Advanced Search (OLGA)

Gene: LOC130006596 (ATAC-STARR-seq lymphoblastoid silent region 3840) Homo sapiens

Subscribe to Updates

Analyze

Symbol:

LOC130006596

Name:

ATAC-STARR-seq lymphoblastoid silent region 3840

RGD ID:

329841712

Description:

This genomic sequence represents an accessible chromatin region that was validated as a silencer based on its 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) massively parallel reporter assay (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 Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	11	93,784,689 - 93,784,818 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	11	93,517,855 - 93,517,984 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
T2T-CHM13v2.0	11	93,701,021 - 93,701,150 (+)	NCBI		T2T-CHM13v2.0

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Object Symbol	Species	Term	Qualifier	Evidence	With	Reference	Notes	Source	Original Reference(s)
LOC130006596	Human	genetic disease		IAGP	(Homo sapiens) and (Homo sapiens)	8554872	ClinVar Annotator: match by term: Inborn genetic diseases	ClinVar	PMID:28492532
LOC130006596	Human	genetic disease		IAGP	(Homo sapiens) more ...	8554872	ClinVar Annotator: match by term: Inborn genetic diseases	ClinVar
LOC130006596	Human	infantile cerebral and cerebellar atrophy with postnatal progressive microcephaly		IAGP	(Homo sapiens) and (Homo sapiens)	8554872	ClinVar Annotator: match by term: Infantile cerebral and cerebellar atrophy with postnatal progressive microcephaly	ClinVar
LOC130006596	Human	infantile cerebral and cerebellar atrophy with postnatal progressive microcephaly		IAGP	(Homo sapiens) and (Homo sapiens)	8554872	ClinVar Annotator: match by term: Infantile cerebral and cerebellar atrophy with postnatal progressive microcephaly	ClinVar	PMID:18414213 more ...
LOC130006596	Human	infantile cerebral and cerebellar atrophy with postnatal progressive microcephaly		IAGP	(Homo sapiens) more ...	8554872	ClinVar more ...	ClinVar	PMID:28492532
LOC130006596	Human	infantile cerebral and cerebellar atrophy with postnatal progressive microcephaly		IAGP	(Homo sapiens)	8554872	ClinVar Annotator: match by term: Infantile cerebral and cerebellar atrophy with postnatal progressive microcephaly	ClinVar	PMID:20950787 more ...

