LOC130001603 (ATAC-STARR-seq lymphoblastoid silent region 19811) - Rat Genome Database

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Gene: LOC130001603 (ATAC-STARR-seq lymphoblastoid silent region 19811) Homo sapiens
Analyze
Symbol: LOC130001603
Name: ATAC-STARR-seq lymphoblastoid silent region 19811
RGD ID: 329827535
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
GRCh38921,974,815 - 21,974,864 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37921,974,814 - 21,974,863 (+)NCBIGRCh37GRCh37hg19GRCh37
T2T-CHM13v2.0921,989,127 - 21,989,176 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
References
Additional References at PubMed
PMID:35858748  


Genomics

Variants

.
Variants in LOC130001603
43 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NM_058195.4(CDKN2A):c.194-3652G>C single nucleotide variant Familial melanoma [RCV001510925]|Hereditary cancer-predisposing syndrome [RCV001188881]|Melanoma-pancreatic cancer syndrome [RCV000663020]|not provided [RCV000679206]|not specified [RCV002268242] Chr9:21974860 [GRCh38]
Chr9:21974859 [GRCh37]
Chr9:9p21.3		 benign|likely benign
NM_000077.5(CDKN2A):c.13G>A (p.Ala5Thr) single nucleotide variant Familial melanoma [RCV000685763]|Hereditary cancer-predisposing syndrome [RCV000213590]|not provided [RCV001566929] Chr9:21974815 [GRCh38]
Chr9:21974814 [GRCh37]
Chr9:9p21.3		 uncertain significance
NM_000077.5(CDKN2A):c.-21C>T single nucleotide variant Familial melanoma [RCV002573191]|Hereditary cancer-predisposing syndrome [RCV002424985]|not provided [RCV001565114] Chr9:21974848 [GRCh38]
Chr9:21974847 [GRCh37]
Chr9:9p21.3		 likely pathogenic|uncertain significance
NM_000077.5(CDKN2A):c.-25C>T single nucleotide variant Familial melanoma [RCV000204607]|Hereditary cancer-predisposing syndrome [RCV000115330]|Melanoma-pancreatic cancer syndrome [RCV000412304]|not provided [RCV001753492]|not specified [RCV000200981] Chr9:21974852 [GRCh38]
Chr9:21974851 [GRCh37]
Chr9:9p21.3		 benign|likely benign|conflicting interpretations of pathogenicity|uncertain significance|conflicting data from submitters
NM_058195.4(CDKN2A):c.194-3653G>A single nucleotide variant Familial melanoma [RCV001460875]|Hereditary cancer-predisposing syndrome [RCV003584595]|Melanoma-pancreatic cancer syndrome [RCV000988166]|not specified [RCV000439448] Chr9:21974861 [GRCh38]
Chr9:21974860 [GRCh37]
Chr9:9p21.3		 likely benign|uncertain significance
NM_000077.5(CDKN2A):c.6G>A (p.Glu2=) single nucleotide variant Familial melanoma [RCV001468804]|Hereditary cancer-predisposing syndrome [RCV000569694]|not provided [RCV001591336] Chr9:21974822 [GRCh38]
Chr9:21974821 [GRCh37]
Chr9:9p21.3		 likely benign
NM_000077.5(CDKN2A):c.11C>T (p.Ala4Val) single nucleotide variant Familial melanoma [RCV001367742]|Hereditary cancer-predisposing syndrome [RCV002350698] Chr9:21974817 [GRCh38]
Chr9:21974816 [GRCh37]
Chr9:9p21.3		 uncertain significance
NM_000077.5(CDKN2A):c.6G>C (p.Glu2Asp) single nucleotide variant Familial melanoma [RCV003746624]|Hereditary cancer-predisposing syndrome [RCV002364782] Chr9:21974822 [GRCh38]
