LOC130058543 (ATAC-STARR-seq lymphoblastoid active region 10486) - Rat Genome Database

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Gene: LOC130058543 (ATAC-STARR-seq lymphoblastoid active region 10486) Homo sapiens
Analyze
Symbol: LOC130058543
Name: ATAC-STARR-seq lymphoblastoid active region 10486
RGD ID: 329834562
Description: This genomic sequence represents an accessible chromatin region that was validated as an enhancer based on its ability to activate 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
GRCh381613,919,998 - 13,920,357 (+)NCBIGRCh38GRCh38hg38GRCh38
T2T-CHM13v2.01613,957,237 - 13,957,596 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
References
Additional References at PubMed
PMID:35858748  


Genomics

Variants

.
Variants in LOC130058543
65 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NM_005236.3(ERCC4):c.127C>T (p.Arg43Trp) single nucleotide variant Fanconi anemia complementation group Q [RCV001788945] Chr16:13920292 [GRCh38]
Chr16:14014149 [GRCh37]
Chr16:16p13.12		 uncertain significance
NM_005236.3(ERCC4):c.86C>T (p.Thr29Ile) single nucleotide variant not specified [RCV001820238] Chr16:13920251 [GRCh38]
Chr16:14014108 [GRCh37]
Chr16:16p13.12		 uncertain significance
GRCh38/hg38 16p13.3-11.2(chr16:4644892-29170820)x3 copy number gain See cases [RCV000133809] Chr16:4644892..29170820 [GRCh38]
Chr16:4694893..29182141 [GRCh37]
Chr16:4634894..29089642 [NCBI36]
Chr16:16p13.3-11.2		 pathogenic
NM_005236.3(ERCC4):c.145C>T (p.Leu49Phe) single nucleotide variant Xeroderma pigmentosum [RCV002258137]|Xeroderma pigmentosum, group F [RCV001116100]|Xeroderma pigmentosum, group F [RCV001359252]|not provided [RCV001759882] Chr16:13920310 [GRCh38]
Chr16:14014167 [GRCh37]
Chr16:16p13.12		 uncertain significance
NM_005236.3(ERCC4):c.109C>T (p.Arg37Cys) single nucleotide variant Xeroderma pigmentosum, group F [RCV001066566]|not provided [RCV003238298] Chr16:13920274 [GRCh38]
Chr16:14014131 [GRCh37]
Chr16:16p13.12		 uncertain significance
NM_005236.3(ERCC4):c.79C>T (p.Leu27Phe) single nucleotide variant Xeroderma pigmentosum [RCV002257427]|Xeroderma pigmentosum, group F [RCV000372597]|Xeroderma pigmentosum, group F [RCV001340956]|Xeroderma pigmentosum, group F [RCV002477312]|not specified [RCV000120804] Chr16:13920244 [GRCh38]
Chr16:14014101 [GRCh37]
Chr16:16p13.12		 uncertain significance|not provided
NM_005236.3(ERCC4):c.137A>G (p.Tyr46Cys) single nucleotide variant Xeroderma pigmentosum, group F [RCV001936424] Chr16:13920302 [GRCh38]
Chr16:14014159 [GRCh37]
Chr16:16p13.12		 uncertain significance
NM_005236.3(ERCC4):c.33C>T (p.Ala11=) single nucleotide variant Xeroderma pigmentosum, group F [RCV000232260]|Xeroderma pigmentosum, group F [RCV001121019]|not provided [RCV001565313]|not specified [RCV000251617] Chr16:13920198 [GRCh38]
Chr16:14014055 [GRCh37]
Chr16:16p13.12		 benign|likely benign
NC_000016.10:g.13920136T>A single nucleotide variant not provided [RCV001663035] Chr16:13920136 [GRCh38]
Chr16:14013993 [GRCh37]
Chr16:16p13.12		 benign
NM_005236.3(ERCC4):c.12G>A (p.Gly4=) single nucleotide variant Xeroderma pigmentosum, group F [RCV001121018] Chr16:13920177 [GRCh38]
Chr16:14014034 [GRCh37]
Chr16:16p13.12		 uncertain significance