PMID:35858748

Variants in LOC130006596
41 total Variants

Name	Type	Condition(s)	Position(s)	Clinical significance
NM_004268.5(MED17):c.195C>G (p.Gly65=)	single nucleotide variant	Infantile cerebral and cerebellar atrophy with postnatal progressive microcephaly [RCV000600983]\|not provided [RCV001510012]\|not specified [RCV000117608]	Chr11:93784708 [GRCh38] Chr11:93517874 [GRCh37] Chr11:11q21	benign
NM_004268.5(MED17):c.207G>C (p.Glu69Asp)	single nucleotide variant	Infantile cerebral and cerebellar atrophy with postnatal progressive microcephaly [RCV000607022]\|not provided [RCV001510013]\|not specified [RCV000117609]	Chr11:93784720 [GRCh38] Chr11:93517886 [GRCh37] Chr11:11q21	benign
GRCh38/hg38 11q13.5-22.1(chr11:75941754-98357960)x1	copy number loss	See cases [RCV000133838]	Chr11:75941754..98357960 [GRCh38] Chr11:75652798..98228688 [GRCh37] Chr11:75330446..97733898 [NCBI36] Chr11:11q13.5-22.1	pathogenic
NM_004268.5(MED17):c.233A>G (p.Asp78Gly)	single nucleotide variant	Inborn genetic diseases [RCV002542903]\|Infantile cerebral and cerebellar atrophy with postnatal progressive microcephaly [RCV001278666]\|not provided [RCV002274177]	Chr11:93784746 [GRCh38] Chr11:93517912 [GRCh37] Chr11:11q21	uncertain significance
NM_004268.5(MED17):c.235C>T (p.Gln79Ter)	single nucleotide variant	Infantile cerebral and cerebellar atrophy with postnatal progressive microcephaly [RCV005008302]\|not provided [RCV001953510]	Chr11:93784748 [GRCh38] Chr11:93517914 [GRCh37] Chr11:11q21	pathogenic\|likely pathogenic
NM_004268.5(MED17):c.180G>A (p.Ala60=)	single nucleotide variant	not provided [RCV002006327]	Chr11:93784693 [GRCh38] Chr11:93517859 [GRCh37] Chr11:11q21	likely benign
NM_004268.5(MED17):c.246G>A (p.Glu82=)	single nucleotide variant	not provided [RCV002090712]	Chr11:93784759 [GRCh38] Chr11:93517925 [GRCh37] Chr11:11q21	likely benign
NM_004268.5(MED17):c.232G>T (p.Asp78Tyr)	single nucleotide variant	Inborn genetic diseases [RCV002812809]	Chr11:93784745 [GRCh38] Chr11:93517911 [GRCh37] Chr11:11q21	uncertain significance
NM_004268.5(MED17):c.243C>T (p.Asp81=)	single nucleotide variant	not provided [RCV002147547]	Chr11:93784756 [GRCh38] Chr11:93517922 [GRCh37] Chr11:11q21	likely benign
NM_004268.5(MED17):c.250G>C (p.Gly84Arg)	single nucleotide variant	not provided [RCV001900592]	Chr11:93784763 [GRCh38] Chr11:93517929 [GRCh37] Chr11:11q21	uncertain significance
NM_004268.5(MED17):c.220G>A (p.Gly74Arg)	single nucleotide variant	Inborn genetic diseases [RCV002697143]	Chr11:93784733 [GRCh38] Chr11:93517899 [GRCh37] Chr11:11q21	likely benign
NM_004268.5(MED17):c.189C>T (p.Thr63=)	single nucleotide variant	not provided [RCV002166879]	Chr11:93784702 [GRCh38] Chr11:93517868 [GRCh37] Chr11:11q21	likely benign
NM_004268.5(MED17):c.250+9dup	duplication	not provided [RCV002168570]	Chr11:93784771..93784772 [GRCh38] Chr11:93517937..93517938 [GRCh37] Chr11:11q21	likely benign
NM_004268.5(MED17):c.210del (p.Trp70fs)	deletion	not provided [RCV002880303]	Chr11:93784722 [GRCh38] Chr11:93517888 [GRCh37] Chr11:11q21	pathogenic
NM_004268.5(MED17):c.241G>A (p.Asp81Asn)	single nucleotide variant	not provided [RCV003070889]	Chr11:93784754 [GRCh38] Chr11:93517920 [GRCh37] Chr11:11q21	uncertain significance
NM_004268.5(MED17):c.203A>C (p.Gln68Pro)	single nucleotide variant	Inborn genetic diseases [RCV002540753]\|Infantile cerebral and cerebellar atrophy with postnatal progressive microcephaly [RCV001274816]\|not provided [RCV000906859]	Chr11:93784716 [GRCh38] Chr11:93517882 [GRCh37] Chr11:11q21	benign\|likely benign\|uncertain significance