Chr9:21974821 [GRCh37]
Chr9:9p21.3		 uncertain significance
NM_058195.4(CDKN2A):c.194-3653G>T single nucleotide variant CDKN2A-related disorder [RCV004754323]|Familial melanoma [RCV000168189]|Hereditary cancer-predisposing syndrome [RCV000493169]|Melanoma and neural system tumor syndrome [RCV003474830]|Melanoma, cutaneous malignant, susceptibility to, 2 [RCV001762350]|Melanoma-pancreatic cancer syndrome [RCV000576396]|Melanoma-pancreatic cancer syndrome [RCV000763194]|Ovarian neoplasm [RCV002243829]|not provided [RCV000160410] Chr9:21974861 [GRCh38]
Chr9:21974860 [GRCh37]
Chr9:9p21.3		 pathogenic|risk factor
NM_058195.4(CDKN2A):c.194-3651G>A single nucleotide variant not specified [RCV000478925] Chr9:21974859 [GRCh38]
Chr9:21974858 [GRCh37]
Chr9:9p21.3		 likely benign
GRCh38/hg38 9p24.3-21.1(chr9:220257-29424848)x3 copy number gain See cases [RCV000134037] Chr9:220257..29424848 [GRCh38]
Chr9:220257..29424846 [GRCh37]
Chr9:210257..29414846 [NCBI36]
Chr9:9p24.3-21.1		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138179445)x3 copy number gain See cases [RCV000050348] Chr9:193412..138179445 [GRCh38]
Chr9:204193..141073897 [GRCh37]
Chr9:194193..140193718 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9p24.3-13.1(chr9:204193-38815478)x3 copy number gain See cases [RCV000050357] Chr9:204193..38815478 [GRCh38]
Chr9:204193..38815475 [GRCh37]
Chr9:194193..38805475 [NCBI36]
Chr9:9p24.3-13.1		 pathogenic|conflicting interpretations of pathogenicity|conflicting data from submitters
NM_058195.4(CDKN2A):c.194-3646_194-3624del deletion Hereditary cancer-predisposing syndrome [RCV000776531]|Melanoma and neural system tumor syndrome [RCV003472302]|not provided [RCV004773135] Chr9:21974832..21974854 [GRCh38]
Chr9:21974831..21974853 [GRCh37]
Chr9:9p21.3		 uncertain significance
NM_000077.5(CDKN2A):c.1A>T (p.Met1Leu) single nucleotide variant Familial melanoma [RCV001976384] Chr9:21974827 [GRCh38]
Chr9:21974826 [GRCh37]
Chr9:9p21.3		 uncertain significance
NM_058195.4(CDKN2A):c.194-3650G>A single nucleotide variant Melanoma-pancreatic cancer syndrome [RCV003315960]|not provided [RCV000679205]|not specified [RCV003321523] Chr9:21974858 [GRCh38]
Chr9:21974857 [GRCh37]
Chr9:9p21.3		 likely benign|uncertain significance
NM_000077.5(CDKN2A):c.8C>T (p.Pro3Leu) single nucleotide variant Familial melanoma [RCV002002200]|Hereditary cancer-predisposing syndrome [RCV002256869] Chr9:21974820 [GRCh38]
Chr9:21974819 [GRCh37]
Chr9:9p21.3		 conflicting interpretations of pathogenicity|uncertain significance
NM_000077.5(CDKN2A):c.-20A>G single nucleotide variant Hereditary cancer-predisposing syndrome [RCV001190556] Chr9:21974847 [GRCh38]
Chr9:21974846 [GRCh37]
Chr9:9p21.3		 likely benign
NM_000077.5(CDKN2A):c.2T>G (p.Met1Arg) single nucleotide variant Familial melanoma [RCV000817301]|Hereditary cancer-predisposing syndrome [RCV001185169] Chr9:21974826 [GRCh38]
Chr9:21974825 [GRCh37]
Chr9:9p21.3		 likely benign|uncertain significance
