LOC130059440 (ATAC-STARR-seq lymphoblastoid silent region 7724) - Rat Genome Database

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Gene: LOC130059440 (ATAC-STARR-seq lymphoblastoid silent region 7724) Homo sapiens
Analyze
Symbol: LOC130059440
Name: ATAC-STARR-seq lymphoblastoid silent region 7724
RGD ID: 329817076
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 AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381675,555,943 - 75,556,022 (+)NCBIGRCh38GRCh38hg38GRCh38
T2T-CHM13v2.01681,604,190 - 81,604,269 (+)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:35858748  


Genomics

Variants

.
Variants in LOC130059440
19 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NM_001077418.3(TMEM231):c.155G>A (p.Arg52Gln) single nucleotide variant Joubert syndrome 20 [RCV002619305] Chr16:75555958 [GRCh38]
Chr16:75589856 [GRCh37]
Chr16:16q23.1		 uncertain significance
NM_001077418.3(TMEM231):c.166G>C (p.Glu56Gln) single nucleotide variant Joubert syndrome 20 [RCV001866223]|not provided [RCV001594355] Chr16:75555947 [GRCh38]
Chr16:75589845 [GRCh37]
Chr16:16q23.1		 uncertain significance
NM_001077418.3(TMEM231):c.140-33C>T single nucleotide variant Joubert syndrome 20 [RCV001988520]|not provided [RCV002300640] Chr16:75556006 [GRCh38]
Chr16:75589904 [GRCh37]
Chr16:16q23.1		 uncertain significance
NM_001077418.3(TMEM231):c.164A>G (p.Tyr55Cys) single nucleotide variant Joubert syndrome 20 [RCV002585057] Chr16:75555949 [GRCh38]
Chr16:75589847 [GRCh37]
Chr16:16q23.1		 uncertain significance
NM_001077418.3(TMEM231):c.140-10T>C single nucleotide variant Joubert syndrome 20 [RCV002008429] Chr16:75555983 [GRCh38]
Chr16:75589881 [GRCh37]
Chr16:16q23.1		 uncertain significance
GRCh38/hg38 16q23.1(chr16:75541502-79154140)x1 copy number loss See cases [RCV000135449] Chr16:75541502..79154140 [GRCh38]
Chr16:75575400..79188037 [GRCh37]
Chr16:74132901..77745538 [NCBI36]
Chr16:16q23.1		 pathogenic
NM_001077418.3(TMEM231):c.140-2A>G single nucleotide variant Joubert syndrome 20 [RCV002078590] Chr16:75555975 [GRCh38]
Chr16:75589873 [GRCh37]
Chr16:16q23.1		 likely benign
GRCh38/hg38 16q22.1-24.1(chr16:70414573-84908120)x1 copy number loss See cases [RCV000133814] Chr16:70414573..84908120 [GRCh38]
Chr16:70448476..84941726 [GRCh37]
Chr16:69005977..83499227 [NCBI36]
Chr16:16q22.1-24.1		 pathogenic
NM_001077418.3(TMEM231):c.140-3C>G single nucleotide variant Joubert syndrome 20 [RCV001950943] Chr16:75555976 [GRCh38]
Chr16:75589874 [GRCh37]
Chr16:16q23.1		 pathogenic
NM_001077418.3(TMEM231):c.168G>T (p.Glu56Asp) single nucleotide variant Inborn genetic diseases [RCV002827104] Chr16:75555945 [GRCh38]
Chr16:75589843 [GRCh37]
Chr16:16q23.1		 uncertain significance
GRCh38/hg38 16q21-24.1(chr16:62925929-84585795)x3 copy number gain See cases [RCV000135863] Chr16:62925929..84585795 [GRCh38]
Chr16:62959833..84619401 [GRCh37]
Chr16:61517334..83176902 [NCBI36]
Chr16:16q21-24.1		 pathogenic
