LOC124625920 (Sharpr-MPRA regulatory region 8059) - Rat Genome Database

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Gene: LOC124625920 (Sharpr-MPRA regulatory region 8059) Homo sapiens
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Symbol: LOC124625920
Name: Sharpr-MPRA regulatory region 8059
RGD ID: 151665657
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. It was validated as a functional repressive element by the Sharpr-MPRA technique (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in both HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 10:DNaseD, primarily Duke DNase, candidate regulatory elements in more likely repressive locations) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 24:Quies, heterochromatin/dead zone). [provided by RefSeq, Mar 2022]
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
GRCh381220,369,575 - 20,369,869 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371220,522,509 - 20,522,803 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map12pNCBI
T2T-CHM13v2.01220,247,983 - 20,248,277 (+)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  


Genomics

Variants

.
Variants in LOC124625920
29 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NM_000921.5(PDE3A):c.293C>G (p.Ala98Gly) single nucleotide variant not provided [RCV001929937] Chr12:20369577 [GRCh38]
Chr12:20522511 [GRCh37]
Chr12:12p12.2		 uncertain significance
NM_000921.5(PDE3A):c.578T>C (p.Val193Ala) single nucleotide variant not provided [RCV000890451] Chr12:20369862 [GRCh38]
Chr12:20522796 [GRCh37]
Chr12:12p12.2		 benign|likely benign
NM_000921.5(PDE3A):c.318A>G (p.Gly106=) single nucleotide variant not provided [RCV000890078] Chr12:20369602 [GRCh38]
Chr12:20522536 [GRCh37]
Chr12:12p12.2		 benign
NM_000921.5(PDE3A):c.296A>C (p.Glu99Ala) single nucleotide variant not provided [RCV000959086] Chr12:20369580 [GRCh38]
Chr12:20522514 [GRCh37]
Chr12:12p12.2		 benign|likely benign
NM_000921.5(PDE3A):c.519C>A (p.Leu173=) single nucleotide variant not provided [RCV000977830] Chr12:20369803 [GRCh38]
Chr12:20522737 [GRCh37]
Chr12:12p12.2		 likely benign
NM_000921.5(PDE3A):c.511dup (p.Glu171fs) duplication not provided [RCV001981955] Chr12:20369788..20369789 [GRCh38]
Chr12:20522722..20522723 [GRCh37]
Chr12:12p12.2		 uncertain significance
GRCh38/hg38 12p13.33-11.1(chr12:77187-34380176)x3 copy number gain See cases [RCV000053660] Chr12:77187..34380176 [GRCh38]
Chr12:282465..34533111 [GRCh37]
Chr12:56614..34424378 [NCBI36]
Chr12:12p13.33-11.1		 pathogenic
NM_000921.5(PDE3A):c.402G>T (p.Ala134=) single nucleotide variant not provided [RCV002109463] Chr12:20369686 [GRCh38]
Chr12:20522620 [GRCh37]
Chr12:12p12.2		 benign|likely benign
GRCh38/hg38 12p12.3-11.23(chr12:19295848-27012560)x1 copy number loss See cases [RCV000052782] Chr12:19295848..27012560 [GRCh38]
Chr12:19448782..27165493 [GRCh37]
Chr12:19340049..27056760 [NCBI36]
Chr12:12p12.3-11.23		 pathogenic
NM_000921.5(PDE3A):c.505G>T (p.Gly169Trp) single nucleotide variant PDE3A-related disorder [RCV003978534]|not provided [RCV002187154] Chr12:20369789 [GRCh38]
Chr12:20522723 [GRCh37]
Chr12:12p12.2		 likely benign
GRCh38/hg38 12p13.33-11.1(chr12:212976-33926913)x4 copy number gain See cases [RCV000053666] Chr12:212976..33926913 [GRCh38]
Chr12:322142..34079848 [GRCh37]
Chr12:192403..33971115 [NCBI36]