GRCh38/hg38 9p24.3-q34.3(chr9:204193-138179445) copy number gain See cases [RCV000133791] Chr9:204193..138179445 [GRCh38]
Chr9:204193..141073897 [GRCh37]
Chr9:194193..140193718 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
NM_000077.5(CDKN2A):c.-11C>G single nucleotide variant Hereditary cancer-predisposing syndrome [RCV001176598] Chr9:21974838 [GRCh38]
Chr9:21974837 [GRCh37]
Chr9:9p21.3		 uncertain significance
NM_000077.5(CDKN2A):c.10G>A (p.Ala4Thr) single nucleotide variant Familial melanoma [RCV002015968] Chr9:21974818 [GRCh38]
Chr9:21974817 [GRCh37]
Chr9:9p21.3		 uncertain significance
GRCh38/hg38 9p24.3-q21.11(chr9:13997-68401065)x3 copy number gain See cases [RCV000135344] Chr9:13997..68401065 [GRCh38]
Chr9:13997..71015981 [GRCh37]
Chr9:3997..70205801 [NCBI36]
Chr9:9p24.3-q21.11		 pathogenic
GRCh38/hg38 9p24.3-13.1(chr9:204193-38741440)x3 copy number gain See cases [RCV000051106] Chr9:204193..38741440 [GRCh38]
Chr9:204193..38741437 [GRCh37]
Chr9:194193..38731437 [NCBI36]
Chr9:9p24.3-13.1		 pathogenic
NM_000077.5(CDKN2A):c.4G>C (p.Glu2Gln) single nucleotide variant Familial melanoma [RCV000470551]|Hereditary cancer-predisposing syndrome [RCV002339143] Chr9:21974824 [GRCh38]
Chr9:21974823 [GRCh37]
Chr9:9p21.3		 uncertain significance
NM_058195.4(CDKN2A):c.194-3652G>A single nucleotide variant Melanoma-pancreatic cancer syndrome [RCV003316971] Chr9:21974860 [GRCh38]
Chr9:21974859 [GRCh37]
Chr9:9p21.3		 uncertain significance
NM_000077.5(CDKN2A):c.-2G>A single nucleotide variant Familial melanoma [RCV001512796]|Hereditary cancer-predisposing syndrome [RCV000129674]|Melanoma-pancreatic cancer syndrome [RCV000410804]|Melanoma-pancreatic cancer syndrome [RCV002505105]|not provided [RCV000590031]|not specified [RCV000212397] Chr9:21974829 [GRCh38]
Chr9:21974828 [GRCh37]
Chr9:9p21.3		 benign|likely benign|conflicting interpretations of pathogenicity|uncertain significance|conflicting data from submitters
GRCh38/hg38 9p24.3-q21.13(chr9:193412-74615913)x3 copy number gain See cases [RCV000135954] Chr9:193412..74615913 [GRCh38]
Chr9:204193..77230829 [GRCh37]
Chr9:194193..76420649 [NCBI36]
Chr9:9p24.3-q21.13		 pathogenic
GRCh38/hg38 9p24.3-q21.12(chr9:193412-70630731)x3 copy number gain See cases [RCV000136152] Chr9:193412..70630731 [GRCh38]
Chr9:220253..73245647 [GRCh37]
Chr9:210253..72435467 [NCBI36]
Chr9:9p24.3-q21.12		 pathogenic
GRCh38/hg38 9p21.3(chr9:21708372-22537070)x3 copy number gain See cases [RCV000051050] Chr9:21708372..22537070 [GRCh38]
Chr9:21708371..22537069 [GRCh37]
Chr9:21698371..22527069 [NCBI36]
Chr9:9p21.3		 uncertain significance
GRCh38/hg38 9p24.3-13.3(chr9:204104-34151476)x3 copy number gain See cases [RCV000139015] Chr9:204104..34151476 [GRCh38]
Chr9:204104..34151474 [GRCh37]
Chr9:194104..34141474 [NCBI36]
Chr9:9p24.3-13.3		 pathogenic|likely benign
GRCh38/hg38 9p24.3-q21.31(chr9:193412-79877816)x3 copy number gain See cases [RCV000143012] Chr9:193412..79877816 [GRCh38]
Chr9:204104..82492731 [GRCh37]
Chr9:194104..81682551 [NCBI36]
Chr9:9p24.3-q21.31		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138179445)x3 copy number gain See cases [RCV000148113] Chr9:193412..138179445 [GRCh38]