NM_001077418.3(TMEM231):c.144T>G (p.Phe48Leu) single nucleotide variant Joubert syndrome 20 [RCV001898066] Chr16:75555969 [GRCh38]
Chr16:75589867 [GRCh37]
Chr16:16q23.1		 uncertain significance
GRCh38/hg38 16q23.1(chr16:75227456-75731127)x3 copy number gain See cases [RCV000143189] Chr16:75227456..75731127 [GRCh38]
Chr16:75261354..75765025 [GRCh37]
Chr16:73818855..74322526 [NCBI36]
Chr16:16q23.1		 uncertain significance
GRCh38/hg38 16q12.2-24.3(chr16:52899183-90088654)x3 copy number gain See cases [RCV000143425] Chr16:52899183..90088654 [GRCh38]
Chr16:52933095..90155062 [GRCh37]
Chr16:51490596..88682563 [NCBI36]
Chr16:16q12.2-24.3		 pathogenic
GRCh38/hg38 16q23.1(chr16:74811982-75698467)x3 copy number gain See cases [RCV000139130] Chr16:74811982..75698467 [GRCh38]
Chr16:74845880..75732365 [GRCh37]
Chr16:73403381..74289866 [NCBI36]
Chr16:16q23.1		 uncertain significance
GRCh38/hg38 16q21-23.3(chr16:65957829-83611443)x3 copy number gain See cases [RCV000143742] Chr16:65957829..83611443 [GRCh38]
Chr16:65991732..83645048 [GRCh37]
Chr16:64549233..82202549 [NCBI36]
Chr16:16q21-23.3		 pathogenic
GRCh38/hg38 16q22.1-24.3(chr16:70749398-90096995)x3 copy number gain See cases [RCV000137495] Chr16:70749398..90096995 [GRCh38]
Chr16:70783301..90163403 [GRCh37]
Chr16:69340802..88690904 [NCBI36]
Chr16:16q22.1-24.3		 pathogenic
NM_001077418.3(TMEM231):c.140-30A>C single nucleotide variant Joubert syndrome 20 [RCV001070947] Chr16:75556003 [GRCh38]
Chr16:75589901 [GRCh37]
Chr16:16q23.1		 likely pathogenic|uncertain significance
GRCh38/hg38 16q23.1-24.3(chr16:75377981-90081992)x3 copy number gain See cases [RCV000139302] Chr16:75377981..90081992 [GRCh38]
Chr16:75411879..90148400 [GRCh37]
Chr16:73969380..88675901 [NCBI36]
Chr16:16q23.1-24.3		 pathogenic
NM_001077418.3(TMEM231):c.140-5C>T single nucleotide variant Joubert syndrome 20 [RCV003026288] Chr16:75555978 [GRCh38]
Chr16:75589876 [GRCh37]
Chr16:16q23.1		 likely benign
NM_001077418.3(TMEM231):c.140-47C>G single nucleotide variant Joubert syndrome 20 [RCV001463558] Chr16:75556020 [GRCh38]
Chr16:75589918 [GRCh37]
Chr16:16q23.1		 likely benign
GRCh38/hg38 16q21-24.3(chr16:65511483-90096995)x3 copy number gain See cases [RCV000139426] Chr16:65511483..90096995 [GRCh38]
Chr16:65545386..90163403 [GRCh37]
Chr16:64102887..88690904 [NCBI36]
Chr16:16q21-24.3		 pathogenic
NM_001077418.3(TMEM231):c.140-15C>T single nucleotide variant Joubert syndrome 20 [RCV000878145] Chr16:75555988 [GRCh38]
Chr16:75589886 [GRCh37]
Chr16:16q23.1		 likely benign
GRCh38/hg38 16q22.1-23.3(chr16:69053457-83274681)x3 copy number gain See cases [RCV000142038] Chr16:69053457..83274681 [GRCh38]
Chr16:69087360..83308286 [GRCh37]
Chr16:67644861..81865787 [NCBI36]
Chr16:16q22.1-23.3		 pathogenic
NM_001077418.3(TMEM231):c.140-17C>A single nucleotide variant not provided [RCV002292929] Chr16:75555990 [GRCh38]
Chr16:75589888 [GRCh37]
Chr16:16q23.1		 likely benign
