LOC128772343 (melanoma risk locus-associated MPRA allelic enhancer 11:16133413) - Rat Genome Database

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Gene: LOC128772343 (melanoma risk locus-associated MPRA allelic enhancer 11:16133413) Homo sapiens
Analyze
Symbol: LOC128772343
Name: melanoma risk locus-associated MPRA allelic enhancer 11:16133413
RGD ID: 156451613
Description: This genomic sequence includes a genetic variant, rs4617548, that is in strong linkage disequilibrium with a melanoma risk locus identified at 11p15.2 in genome-wide association studies (GWASs), and for which the reference allele has a protective effect. This region was validated as a functional enhancer by massively parallel reporter assays (MPRAs) in UACC903 melanoma cells, where differences in transcriptional activity were observed between the reference and alternative rs4617548 alleles. [provided by RefSeq, Mar 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
GRCh381116,111,795 - 16,111,939 (+)NCBIGRCh38GRCh38hg38GRCh38
T2T-CHM13v2.01116,209,741 - 16,209,885 (+)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:32341527   PMID:36423637  


Genomics

Variants

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Variants in LOC128772343
11 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 11p15.2(chr11:16101236-16446623)x1 copy number loss See cases [RCV000051188] Chr11:16101236..16446623 [GRCh38]
Chr11:16122782..16468170 [GRCh37]
Chr11:16079358..16424746 [NCBI36]
Chr11:11p15.2		 uncertain significance
NM_001367873.1(SOX6):c.878dup (p.Gly294fs) duplication Intellectual disability [RCV001254915] Chr11:16111822..16111823 [GRCh38]
Chr11:16133368..16133369 [GRCh37]
Chr11:11p15.2		 pathogenic
NM_001367873.1(SOX6):c.834T>C (p.Thr278=) single nucleotide variant not provided [RCV001691868] Chr11:16111867 [GRCh38]
Chr11:16133413 [GRCh37]
Chr11:11p15.2		 benign
NM_001367873.1(SOX6):c.841G>A (p.Ala281Thr) single nucleotide variant not provided [RCV002265236] Chr11:16111860 [GRCh38]
Chr11:16133406 [GRCh37]
Chr11:11p15.2		 uncertain significance
NM_001367873.1(SOX6):c.829C>T (p.Arg277Trp) single nucleotide variant not provided [RCV002225986] Chr11:16111872 [GRCh38]
Chr11:16133418 [GRCh37]
Chr11:11p15.2		 uncertain significance
NM_001367873.1(SOX6):c.790A>G (p.Met264Val) single nucleotide variant Inborn genetic diseases [RCV002714699] Chr11:16111911 [GRCh38]
Chr11:16133457 [GRCh37]
Chr11:11p15.2		 uncertain significance
GRCh38/hg38 11p15.4-15.2(chr11:9989516-16825806)x1 copy number loss See cases [RCV000136773] Chr11:9989516..16825806 [GRCh38]
Chr11:10011063..16847353 [GRCh37]
Chr11:9967639..16803929 [NCBI36]
Chr11:11p15.4-15.2		 pathogenic
NM_001367873.1(SOX6):c.884T>A (p.Ile295Lys) single nucleotide variant not provided [RCV002638624] Chr11:16111817 [GRCh38]
Chr11:16133363 [GRCh37]
Chr11:11p15.2		 uncertain significance
GRCh38/hg38 11p15.5-15.1(chr11:446754-18904742)x3 copy number gain See cases [RCV000133997] Chr11:446754..18904742 [GRCh38]
Chr11:446754..18926289 [GRCh37]
Chr11:436754..18882865 [NCBI36]
Chr11:11p15.5-15.1		 pathogenic
NM_001367873.1(SOX6):c.811A>G (p.Ile271Val) single nucleotide variant not provided [RCV003129162] Chr11:16111890 [GRCh38]
Chr11:16133436 [GRCh37]
Chr11:11p15.2		 likely pathogenic
NM_001367873.1(SOX6):c.877C>T (p.Pro293Ser) single nucleotide variant Inborn genetic diseases [RCV002989237] Chr11:16111824 [GRCh38]
Chr11:16133370 [GRCh37]
Chr11:11p15.2		 uncertain significance
NM_001367873.1(SOX6):c.871T>C (p.Phe291Leu) single nucleotide variant not provided [RCV003159337] Chr11:16111830 [GRCh38]
Chr11:16133376 [GRCh37]
Chr11:11p15.2		 uncertain significance
NM_001367873.1(SOX6):c.873C>A (p.Phe291Leu) single nucleotide variant not provided [RCV003879863] Chr11:16111828 [GRCh38]
Chr11:16133374 [GRCh37]
Chr11:11p15.2		 uncertain significance
NM_001367873.1(SOX6):c.877C>G (p.Pro293Ala) single nucleotide variant not provided [RCV003817415] Chr11:16111824 [GRCh38]
Chr11:16133370 [GRCh37]
Chr11:11p15.2		 uncertain significance

Expression


Sequence



Additional Information

Database Acc Id Source(s)
COSMIC LOC128772343 COSMIC
GTEx LOC128772343 GTEx
Human Proteome Map LOC128772343 Human Proteome Map
NCBI Gene LOC128772343 ENTREZGENE