NM_004268.5(MED17):c.224C>G (p.Ser75Cys)	single nucleotide variant	Inborn genetic diseases [RCV002540164]\|Infantile cerebral and cerebellar atrophy with postnatal progressive microcephaly [RCV001274818]\|MED17-related disorder [RCV003922905]\|not provided [RCV000898028]	Chr11:93784737 [GRCh38] Chr11:93517903 [GRCh37] Chr11:11q21	benign\|likely benign\|uncertain significance
NM_004268.5(MED17):c.250+7C>T	single nucleotide variant	Infantile cerebral and cerebellar atrophy with postnatal progressive microcephaly [RCV001274819]\|not provided [RCV000932783]	Chr11:93784770 [GRCh38] Chr11:93517936 [GRCh37] Chr11:11q21	benign\|uncertain significance
NM_004268.5(MED17):c.201G>T (p.Ala67=)	single nucleotide variant	Infantile cerebral and cerebellar atrophy with postnatal progressive microcephaly [RCV001274815]\|MED17-related disorder [RCV003960377]\|not provided [RCV000919379]	Chr11:93784714 [GRCh38] Chr11:93517880 [GRCh37] Chr11:11q21	likely benign\|uncertain significance
NM_004268.5(MED17):c.219C>T (p.Ala73=)	single nucleotide variant	Infantile cerebral and cerebellar atrophy with postnatal progressive microcephaly [RCV001274817]\|not provided [RCV000942141]	Chr11:93784732 [GRCh38] Chr11:93517898 [GRCh37] Chr11:11q21	likely benign\|uncertain significance
NC_000011.10:g.(?_93784504)_(93788177_?)del	deletion	not provided [RCV000800037]	Chr11:93784504..93788177 [GRCh38] Chr11:93517670..93521343 [GRCh37] Chr11:11q21	pathogenic
NM_004268.5(MED17):c.212C>T (p.Pro71Leu)	single nucleotide variant	Inborn genetic diseases [RCV004951440]\|Infantile cerebral and cerebellar atrophy with postnatal progressive microcephaly [RCV001278665]	Chr11:93784725 [GRCh38] Chr11:93517891 [GRCh37] Chr11:11q21	uncertain significance
NM_004268.5(MED17):c.198C>T (p.Asp66=)	single nucleotide variant	not provided [RCV001489845]	Chr11:93784711 [GRCh38] Chr11:93517877 [GRCh37] Chr11:11q21	likely benign
NM_004268.5(MED17):c.195C>A (p.Gly65=)	single nucleotide variant	not provided [RCV001485307]	Chr11:93784708 [GRCh38] Chr11:93517874 [GRCh37] Chr11:11q21	likely benign
NM_004268.5(MED17):c.177G>A (p.Glu59=)	single nucleotide variant	not provided [RCV002625084]	Chr11:93784690 [GRCh38] Chr11:93517856 [GRCh37] Chr11:11q21	likely benign
NM_004268.5(MED17):c.250+8C>T	single nucleotide variant	not provided [RCV001409720]	Chr11:93784771 [GRCh38] Chr11:93517937 [GRCh37] Chr11:11q21	likely benign
GRCh38/hg38 11q14.1-22.3(chr11:78232836-106779420)x1	copy number loss	See cases [RCV000052710]	Chr11:78232836..106779420 [GRCh38] Chr11:77943882..106650146 [GRCh37] Chr11:77621530..106155356 [NCBI36] Chr11:11q14.1-22.3	pathogenic
NM_004268.5(MED17):c.221G>C (p.Gly74Ala)	single nucleotide variant	Inborn genetic diseases [RCV003210595]	Chr11:93784734 [GRCh38] Chr11:93517900 [GRCh37] Chr11:11q21	uncertain significance
NM_004268.5(MED17):c.183G>A (p.Ala61=)	single nucleotide variant	not provided [RCV003577578]	Chr11:93784696 [GRCh38] Chr11:93517862 [GRCh37] Chr11:11q21	likely benign
NM_004268.5(MED17):c.228C>T (p.Ser76=)	single nucleotide variant	not provided [RCV003686845]	Chr11:93784741 [GRCh38] Chr11:93517907 [GRCh37] Chr11:11q21	likely benign
NM_004268.5(MED17):c.250+20C>T	single nucleotide variant	not provided [RCV003880649]	Chr11:93784783 [GRCh38] Chr11:93517949 [GRCh37] Chr11:11q21	likely benign
