LOC117125591 (CRISPRi-FlowFISH-validated PRDX2 and RAD23A regulatory element) - Rat Genome Database
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Gene: LOC117125591 (CRISPRi-FlowFISH-validated PRDX2 and RAD23A regulatory element) Homo sapiens
Analyze
Symbol: LOC117125591
Name: CRISPRi-FlowFISH-validated PRDX2 and RAD23A regulatory element
RGD ID: 38615121
Description: This genomic region was predicted to be an enhancer based on an activity-by-contact (ABC) model that predicts enhancer-gene connections, where the putative enhancer strength is measured by DNase I hypersensitivity and H3K27 acetylation, and the contact frequency by Hi-C. It was validated as a positively-acting cis-regulatory element for both the PRDX2 (peroxiredoxin 2) and RAD23A (RAD23 homolog A, nucleotide excision repair protein) genes based on CRISPR/Cas9-mediated perturbation (CRISPRi-FlowFISH method) in K562 erythroleukemia cells. [provided by RefSeq, Mar 2020]
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
GRCh381912,885,011 - 12,885,511 (+)NCBIGRCh38GRCh38hg38GRCh38
Cytogenetic Map19pNCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

References
Additional References at PubMed
PMID:31784727  


Genomics


Expression


Sequence

Nucleotide Sequences
RefSeq Transcripts NG_068129 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AD000092 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 19p13.13(chr19:12850595-13290954)x3 copy number gain See cases [RCV000052911] Chr19:12850595..13290954 [GRCh38]
Chr19:12961409..13401768 [GRCh37]
Chr19:12822409..13262768 [NCBI36]
Chr19:19p13.13
pathogenic
GRCh38/hg38 19p13.2-13.13(chr19:11517825-13225287)x1 copy number loss See cases [RCV000053945] Chr19:11517825..13225287 [GRCh38]
Chr19:11628640..13336101 [GRCh37]
Chr19:11489640..13197101 [NCBI36]
Chr19:19p13.2-13.13
pathogenic
NM_006563.5(KLF1):c.809C>G (p.Ser270Trp) single nucleotide variant BLOOD GROUP--LUTHERAN INHIBITOR [RCV000990154] Chr19:12885421 [GRCh38]
Chr19:12996235 [GRCh37]
Chr19:19p13.13
benign
NM_006563.4(KLF1):c.954dup (p.Arg319fs) duplication BLOOD GROUP--LUTHERAN INHIBITOR [RCV000009562] Chr19:12885019..12885020 [GRCh38]
Chr19:12995833..12995834 [GRCh37]
Chr19:19p13.13
pathogenic
GRCh38/hg38 19p13.2-13.13(chr19:8831147-13331227)x3 copy number gain See cases [RCV000052908] Chr19:8831147..13331227 [GRCh38]
Chr19:8941823..13442041 [GRCh37]
Chr19:8802823..13303041 [NCBI36]
Chr19:19p13.2-13.13
likely pathogenic
GRCh38/hg38 19p13.13(chr19:12813597-13119698)x3 copy number gain See cases [RCV000054144] Chr19:12813597..13119698 [GRCh38]
Chr19:12924411..13230512 [GRCh37]
Chr19:12785411..13091512 [NCBI36]
Chr19:19p13.13
uncertain significance
NM_006563.4(KLF1):c.913+1G>A single nucleotide variant not provided [RCV000087159] Chr19:12885316 [GRCh38]
Chr19:12996130 [GRCh37]
Chr19:19p13.13
likely pathogenic
NM_006563.4(KLF1):c.895C>T (p.His299Tyr) single nucleotide variant BLOOD GROUP--LUTHERAN INHIBITOR [RCV000009565] Chr19:12885335 [GRCh38]
