LOC117125594 (CRISPRi-FlowFISH-validated KLF1 regulatory element) - Rat Genome Database
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Gene: LOC117125594 (CRISPRi-FlowFISH-validated KLF1 regulatory element) Homo sapiens
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Symbol: LOC117125594
Name: CRISPRi-FlowFISH-validated KLF1 regulatory element
RGD ID: 38670194
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 the KLF1 (Kruppel like factor 1) gene 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
GRCh381912,890,691 - 12,891,378 (+)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_068132 (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
NM_000159.4(GCDH):c.38G>A (p.Arg13His) single nucleotide variant Glutaric aciduria, type 1 [RCV000910751] Chr19:12891342 [GRCh38]
Chr19:13002156 [GRCh37]
Chr19:19p13.13
benign|conflicting interpretations of pathogenicity
NM_000159.4(GCDH):c.-35+3A>G single nucleotide variant not specified [RCV000435483] Chr19:12891205 [GRCh38]
Chr19:13002019 [GRCh37]
Chr19:19p13.13
likely benign
NM_000159.4(GCDH):c.-47G>A single nucleotide variant Polymalformative syndrome [RCV001197962] Chr19:12891190 [GRCh38]
Chr19:13002004 [GRCh37]
Chr19:19p13.13
uncertain significance
NM_000159.4(GCDH):c.-35+9G>A single nucleotide variant Glutaric aciduria, type 1 [RCV000267770] Chr19:12891211 [GRCh38]
Chr19:13002025 [GRCh37]
Chr19:19p13.13
uncertain significance
NM_000159.4(GCDH):c.-35+17_-35+19delinsGG indel not specified [RCV000611096] Chr19:12891219..12891221 [GRCh38]
Chr19:13002033..13002035 [GRCh37]
Chr19:19p13.13
likely benign
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_000159.4(GCDH):c.-67dup duplication Glutaric acidemia [RCV000298201] Chr19:12891169..12891170 [GRCh38]
Chr19:13001983..13001984 [GRCh37]
Chr19:19p13.13
uncertain significance
NM_000159.4(GCDH):c.-49G>A single nucleotide variant Glutaric aciduria, type 1 [RCV000353123] Chr19:12891188 [GRCh38]
Chr19:13002002 [GRCh37]
Chr19:19p13.13
uncertain significance
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_000159.4(GCDH):c.-35G>A single nucleotide variant Glutaric aciduria, type 1 [RCV001124037]|not specified [RCV000443628] Chr19:12891202 [GRCh38]
Chr19:13002016 [GRCh37]
Chr19:19p13.13
likely benign|uncertain significance
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 19p13.2-13.12(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
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_000159.4(GCDH):c.3G>A (p.Met1Ile) single nucleotide variant Glutaric aciduria, type 1 [RCV000666241] Chr19:12891307 [GRCh38]
Chr19:13002121 [GRCh37]
Chr19:19p13.13
likely pathogenic
NM_000159.4(GCDH):c.1A>C (p.Met1Leu) single nucleotide variant Glutaric aciduria, type 1 [RCV000668267] Chr19:12891305 [GRCh38]
Chr19:13002119 [GRCh37]
Chr19:19p13.13
likely pathogenic
NM_000159.4(GCDH):c.-50C>T single nucleotide variant Glutaric aciduria, type 1 [RCV001124036] Chr19:12891187 [GRCh38]
Chr19:13002001 [GRCh37]
Chr19:19p13.13
uncertain significance
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
NM_000159.4(GCDH):c.-35+19C>T single nucleotide variant not provided [RCV000839909] Chr19:12891221 [GRCh38]
Chr19:13002035 [GRCh37]
Chr19:19p13.13
likely benign
NM_000159.4(GCDH):c.54C>T (p.His18=) single nucleotide variant Glutaric aciduria, type 1 [RCV000872580] Chr19:12891358 [GRCh38]
Chr19:13002172 [GRCh37]
Chr19:19p13.13
likely benign
NM_000159.4(GCDH):c.-69T>C single nucleotide variant Glutaric aciduria, type 1 [RCV001122970] Chr19:12891168 [GRCh38]
Chr19:13001982 [GRCh37]
Chr19:19p13.13
uncertain significance
NM_000159.4(GCDH):c.-34-11C>A single nucleotide variant Glutaric aciduria, type 1 [RCV001124038] Chr19:12891260 [GRCh38]
Chr19:13002074 [GRCh37]
Chr19:19p13.13
uncertain significance
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
NM_000159.4(GCDH):c.73_75TCG[1] (p.Ser26del) microsatellite Glutaric aciduria, type 1 [RCV000666490] Chr19:12891377..12891379 [GRCh38]
Chr19:13002191..13002193 [GRCh37]
Chr19:19p13.13
uncertain significance
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 LOC117125594 COSMIC
GTEx LOC117125594 GTEx
Human Proteome Map LOC117125594 Human Proteome Map
NCBI Gene LOC117125594 ENTREZGENE