Chr9:204193..141073897 [GRCh37]
Chr9:194193..140193718 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9p24.1-13.2(chr9:7162304-37038771)x3 copy number gain See cases [RCV000137741] Chr9:7162304..37038771 [GRCh38]
Chr9:7162304..37038768 [GRCh37]
Chr9:7152304..37028768 [NCBI36]
Chr9:9p24.1-13.2		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:203862-138125937)x3 copy number gain See cases [RCV000143476] Chr9:203862..138125937 [GRCh38]
Chr9:203862..141020389 [GRCh37]
Chr9:193862..140140210 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9p24.3-21.3(chr9:459131-24207894)x3 copy number gain See cases [RCV000138499] Chr9:459131..24207894 [GRCh38]
Chr9:459131..24207892 [GRCh37]
Chr9:449131..24197892 [NCBI36]
Chr9:9p24.3-21.3		 pathogenic
GRCh38/hg38 9p24.3-13.1(chr9:204193-38815478)x3 copy number gain See cases [RCV000148159] Chr9:204193..38815478 [GRCh38]
Chr9:204193..38815475 [GRCh37]
Chr9:194193..38805475 [NCBI36]
Chr9:9p24.3-13.1		 pathogenic
NM_000077.5(CDKN2A):c.8CGG[1] (p.Ala4_Ala5del) microsatellite Familial melanoma [RCV000638967]|not provided [RCV000486109] Chr9:21974812..21974817 [GRCh38]
Chr9:21974811..21974816 [GRCh37]
Chr9:9p21.3		 uncertain significance
NM_000077.5(CDKN2A):c.11C>G (p.Ala4Gly) single nucleotide variant Familial melanoma [RCV000804694]|Hereditary cancer-predisposing syndrome [RCV000772904] Chr9:21974817 [GRCh38]
Chr9:21974816 [GRCh37]
Chr9:9p21.3		 uncertain significance
NM_000077.5(CDKN2A):c.-10G>A single nucleotide variant Hereditary cancer-predisposing syndrome [RCV000771487] Chr9:21974837 [GRCh38]
Chr9:21974836 [GRCh37]
Chr9:9p21.3		 uncertain significance
NM_000077.5(CDKN2A):c.7C>T (p.Pro3Ser) single nucleotide variant Familial melanoma [RCV000638971]|Hereditary cancer-predisposing syndrome [RCV004609463] Chr9:21974821 [GRCh38]
Chr9:21974820 [GRCh37]
Chr9:9p21.3		 likely benign|uncertain significance
GRCh38/hg38 9p24.3-13.1(chr9:220253-38815419)x3 copy number gain See cases [RCV000053747] Chr9:220253..38815419 [GRCh38]
Chr9:220253..38815416 [GRCh37]
Chr9:210253..38805416 [NCBI36]
Chr9:9p24.3-13.1		 pathogenic
GRCh38/hg38 9p23-21.1(chr9:9543538-30266463)x3 copy number gain See cases [RCV000053749] Chr9:9543538..30266463 [GRCh38]
Chr9:9543538..30266461 [GRCh37]
Chr9:9533538..30256461 [NCBI36]
Chr9:9p23-21.1		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138114463)x3 copy number gain See cases [RCV000053746] Chr9:193412..138114463 [GRCh38]
Chr9:214367..141008915 [GRCh37]
Chr9:204367..140128736 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9p24.3-21.3(chr9:204193-22086858)x3 copy number gain See cases [RCV000053704] Chr9:204193..22086858 [GRCh38]
Chr9:204193..22086857 [GRCh37]
Chr9:194193..22076857 [NCBI36]
Chr9:9p24.3-21.3		 pathogenic
NM_000077.5(CDKN2A):c.1A>G (p.Met1Val) single nucleotide variant Familial melanoma [RCV001229625]|Hereditary cancer-predisposing syndrome [RCV001013980]|not provided [RCV003442143] Chr9:21974827 [GRCh38]
Chr9:21974826 [GRCh37]