NM_005236.3(ERCC4):c.2T>C (p.Met1Thr) single nucleotide variant not provided [RCV001774849] Chr16:13920167 [GRCh38]
Chr16:14014024 [GRCh37]
Chr16:16p13.12		 uncertain significance
NM_005236.3(ERCC4):c.122C>G (p.Ala41Gly) single nucleotide variant Xeroderma pigmentosum, group F [RCV001201434] Chr16:13920287 [GRCh38]
Chr16:14014144 [GRCh37]
Chr16:16p13.12		 uncertain significance
NM_005236.3(ERCC4):c.37G>A (p.Ala13Thr) single nucleotide variant Behavioral variant of frontotemporal dementia [RCV002508160]|Xeroderma pigmentosum, group F [RCV002541036]|not provided [RCV003238123] Chr16:13920202 [GRCh38]
Chr16:14014059 [GRCh37]
Chr16:16p13.12		 uncertain significance
NM_005236.3(ERCC4):c.4G>C (p.Glu2Gln) single nucleotide variant Xeroderma pigmentosum, group F [RCV001219171] Chr16:13920169 [GRCh38]
Chr16:14014026 [GRCh37]
Chr16:16p13.12		 uncertain significance
NM_005236.3(ERCC4):c.176T>A (p.Val59Glu) single nucleotide variant not specified [RCV000120805] Chr16:13920341 [GRCh38]
Chr16:14014198 [GRCh37]
Chr16:16p13.12		 not provided
NM_005236.3(ERCC4):c.98T>C (p.Val33Ala) single nucleotide variant Xeroderma pigmentosum [RCV002258703] Chr16:13920263 [GRCh38]
Chr16:14014120 [GRCh37]
Chr16:16p13.12		 uncertain significance
NM_005236.3(ERCC4):c.143T>A (p.Phe48Tyr) single nucleotide variant Xeroderma pigmentosum, group F [RCV001895360] Chr16:13920308 [GRCh38]
Chr16:14014165 [GRCh37]
Chr16:16p13.12		 uncertain significance
NM_005236.3(ERCC4):c.69G>A (p.Val23=) single nucleotide variant Xeroderma pigmentosum, group F [RCV002156447] Chr16:13920234 [GRCh38]
Chr16:14014091 [GRCh37]
Chr16:16p13.12		 likely benign
NM_005236.3(ERCC4):c.22C>A (p.Arg8=) single nucleotide variant Xeroderma pigmentosum, group F [RCV002095302] Chr16:13920187 [GRCh38]
Chr16:14014044 [GRCh37]
Chr16:16p13.12		 likely benign
NM_005236.3(ERCC4):c.183G>A (p.Val61=) single nucleotide variant Xeroderma pigmentosum, group F [RCV002140107] Chr16:13920348 [GRCh38]
Chr16:14014205 [GRCh37]
Chr16:16p13.12		 likely benign
NM_005236.3(ERCC4):c.125A>G (p.Asp42Gly) single nucleotide variant Xeroderma pigmentosum, group F [RCV001930722] Chr16:13920290 [GRCh38]
Chr16:14014147 [GRCh37]
Chr16:16p13.12		 uncertain significance
NM_005236.3(ERCC4):c.187A>C (p.Asn63His) single nucleotide variant Xeroderma pigmentosum, group F [RCV003101505]|not specified [RCV002266411] Chr16:13920352 [GRCh38]
Chr16:14014209 [GRCh37]
Chr16:16p13.12		 uncertain significance
NM_005236.3(ERCC4):c.105C>T (p.Cys35=) single nucleotide variant Xeroderma pigmentosum, group F [RCV000285190]|Xeroderma pigmentosum, group F [RCV002061190] Chr16:13920270 [GRCh38]
Chr16:14014127 [GRCh37]
Chr16:16p13.12		 likely benign|uncertain significance
NM_005236.3(ERCC4):c.32C>T (p.Ala11Val) single nucleotide variant Xeroderma pigmentosum, group F [RCV001220164] Chr16:13920197 [GRCh38]
Chr16:14014054 [GRCh37]
Chr16:16p13.12		 uncertain significance
NM_005236.3(ERCC4):c.58C>T (p.Arg20Ter) single nucleotide variant Xeroderma pigmentosum, group F [RCV002037756] Chr16:13920223 [GRCh38]
Chr16:14014080 [GRCh37]
Chr16:16p13.12		 pathogenic
NM_005236.3(ERCC4):c.2T>G (p.Met1Arg) single nucleotide variant Xeroderma pigmentosum, group F [RCV002957387] Chr16:13920167 [GRCh38]
Chr16:14014024 [GRCh37]
Chr16:16p13.12		 uncertain significance