NM_001077418.3(TMEM231):c.140-28C>G single nucleotide variant Joubert syndrome 20 [RCV000544987]|not provided [RCV003884433]|not specified [RCV000248641] Chr16:75556001 [GRCh38]
Chr16:75589899 [GRCh37]
Chr16:16q23.1		 benign|likely benign|conflicting interpretations of pathogenicity
GRCh38/hg38 16q21-24.3(chr16:64389378-90081985)x3 copy number gain See cases [RCV000142578] Chr16:64389378..90081985 [GRCh38]
Chr16:64423281..90148393 [GRCh37]
Chr16:62980782..88675894 [NCBI36]
Chr16:16q21-24.3		 pathogenic|likely pathogenic
NM_001077418.3(TMEM231):c.140-39G>A single nucleotide variant Joubert syndrome 20 [RCV002628957] Chr16:75556012 [GRCh38]
Chr16:75589910 [GRCh37]
Chr16:16q23.1		 uncertain significance
GRCh38/hg38 16q22.1-23.1(chr16:69918076-76723348)x1 copy number loss See cases [RCV000053356] Chr16:69918076..76723348 [GRCh38]
Chr16:69951979..76757245 [GRCh37]
Chr16:68509480..75314746 [NCBI36]
Chr16:16q22.1-23.1		 pathogenic
GRCh38/hg38 16q21-24.3(chr16:65313395-90081985)x3 copy number gain See cases [RCV000052421] Chr16:65313395..90081985 [GRCh38]
Chr16:65347298..90148393 [GRCh37]
Chr16:63904799..88675894 [NCBI36]
Chr16:16q21-24.3		 pathogenic
GRCh38/hg38 16q22.3-23.3(chr16:73049467-82576326)x1 copy number loss See cases [RCV000053357] Chr16:73049467..82576326 [GRCh38]
Chr16:73083366..82609931 [GRCh37]
Chr16:71640867..81167432 [NCBI36]
Chr16:16q22.3-23.3		 pathogenic
GRCh38/hg38 16q22.1-24.3(chr16:70514631-90081985)x3 copy number gain See cases [RCV000052422] Chr16:70514631..90081985 [GRCh38]
Chr16:70548534..90148393 [GRCh37]
Chr16:69106035..88675894 [NCBI36]
Chr16:16q22.1-24.3		 pathogenic
NM_001077418.3(TMEM231):c.140-35C>T single nucleotide variant Joubert syndrome 20 [RCV003767538]|not specified [RCV000606378] Chr16:75556008 [GRCh38]
Chr16:75589906 [GRCh37]
Chr16:16q23.1		 likely benign
NM_001077418.3(TMEM231):c.140-33C>G single nucleotide variant Joubert syndrome 20 [RCV001329561] Chr16:75556006 [GRCh38]
Chr16:75589904 [GRCh37]
Chr16:16q23.1		 uncertain significance
GRCh38/hg38 16q23.1(chr16:75485676-75603079)x3 copy number gain See cases [RCV000053894] Chr16:75485676..75603079 [GRCh38]
Chr16:75519574..75636977 [GRCh37]
Chr16:74077075..74194478 [NCBI36]
Chr16:16q23.1		 uncertain significance
NM_001077418.3(TMEM231):c.140-8dup duplication Joubert syndrome 20 [RCV003806770] Chr16:75555980..75555981 [GRCh38]
Chr16:75589878..75589879 [GRCh37]
Chr16:16q23.1		 pathogenic
NM_001077418.3(TMEM231):c.140-9_140-8del deletion Joubert syndrome 20 [RCV003798227] Chr16:75555981..75555982 [GRCh38]
Chr16:75589879..75589880 [GRCh37]
Chr16:16q23.1		 pathogenic
NM_001077418.3(TMEM231):c.140-29C>T single nucleotide variant Joubert syndrome 20 [RCV003800094] Chr16:75556002 [GRCh38]
Chr16:75589900 [GRCh37]
Chr16:16q23.1		 likely benign

Expression


Sequence



Additional Information

Database Acc Id Source(s)
COSMIC LOC130059440 COSMIC
GTEx LOC130059440 GTEx
Human Proteome Map LOC130059440 Human Proteome Map
NCBI Gene LOC130059440 ENTREZGENE