Chr9:9p21.3		 uncertain significance
NM_000077.5(CDKN2A):c.-10G>T single nucleotide variant Hereditary cancer-predisposing syndrome [RCV000772306] Chr9:21974837 [GRCh38]
Chr9:21974836 [GRCh37]
Chr9:9p21.3		 likely benign|uncertain significance
NM_000077.5(CDKN2A):c.9G>A (p.Pro3=) single nucleotide variant Familial melanoma [RCV000461178]|Hereditary cancer-predisposing syndrome [RCV000566902]|not provided [RCV000418358] Chr9:21974819 [GRCh38]
Chr9:21974818 [GRCh37]
Chr9:9p21.3		 likely benign
NM_000077.5(CDKN2A):c.-14C>A single nucleotide variant Hereditary cancer-predisposing syndrome [RCV003585107] Chr9:21974841 [GRCh38]
Chr9:21974840 [GRCh37]
Chr9:9p21.3		 uncertain significance
NM_000077.5(CDKN2A):c.-12G>A single nucleotide variant Hereditary cancer-predisposing syndrome [RCV003585106] Chr9:21974839 [GRCh38]
Chr9:21974838 [GRCh37]
Chr9:9p21.3		 uncertain significance
NM_000077.5(CDKN2A):c.-5G>A single nucleotide variant Hereditary cancer-predisposing syndrome [RCV004520413] Chr9:21974832 [GRCh38]
Chr9:21974831 [GRCh37]
Chr9:9p21.3		 uncertain significance
NM_000077.5(CDKN2A):c.-4C>A single nucleotide variant Hereditary cancer-predisposing syndrome [RCV004520412] Chr9:21974831 [GRCh38]
Chr9:21974830 [GRCh37]
Chr9:9p21.3		 uncertain significance
NM_000077.5(CDKN2A):c.-1C>T single nucleotide variant Hereditary cancer-predisposing syndrome [RCV003387339] Chr9:21974828 [GRCh38]
Chr9:21974827 [GRCh37]
Chr9:9p21.3		 uncertain significance
NM_000077.5(CDKN2A):c.2T>C (p.Met1Thr) single nucleotide variant Familial melanoma [RCV001858285]|Hereditary cancer-predisposing syndrome [RCV000563258] Chr9:21974826 [GRCh38]
Chr9:21974825 [GRCh37]
Chr9:9p21.3		 uncertain significance
GRCh38/hg38 9p24.3-q21.11(chr9:204104-67549861)x3 copy number gain See cases [RCV000139208] Chr9:204104..67549861 [GRCh38]
Chr9:204104..66516698 [GRCh37]
Chr9:194104..66256518 [NCBI36]
Chr9:9p24.3-q21.11		 pathogenic
GRCh38/hg38 9p11.2-q34.3(chr9:193412-138159073)x3 copy number gain See cases [RCV000139207] Chr9:193412..138159073 [GRCh38]
Chr9:68420641..141053525 [GRCh37]
Chr9:67910461..140173346 [NCBI36]
Chr9:9p11.2-q34.3		 pathogenic
GRCh38/hg38 9p24.3-13.1(chr9:204104-38768294)x3 copy number gain See cases [RCV000139126] Chr9:204104..38768294 [GRCh38]
Chr9:204104..38768291 [GRCh37]
Chr9:194104..38758291 [NCBI36]
Chr9:9p24.3-13.1		 pathogenic
NM_000077.5(CDKN2A):c.2T>A (p.Met1Lys) single nucleotide variant Familial melanoma [RCV000638963]|Gastric cancer [RCV003159969]|Hereditary cancer-predisposing syndrome [RCV000567259]|not provided [RCV000586260]|not specified [RCV003321685] Chr9:21974826 [GRCh38]
Chr9:21974825 [GRCh37]
Chr9:9p21.3		 pathogenic|uncertain significance
NM_000077.5(CDKN2A):c.-4C>T single nucleotide variant Hereditary cancer-predisposing syndrome [RCV003306244] Chr9:21974831 [GRCh38]
Chr9:21974830 [GRCh37]
Chr9:9p21.3		 uncertain significance
NM_000077.5(CDKN2A):c.-3A>C single nucleotide variant not provided [RCV003321165] Chr9:21974830 [GRCh38]
Chr9:21974829 [GRCh37]
Chr9:9p21.3		 uncertain significance