NM_005236.3(ERCC4):c.91G>C (p.Gly31Arg) single nucleotide variant Inborn genetic diseases [RCV002931210] Chr16:13920256 [GRCh38]
Chr16:14014113 [GRCh37]
Chr16:16p13.12		 uncertain significance
NM_005236.3(ERCC4):c.167C>T (p.Ala56Val) single nucleotide variant Xeroderma pigmentosum, group F [RCV003000123] Chr16:13920332 [GRCh38]
Chr16:14014189 [GRCh37]
Chr16:16p13.12		 uncertain significance
NM_005236.3(ERCC4):c.20C>T (p.Ala7Val) single nucleotide variant Xeroderma pigmentosum, group F [RCV003016417] Chr16:13920185 [GRCh38]
Chr16:14014042 [GRCh37]
Chr16:16p13.12		 uncertain significance
NM_005236.3(ERCC4):c.178C>T (p.Leu60=) single nucleotide variant Xeroderma pigmentosum, group F [RCV002102669] Chr16:13920343 [GRCh38]
Chr16:14014200 [GRCh37]
Chr16:16p13.12		 likely benign
NM_005236.3(ERCC4):c.96A>G (p.Leu32=) single nucleotide variant Xeroderma pigmentosum, group F [RCV002972285] Chr16:13920261 [GRCh38]
Chr16:14014118 [GRCh37]
Chr16:16p13.12		 likely benign
GRCh38/hg38 16p13.13-13.11(chr16:11952467-15186199)x1 copy number loss See cases [RCV000137596] Chr16:11952467..15186199 [GRCh38]
Chr16:12046324..15280056 [GRCh37]
Chr16:11953825..15187557 [NCBI36]
Chr16:16p13.13-13.11		 likely pathogenic
NM_005236.3(ERCC4):c.89A>C (p.Asp30Ala) single nucleotide variant not provided [RCV000224195] Chr16:13920254 [GRCh38]
Chr16:14014111 [GRCh37]
Chr16:16p13.12		 uncertain significance
GRCh38/hg38 16p13.3-13.11(chr16:666662-15743104)x3 copy number gain See cases [RCV000143710] Chr16:666662..15743104 [GRCh38]
Chr16:716662..15836961 [GRCh37]
Chr16:656663..15744462 [NCBI36]
Chr16:16p13.3-13.11		 pathogenic
NM_005236.3(ERCC4):c.1A>G (p.Met1Val) single nucleotide variant Fanconi anemia complementation group Q [RCV003154575] Chr16:13920166 [GRCh38]
Chr16:14014023 [GRCh37]
Chr16:16p13.12		 uncertain significance
NM_005236.3(ERCC4):c.100G>A (p.Val34Met) single nucleotide variant Ovarian cancer [RCV003154735]|Xeroderma pigmentosum, group F [RCV003778920] Chr16:13920265 [GRCh38]
Chr16:14014122 [GRCh37]
Chr16:16p13.12		 likely pathogenic|uncertain significance
NC_000016.10:g.(?_13920156)_(13948357_?)del deletion Xeroderma pigmentosum, group F [RCV000819225] Chr16:13920156..13948357 [GRCh38]
Chr16:14014013..14042214 [GRCh37]
Chr16:16p13.12		 pathogenic
NM_005236.3(ERCC4):c.42G>A (p.Pro14=) single nucleotide variant Xeroderma pigmentosum, group F [RCV001412669] Chr16:13920207 [GRCh38]
Chr16:14014064 [GRCh37]
Chr16:16p13.12		 likely benign
GRCh38/hg38 16p13.13-13.11(chr16:11967831-15162888)x1 copy number loss See cases [RCV000052484] Chr16:11967831..15162888 [GRCh38]
Chr16:12061688..15256745 [GRCh37]
Chr16:11969189..15164246 [NCBI36]
Chr16:16p13.13-13.11		 pathogenic
NM_005236.3(ERCC4):c.61C>G (p.Gln21Glu) single nucleotide variant Xeroderma pigmentosum, group F [RCV000334401]|Xeroderma pigmentosum, group F [RCV001362330] Chr16:13920226 [GRCh38]
Chr16:14014083 [GRCh37]
Chr16:16p13.12		 uncertain significance
NM_005236.3(ERCC4):c.19G>A (p.Ala7Thr) single nucleotide variant Xeroderma pigmentosum, group F [RCV000688763] Chr16:13920184 [GRCh38]
Chr16:14014041 [GRCh37]
Chr16:16p13.12		 uncertain significance
NM_005236.3(ERCC4):c.15G>A (p.Gln5=) single nucleotide variant Xeroderma pigmentosum, group F [RCV001485566] Chr16:13920180 [GRCh38]
Chr16:14014037 [GRCh37]
Chr16:16p13.12		 likely benign