Chr19:12996149 [GRCh37]
Chr19:19p13.13
pathogenic
NM_006563.4(KLF1):c.892G>C (p.Ala298Pro) single nucleotide variant BLOOD GROUP--LUTHERAN INHIBITOR [RCV000050236] Chr19:12885338 [GRCh38]
Chr19:12996152 [GRCh37]
Chr19:19p13.13
pathogenic
NM_006563.4(KLF1):c.895C>G (p.His299Asp) single nucleotide variant not provided [RCV000087158] Chr19:12885335 [GRCh38]
Chr19:12996149 [GRCh37]
Chr19:19p13.13
likely pathogenic
GRCh38/hg38 19p13.2-13.12(chr19:11525163-14155021)x1 copy number loss See cases [RCV000136909] Chr19:11525163..14155021 [GRCh38]
Chr19:11635978..14265833 [GRCh37]
Chr19:11496978..14126833 [NCBI36]
Chr19:19p13.2-13.12
pathogenic
NM_006563.5(KLF1):c.803G>T (p.Arg268Leu) single nucleotide variant Congenital dyserythropoietic anemia, type IV [RCV001126602] Chr19:12885427 [GRCh38]
Chr19:12996241 [GRCh37]
Chr19:19p13.13
benign
NM_006563.4(KLF1):c.954G>C (p.Trp318Cys) single nucleotide variant BLOOD GROUP--LUTHERAN INHIBITOR [RCV000240027] Chr19:12885020 [GRCh38]
Chr19:12995834 [GRCh37]
Chr19:19p13.13
affects
GRCh38/hg38 19p13.2-13.12(chr19:10315258-14048994)x3 copy number gain See cases [RCV000052909] Chr19:10315258..14048994 [GRCh38]
Chr19:10425934..14159806 [GRCh37]
Chr19:10286934..14020806 [NCBI36]
Chr19:19p13.2-13.12
pathogenic
NM_006563.5(KLF1):c.757G>A (p.Glu253Lys) single nucleotide variant Congenital dyserythropoietic anemia, type IV [RCV001126603] Chr19:12885473 [GRCh38]
Chr19:12996287 [GRCh37]
Chr19:19p13.13
benign
NM_006563.4(KLF1):c.874A>T (p.Lys292Ter) single nucleotide variant BLOOD GROUP--LUTHERAN INHIBITOR [RCV000009564] Chr19:12885356 [GRCh38]
Chr19:12996170 [GRCh37]
Chr19:19p13.13
pathogenic
NM_006563.4(KLF1):c.862A>T (p.Lys288Ter) single nucleotide variant HEREDITARY PERSISTENCE OF FETAL HEMOGLOBIN, KLF1-RELATED [RCV000009566] Chr19:12885368 [GRCh38]
Chr19:12996182 [GRCh37]
Chr19:19p13.13
pathogenic
GRCh38/hg38 19p13.2-13.12(chr19:12132052-14751798)x3 copy number gain See cases [RCV000052910] Chr19:12132052..14751798 [GRCh38]
Chr19:12242867..14862610 [GRCh37]
Chr19:12103867..14723610 [NCBI36]
Chr19:19p13.2-13.12
pathogenic
GRCh38/hg38 19p13.2-q13.31(chr19:11227942-44626354)x3 copy number gain See cases [RCV000133888] Chr19:11227942..44626354 [GRCh38]
Chr19:11338618..45129651 [GRCh37]
Chr19:11199618..49821491 [NCBI36]
Chr19:19p13.2-q13.31
pathogenic
GRCh38/hg38 19p13.2-13.12(chr19:12580427-14742673)x1 copy number loss See cases [RCV000135937] Chr19:12580427..14742673 [GRCh38]
Chr19:12691241..14853485 [GRCh37]
Chr19:12552241..14714485 [NCBI36]
Chr19:19p13.2-13.12
pathogenic|likely pathogenic
GRCh38/hg38 19p13.2-13.13(chr19:10319474-13777860)x1 copy number loss See cases [RCV000141568] Chr19:10319474..13777860 [GRCh38]
Chr19:10430150..13888674 [GRCh37]
Chr19:10291150..13749674 [NCBI36]
Chr19:19p13.2-13.13
pathogenic

Additional Information

Database Acc Id Source(s)
COSMIC LOC117125591 COSMIC
GTEx LOC117125591 GTEx
Human Proteome Map LOC117125591 Human Proteome Map
NCBI Gene LOC117125591 ENTREZGENE