NM_004268.5(MED17):c.250+10G>A	single nucleotide variant	not provided [RCV003687843]	Chr11:93784773 [GRCh38] Chr11:93517939 [GRCh37] Chr11:11q21	likely benign
NM_004268.5(MED17):c.250+16G>A	single nucleotide variant	not provided [RCV003812206]	Chr11:93784779 [GRCh38] Chr11:93517945 [GRCh37] Chr11:11q21	likely benign
NM_004268.5(MED17):c.213G>A (p.Pro71=)	single nucleotide variant	not provided [RCV003559604]	Chr11:93784726 [GRCh38] Chr11:93517892 [GRCh37] Chr11:11q21	likely benign
NM_004268.5(MED17):c.250+11C>T	single nucleotide variant	not provided [RCV003706775]	Chr11:93784774 [GRCh38] Chr11:93517940 [GRCh37] Chr11:11q21	likely benign
NM_004268.5(MED17):c.250+7C>G	single nucleotide variant	not provided [RCV003719268]	Chr11:93784770 [GRCh38] Chr11:93517936 [GRCh37] Chr11:11q21	likely benign
NM_004268.5(MED17):c.219C>G (p.Ala73=)	single nucleotide variant	not provided [RCV003711758]	Chr11:93784732 [GRCh38] Chr11:93517898 [GRCh37] Chr11:11q21	likely benign
NM_004268.5(MED17):c.250+1G>A	single nucleotide variant	not provided [RCV003718768]	Chr11:93784764 [GRCh38] Chr11:93517930 [GRCh37] Chr11:11q21	likely pathogenic
NM_004268.5(MED17):c.216C>A (p.Gly72=)	single nucleotide variant	not provided [RCV003685450]	Chr11:93784729 [GRCh38] Chr11:93517895 [GRCh37] Chr11:11q21	likely benign
NM_004268.5(MED17):c.250+2T>A	single nucleotide variant	not provided [RCV003737807]	Chr11:93784765 [GRCh38] Chr11:93517931 [GRCh37] Chr11:11q21	likely pathogenic
NM_004268.5(MED17):c.176A>C (p.Glu59Ala)	single nucleotide variant	Inborn genetic diseases [RCV004645116]	Chr11:93784689 [GRCh38] Chr11:93517855 [GRCh37] Chr11:11q21	uncertain significance
GRCh38/hg38 11q14.1-22.2(chr11:85242847-102920097)x1	copy number loss	See cases [RCV000052711]	Chr11:85242847..102920097 [GRCh38] Chr11:84953891..102738968 [GRCh37] Chr11:84631539..102296037 [NCBI36] Chr11:11q14.1-22.2	pathogenic
NM_004268.5(MED17):c.200C>G (p.Ala67Gly)	single nucleotide variant	not provided [RCV002039905]	Chr11:93784713 [GRCh38] Chr11:93517879 [GRCh37] Chr11:11q21	uncertain significance
NM_004268.5(MED17):c.192G>A (p.Glu64=)	single nucleotide variant	not provided [RCV002824279]	Chr11:93784705 [GRCh38] Chr11:93517871 [GRCh37] Chr11:11q21	likely benign
GRCh38/hg38 11q14.3-22.3(chr11:91086659-109595582)x1	copy number loss	See cases [RCV000138038]	Chr11:91086659..109595582 [GRCh38] Chr11:90819827..109466308 [GRCh37] Chr11:90459475..108971518 [NCBI36] Chr11:11q14.3-22.3	pathogenic
NM_004268.5(MED17):c.236A>G (p.Gln79Arg)	single nucleotide variant	Inborn genetic diseases [RCV003302335]	Chr11:93784749 [GRCh38] Chr11:93517915 [GRCh37] Chr11:11q21	uncertain significance

Click on a value in the shaded box below the category label to view a detailed expression data table for that system.


RefSeq Transcripts	NG_186041	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AP001894	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CP068267	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Database	Acc Id	Source(s)
COSMIC	LOC130006596	COSMIC
GTEx	LOC130006596	GTEx
Human Proteome Map	LOC130006596	Human Proteome Map
NCBI Gene	LOC130006596	ENTREZGENE

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailable


InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailable


Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
		Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable

Send us a Message

Imported Disease Annotations - ClinVar