NM_005236.3(ERCC4):c.22C>T (p.Arg8Ter) single nucleotide variant Xeroderma pigmentosum, group F [RCV001389442] Chr16:13920187 [GRCh38]
Chr16:14014044 [GRCh37]
Chr16:16p13.12		 pathogenic
NM_005236.3(ERCC4):c.25C>G (p.Arg9Gly) single nucleotide variant Xeroderma pigmentosum, group F [RCV002650366] Chr16:13920190 [GRCh38]
Chr16:14014047 [GRCh37]
Chr16:16p13.12		 uncertain significance
NM_005236.3(ERCC4):c.130C>T (p.Leu44Phe) single nucleotide variant Xeroderma pigmentosum, group F [RCV001298474] Chr16:13920295 [GRCh38]
Chr16:14014152 [GRCh37]
Chr16:16p13.12		 uncertain significance
NM_005236.3(ERCC4):c.17C>T (p.Pro6Leu) single nucleotide variant Fanconi anemia complementation group Q [RCV001294107] Chr16:13920182 [GRCh38]
Chr16:14014039 [GRCh37]
Chr16:16p13.12		 uncertain significance
NM_005236.3(ERCC4):c.124G>A (p.Asp42Asn) single nucleotide variant Xeroderma pigmentosum, group F [RCV001349621] Chr16:13920289 [GRCh38]
Chr16:14014146 [GRCh37]
Chr16:16p13.12		 uncertain significance
NM_005236.3(ERCC4):c.41C>T (p.Pro14Leu) single nucleotide variant Xeroderma pigmentosum, group F [RCV000462139] Chr16:13920206 [GRCh38]
Chr16:14014063 [GRCh37]
Chr16:16p13.12		 uncertain significance
NM_005236.3(ERCC4):c.8C>T (p.Ser3Leu) single nucleotide variant Xeroderma pigmentosum, group F [RCV003765689]|not provided [RCV000362531] Chr16:13920173 [GRCh38]
Chr16:14014030 [GRCh37]
Chr16:16p13.12		 uncertain significance
NM_005236.3(ERCC4):c.190A>T (p.Thr64Ser) single nucleotide variant Xeroderma pigmentosum, group F [RCV003805972] Chr16:13920355 [GRCh38]
Chr16:14014212 [GRCh37]
Chr16:16p13.12		 uncertain significance
NM_005236.3(ERCC4):c.43C>T (p.Leu15=) single nucleotide variant Xeroderma pigmentosum, group F [RCV003780459] Chr16:13920208 [GRCh38]
Chr16:14014065 [GRCh37]
Chr16:16p13.12		 likely benign
NM_005236.3(ERCC4):c.90C>G (p.Asp30Glu) single nucleotide variant Xeroderma pigmentosum, group F [RCV003806866] Chr16:13920255 [GRCh38]
Chr16:14014112 [GRCh37]
Chr16:16p13.12		 uncertain significance
NM_005236.3(ERCC4):c.83A>G (p.Asp28Gly) single nucleotide variant Xeroderma pigmentosum, group F [RCV003788050] Chr16:13920248 [GRCh38]
Chr16:14014105 [GRCh37]
Chr16:16p13.12		 uncertain significance
NM_005236.3(ERCC4):c.9A>C (p.Ser3=) single nucleotide variant Xeroderma pigmentosum, group F [RCV003785957] Chr16:13920174 [GRCh38]
Chr16:14014031 [GRCh37]
Chr16:16p13.12		 likely benign
NM_005236.3(ERCC4):c.129G>A (p.Arg43=) single nucleotide variant Xeroderma pigmentosum, group F [RCV003790997] Chr16:13920294 [GRCh38]
Chr16:14014151 [GRCh37]
Chr16:16p13.12		 likely benign
NM_005236.3(ERCC4):c.152T>G (p.Leu51Arg) single nucleotide variant Xeroderma pigmentosum, group F [RCV003787934] Chr16:13920317 [GRCh38]
Chr16:14014174 [GRCh37]
Chr16:16p13.12		 uncertain significance
NM_005236.3(ERCC4):c.158G>A (p.Cys53Tyr) single nucleotide variant Xeroderma pigmentosum, group F [RCV003790085] Chr16:13920323 [GRCh38]
Chr16:14014180 [GRCh37]
Chr16:16p13.12		 uncertain significance
NM_005236.3(ERCC4):c.81C>T (p.Leu27=) single nucleotide variant Xeroderma pigmentosum, group F [RCV003781335] Chr16:13920246 [GRCh38]
Chr16:14014103 [GRCh37]
Chr16:16p13.12		 likely benign
NM_005236.3(ERCC4):c.148C>T (p.Gln50Ter) single nucleotide variant Xeroderma pigmentosum, group F [RCV003797867] Chr16:13920313 [GRCh38]