Chr12:12p13.33-11.1		 pathogenic
GRCh38/hg38 12p13.33-12.1(chr12:80412-25470329)x3 copy number gain See cases [RCV000053662] Chr12:80412..25470329 [GRCh38]
Chr12:282465..25623263 [GRCh37]
Chr12:59839..25514530 [NCBI36]
Chr12:12p13.33-12.1		 pathogenic
GRCh38/hg38 12p12.3-12.1(chr12:19265334-25482589)x1 copy number loss See cases [RCV000135588] Chr12:19265334..25482589 [GRCh38]
Chr12:19418268..25635523 [GRCh37]
Chr12:19309535..25526790 [NCBI36]
Chr12:12p12.3-12.1		 likely pathogenic
GRCh38/hg38 12p13.33-11.1(chr12:121255-34603274)x3 copy number gain See cases [RCV000136611] Chr12:121255..34603274 [GRCh38]
Chr12:282465..34756209 [GRCh37]
Chr12:100682..34647476 [NCBI36]
Chr12:12p13.33-11.1		 pathogenic
GRCh38/hg38 12p13.33-q24.33(chr12:121271-133196807)x3 copy number gain See cases [RCV000139555] Chr12:121271..133196807 [GRCh38]
Chr12:282465..133773393 [GRCh37]
Chr12:100698..132283466 [NCBI36]
Chr12:12p13.33-q24.33		 pathogenic
GRCh38/hg38 12p12.2(chr12:20349065-20561597)x1 copy number loss See cases [RCV000141845] Chr12:20349065..20561597 [GRCh38]
Chr12:20501999..20714531 [GRCh37]
Chr12:20393266..20605798 [NCBI36]
Chr12:12p12.2		 uncertain significance
GRCh38/hg38 12p13.33-11.1(chr12:54427-34608071)x4 copy number gain See cases [RCV000139787] Chr12:54427..34608071 [GRCh38]
Chr12:282465..34761006 [GRCh37]
Chr12:33854..34652273 [NCBI36]
Chr12:12p13.33-11.1		 pathogenic
GRCh38/hg38 12p13.33-11.1(chr12:121271-34603261)x3 copy number gain See cases [RCV000139052] Chr12:121271..34603261 [GRCh38]
Chr12:282465..34756196 [GRCh37]
Chr12:100698..34647463 [NCBI36]
Chr12:12p13.33-11.1		 pathogenic
GRCh38/hg38 12p12.3-12.1(chr12:15840854-22021652)x1 copy number loss See cases [RCV000135620] Chr12:15840854..22021652 [GRCh38]
Chr12:15993788..22174586 [GRCh37]
Chr12:15885055..22065853 [NCBI36]
Chr12:12p12.3-12.1		 pathogenic
NM_000921.5(PDE3A):c.459C>T (p.Ala153=) single nucleotide variant not provided [RCV002928614] Chr12:20369743 [GRCh38]
Chr12:20522677 [GRCh37]
Chr12:12p12.2		 likely benign
NM_000921.5(PDE3A):c.577G>C (p.Val193Leu) single nucleotide variant not provided [RCV002996922] Chr12:20369861 [GRCh38]
Chr12:20522795 [GRCh37]
Chr12:12p12.2		 uncertain significance
NM_000921.5(PDE3A):c.465G>A (p.Val155=) single nucleotide variant not provided [RCV003100243] Chr12:20369749 [GRCh38]
Chr12:20522683 [GRCh37]
Chr12:12p12.2		 likely benign
NM_000921.5(PDE3A):c.438G>A (p.Met146Ile) single nucleotide variant Inborn genetic diseases [RCV002960956] Chr12:20369722 [GRCh38]
Chr12:20522656 [GRCh37]
Chr12:12p12.2		 uncertain significance
GRCh38/hg38 12p13.33-11.1(chr12:64620-34682902)x4 copy number gain See cases [RCV000142149] Chr12:64620..34682902 [GRCh38]
Chr12:173786..34835837 [GRCh37]
Chr12:44047..34727104 [NCBI36]
Chr12:12p13.33-11.1		 pathogenic
NM_000921.5(PDE3A):c.585C>T (p.Leu195=) single nucleotide variant not provided [RCV003100311] Chr12:20369869 [GRCh38]
Chr12:20522803 [GRCh37]
Chr12:12p12.2		 likely benign
NM_000921.5(PDE3A):c.506G>C (p.Gly169Ala) single nucleotide variant Inborn genetic diseases [RCV002949664]|not provided [RCV002967403] Chr12:20369790 [GRCh38]
Chr12:20522724 [GRCh37]
Chr12:12p12.2		 uncertain significance
GRCh38/hg38 12p13.33-12.2(chr12:1258274-20657577)x3 copy number gain See cases [RCV000141905] Chr12:1258274..20657577 [GRCh38]
Chr12:1367440..20810511 [GRCh37]