NM_058195.4(CDKN2A):c.194-3653G>C single nucleotide variant CDKN2A-related disorder [RCV003897575]|Familial melanoma [RCV001454127]|Hereditary cancer-predisposing syndrome [RCV001020466]|Melanoma-pancreatic cancer syndrome [RCV000410324]|not provided [RCV001722275]|not specified [RCV000236694] Chr9:21974861 [GRCh38]
Chr9:21974860 [GRCh37]
Chr9:9p21.3		 likely benign|conflicting interpretations of pathogenicity|uncertain significance
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138159073)x3 copy number gain See cases [RCV000138962] Chr9:193412..138159073 [GRCh38]
Chr9:204104..141053525 [GRCh37]
Chr9:194104..140173346 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic|conflicting data from submitters
GRCh38/hg38 9p24.1-21.2(chr9:4661872-27661572)x3 copy number gain See cases [RCV000136680] Chr9:4661872..27661572 [GRCh38]
Chr9:4661872..27661570 [GRCh37]
Chr9:4651872..27651570 [NCBI36]
Chr9:9p24.1-21.2		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138124524)x3 copy number gain See cases [RCV000138783] Chr9:193412..138124524 [GRCh38]
Chr9:204090..141018976 [GRCh37]
Chr9:194090..140138797 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
NM_058195.4(CDKN2A):c.194-3652G>T single nucleotide variant Hereditary cancer-predisposing syndrome [RCV002257067] Chr9:21974860 [GRCh38]
Chr9:21974859 [GRCh37]
Chr9:9p21.3		 uncertain significance
GRCh38/hg38 9p22.2-q21.11(chr9:18344605-68257015) copy number gain See cases [RCV000140448] Chr9:18344605..68257015 [GRCh38]
Chr9:18344603..68995221 [GRCh37]
Chr9:18334603..68285041 [NCBI36]
Chr9:9p22.2-q21.11		 pathogenic
NC_000009.12:g.(?_21967752)_(21975133_?)del deletion Familial melanoma [RCV000199878] Chr9:21967752..21975133 [GRCh38]
Chr9:9p21.3		 pathogenic
GRCh38/hg38 9p24.3-21.2(chr9:204104-27963369)x3 copy number gain See cases [RCV000139621] Chr9:204104..27963369 [GRCh38]
Chr9:204104..27963367 [GRCh37]
Chr9:194104..27953367 [NCBI36]
Chr9:9p24.3-21.2		 pathogenic
GRCh38/hg38 9p22.1-21.1(chr9:19564275-28106622)x1 copy number loss See cases [RCV000139905] Chr9:19564275..28106622 [GRCh38]
Chr9:19564273..28106620 [GRCh37]
Chr9:19554273..28096620 [NCBI36]
Chr9:9p22.1-21.1		 pathogenic
GRCh38/hg38 9p24.3-13.1(chr9:203861-38381642) copy number gain See cases [RCV000143411] Chr9:203861..38381642 [GRCh38]
Chr9:203861..38381639 [GRCh37]
Chr9:193861..38371639 [NCBI36]
Chr9:9p24.3-13.1		 pathogenic
GRCh38/hg38 9p24.3-q21.11(chr9:204104-66233120)x4 copy number gain See cases [RCV000137888] Chr9:204104..66233120 [GRCh38]
Chr9:204104..47212321 [GRCh37]
Chr9:194104..47002141 [NCBI36]
Chr9:9p24.3-q21.11		 pathogenic|conflicting data from submitters
NM_000077.5(CDKN2A):c.-16GGCGGCGGGGAGCAGCATGGAGCC[1] (p.Ala4_Pro11del) microsatellite Familial melanoma [RCV000197052]|Hereditary cancer-predisposing syndrome [RCV000566263]|Melanoma and neural system tumor syndrome [RCV003474958]|Melanoma-pancreatic cancer syndrome [RCV000409781]|not provided [RCV000587112]|not specified [RCV001255216] Chr9:21974796..21974819 [GRCh38]
Chr9:21974795..21974818 [GRCh37]