Chr16:14014170 [GRCh37]
Chr16:16p13.12		 pathogenic
NM_005236.3(ERCC4):c.73G>C (p.Glu25Gln) single nucleotide variant Xeroderma pigmentosum, group F [RCV003800214] Chr16:13920238 [GRCh38]
Chr16:14014095 [GRCh37]
Chr16:16p13.12		 uncertain significance
NM_005236.3(ERCC4):c.147C>T (p.Leu49=) single nucleotide variant Xeroderma pigmentosum, group F [RCV003801952] Chr16:13920312 [GRCh38]
Chr16:14014169 [GRCh37]
Chr16:16p13.12		 likely benign
NM_005236.3(ERCC4):c.165A>G (p.Pro55=) single nucleotide variant Xeroderma pigmentosum, group F [RCV003802803] Chr16:13920330 [GRCh38]
Chr16:14014187 [GRCh37]
Chr16:16p13.12		 likely benign
NM_005236.3(ERCC4):c.118G>C (p.Gly40Arg) single nucleotide variant XFE progeroid syndrome [RCV003990101] Chr16:13920283 [GRCh38]
Chr16:14014140 [GRCh37]
Chr16:16p13.12		 uncertain significance
NM_005236.3(ERCC4):c.55G>A (p.Glu19Lys) single nucleotide variant XFE progeroid syndrome [RCV003990100] Chr16:13920220 [GRCh38]
Chr16:14014077 [GRCh37]
Chr16:16p13.12		 uncertain significance
NM_005236.3(ERCC4):c.106G>C (p.Ala36Pro) single nucleotide variant Xeroderma pigmentosum, group F [RCV002608594] Chr16:13920271 [GRCh38]
Chr16:14014128 [GRCh37]
Chr16:16p13.12		 uncertain significance
NM_005236.3(ERCC4):c.68del (p.Val23fs) deletion Xeroderma pigmentosum, group F [RCV003061403] Chr16:13920233 [GRCh38]
Chr16:14014090 [GRCh37]
Chr16:16p13.12		 pathogenic
NM_005236.3(ERCC4):c.16C>T (p.Pro6Ser) single nucleotide variant Fanconi anemia complementation group Q [RCV001292633]|Inborn genetic diseases [RCV004019681]|Xeroderma pigmentosum [RCV002257426]|Xeroderma pigmentosum, group F [RCV000475143]|Xeroderma pigmentosum, group F [RCV000989531]|Xeroderma pigmentosum, group F [RCV002477311]|not provided [RCV000734582]|not specified [RCV000120803] Chr16:13920181 [GRCh38]
Chr16:14014038 [GRCh37]
Chr16:16p13.12		 uncertain significance|not provided
NM_005236.3(ERCC4):c.34A>G (p.Met12Val) single nucleotide variant Xeroderma pigmentosum, group F [RCV003062927] Chr16:13920199 [GRCh38]
Chr16:14014056 [GRCh37]
Chr16:16p13.12		 uncertain significance
NM_005236.3(ERCC4):c.37G>T (p.Ala13Ser) single nucleotide variant Xeroderma pigmentosum, group F [RCV001056526] Chr16:13920202 [GRCh38]
Chr16:14014059 [GRCh37]
Chr16:16p13.12		 uncertain significance
NM_005236.3(ERCC4):c.114G>A (p.Gly38=) single nucleotide variant Xeroderma pigmentosum, group F [RCV003086579] Chr16:13920279 [GRCh38]
Chr16:14014136 [GRCh37]
Chr16:16p13.12		 likely benign
NM_005236.3(ERCC4):c.26G>C (p.Arg9Pro) single nucleotide variant Xeroderma pigmentosum, group F [RCV001059205] Chr16:13920191 [GRCh38]
Chr16:14014048 [GRCh37]
Chr16:16p13.12		 uncertain significance
NM_005236.3(ERCC4):c.41C>G (p.Pro14Arg) single nucleotide variant Xeroderma pigmentosum, group F [RCV000281667] Chr16:13920206 [GRCh38]
Chr16:14014063 [GRCh37]
Chr16:16p13.12		 uncertain significance
NM_005236.3(ERCC4):c.132C>T (p.Leu44=) single nucleotide variant Xeroderma pigmentosum, group F [RCV001433010] Chr16:13920297 [GRCh38]
Chr16:14014154 [GRCh37]
Chr16:16p13.12		 likely benign

Expression


Sequence



Additional Information

Database Acc Id Source(s)
COSMIC LOC130058543 COSMIC
GTEx LOC130058543 GTEx
Human Proteome Map LOC130058543 Human Proteome Map
NCBI Gene LOC130058543 ENTREZGENE