Chr12:1237701..20701778 [NCBI36]
Chr12:12p13.33-12.2		 pathogenic
NM_000921.5(PDE3A):c.293C>A (p.Ala98Glu) single nucleotide variant not provided [RCV002947903] Chr12:20369577 [GRCh38]
Chr12:20522511 [GRCh37]
Chr12:12p12.2		 uncertain significance
NM_000921.5(PDE3A):c.507G>T (p.Gly169=) single nucleotide variant Brachydactyly-arterial hypertension syndrome [RCV003134777] Chr12:20369791 [GRCh38]
Chr12:20522725 [GRCh37]
Chr12:12p12.2		 uncertain significance
NM_000921.5(PDE3A):c.569C>T (p.Ala190Val) single nucleotide variant Inborn genetic diseases [RCV003261741] Chr12:20369853 [GRCh38]
Chr12:20522787 [GRCh37]
Chr12:12p12.2		 uncertain significance
NM_000921.5(PDE3A):c.575G>A (p.Gly192Glu) single nucleotide variant Inborn genetic diseases [RCV003342983] Chr12:20369859 [GRCh38]
Chr12:20522793 [GRCh37]
Chr12:12p12.2		 uncertain significance
NM_000921.5(PDE3A):c.458C>T (p.Ala153Val) single nucleotide variant Inborn genetic diseases [RCV003369977] Chr12:20369742 [GRCh38]
Chr12:20522676 [GRCh37]
Chr12:12p12.2		 uncertain significance
NM_000921.5(PDE3A):c.454C>A (p.Arg152Ser) single nucleotide variant PDE3A-related disorder [RCV003420939] Chr12:20369738 [GRCh38]
Chr12:20522672 [GRCh37]
Chr12:12p12.2		 uncertain significance
NM_000921.5(PDE3A):c.506G>T (p.Gly169Val) single nucleotide variant not provided [RCV003717125] Chr12:20369790 [GRCh38]
Chr12:20522724 [GRCh37]
Chr12:12p12.2		 likely benign
NM_000921.5(PDE3A):c.419T>A (p.Leu140Gln) single nucleotide variant not provided [RCV003717546] Chr12:20369703 [GRCh38]
Chr12:20522637 [GRCh37]
Chr12:12p12.2		 uncertain significance
NM_000921.5(PDE3A):c.507G>C (p.Gly169=) single nucleotide variant PDE3A-related disorder [RCV003939159]|not provided [RCV003724463] Chr12:20369791 [GRCh38]
Chr12:20522725 [GRCh37]
Chr12:12p12.2		 benign|likely benign
NM_000921.5(PDE3A):c.381C>T (p.Ser127=) single nucleotide variant not provided [RCV003724834] Chr12:20369665 [GRCh38]
Chr12:20522599 [GRCh37]
Chr12:12p12.2		 likely benign
NM_000921.5(PDE3A):c.324A>G (p.Glu108=) single nucleotide variant not provided [RCV003860065] Chr12:20369608 [GRCh38]
Chr12:20522542 [GRCh37]
Chr12:12p12.2		 likely benign
NM_000921.5(PDE3A):c.340G>A (p.Gly114Arg) single nucleotide variant not provided [RCV003818887] Chr12:20369624 [GRCh38]
Chr12:20522558 [GRCh37]
Chr12:12p12.2		 uncertain significance
NM_000921.5(PDE3A):c.311C>T (p.Ala104Val) single nucleotide variant Inborn genetic diseases [RCV004503081] Chr12:20369595 [GRCh38]
Chr12:20522529 [GRCh37]
Chr12:12p12.2		 uncertain significance
NM_000921.5(PDE3A):c.344C>G (p.Pro115Arg) single nucleotide variant Inborn genetic diseases [RCV004503085] Chr12:20369628 [GRCh38]
Chr12:20522562 [GRCh37]
Chr12:12p12.2		 uncertain significance
NM_000921.5(PDE3A):c.494C>A (p.Ala165Asp) single nucleotide variant Inborn genetic diseases [RCV004653500] Chr12:20369778 [GRCh38]
Chr12:20522712 [GRCh37]
Chr12:12p12.2		 uncertain significance
NM_000921.5(PDE3A):c.401C>T (p.Ala134Val) single nucleotide variant not provided [RCV004697431] Chr12:20369685 [GRCh38]
Chr12:20522619 [GRCh37]
Chr12:12p12.2		 uncertain significance

Expression

RNA-SEQ Expression


Sequence



Additional Information

Database Acc Id Source(s)
COSMIC LOC124625920 COSMIC
GTEx LOC124625920 GTEx
Human Proteome Map LOC124625920 Human Proteome Map
NCBI Gene LOC124625920 ENTREZGENE