTCAC insertion PTPRU-related condition [RCV003958965] Chr1:29325331..29325332 [GRCh38]
Chr1:29651843..29651844 [GRCh37]
Chr1:1p35.3		 likely benign

Expression


Sequence



Additional Information

Database Acc Id Source(s)
COSMIC LOC122056818 COSMIC
GTEx LOC122056818 GTEx
Human Proteome Map LOC122056818 Human Proteome Map
NCBI Gene LOC122056818 ENTREZGENE