Chr9:9p21.3		 likely benign|conflicting interpretations of pathogenicity|uncertain significance
NM_000077.5(CDKN2A):c.-14C>T single nucleotide variant CDKN2A-related disorder [RCV003947681]|Familial melanoma [RCV000205775]|Hereditary cancer-predisposing syndrome [RCV000579472]|Melanoma-pancreatic cancer syndrome [RCV000411551]|not specified [RCV000428256] Chr9:21974841 [GRCh38]
Chr9:21974840 [GRCh37]
Chr9:9p21.3		 benign|likely benign|conflicting interpretations of pathogenicity|uncertain significance
NM_000077.5(CDKN2A):c.1_14del (p.Met1fs) deletion Familial melanoma [RCV000813492] Chr9:21974814..21974827 [GRCh38]
Chr9:21974813..21974826 [GRCh37]
Chr9:9p21.3		 uncertain significance
NC_000009.12:g.(?_21968219)_(21994341_?)del deletion Familial melanoma [RCV000707967] Chr9:21968219..21994341 [GRCh38]
Chr9:21968218..21994340 [GRCh37]
Chr9:9p21.3		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:203861-138125937)x3 copy number gain See cases [RCV000141876] Chr9:203861..138125937 [GRCh38]
Chr9:203861..141020389 [GRCh37]
Chr9:193861..140140210 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
NC_000009.11:g.(?_21968218)_(21994340_?)dup duplication Familial melanoma [RCV000708308] Chr9:21968219..21994341 [GRCh38]
Chr9:21968218..21994340 [GRCh37]
Chr9:9p21.3		 uncertain significance
GRCh38/hg38 9p24.3-21.1(chr9:203861-31423873)x4 copy number gain See cases [RCV000141662] Chr9:203861..31423873 [GRCh38]
Chr9:203861..31423871 [GRCh37]
Chr9:193861..31413871 [NCBI36]
Chr9:9p24.3-21.1		 pathogenic
NC_000009.12:g.(?_21970896)_(21974833_?)del deletion Familial melanoma [RCV000535268] Chr9:21970896..21974833 [GRCh38]
Chr9:21970895..21974832 [GRCh37]
Chr9:9p21.3		 pathogenic
GRCh38/hg38 9p24.3-q22.1(chr9:203861-88130444)x4 copy number gain See cases [RCV000141904] Chr9:203861..88130444 [GRCh38]
Chr9:203861..90745359 [GRCh37]
Chr9:193861..89935179 [NCBI36]
Chr9:9p24.3-q22.1		 pathogenic
NM_000077.5(CDKN2A):c.-30G>A single nucleotide variant not provided [RCV000481097] Chr9:21974857 [GRCh38]
Chr9:21974856 [GRCh37]
Chr9:9p21.3		 uncertain significance
NC_000009.11:g.(?_21968222)_(21994330_?)dup duplication Familial melanoma [RCV000639011] Chr9:21968223..21994331 [GRCh38]
Chr9:21968222..21994330 [GRCh37]
Chr9:9p21.3		 uncertain significance
NC_000009.11:g.(?_21970895)_(21994330_?)dup duplication Familial melanoma [RCV000639010] Chr9:21970896..21994331 [GRCh38]
Chr9:21970895..21994330 [GRCh37]
Chr9:9p21.3		 uncertain significance
GRCh38/hg38 9p21.3(chr9:21879075-22096084)x0 copy number loss Vascular endothelial growth factor (VEGF) inhibitor response [RCV000626437] Chr9:21879075..22096084 [GRCh38]
Chr9:21879074..22096083 [GRCh37]
Chr9:9p21.3		 drug response
GRCh38/hg38 9p21.3(chr9:21939409-22706614)x0 copy number loss Vascular endothelial growth factor (VEGF) inhibitor response [RCV000626440] Chr9:21939409..22706614 [GRCh38]
Chr9:21939408..22706613 [GRCh37]
Chr9:9p21.3		 drug response
NM_058195.4(CDKN2A):c.194-3654_194-3641del deletion Hereditary cancer-predisposing syndrome [RCV001805551] Chr9:21974849..21974862 [GRCh38]
Chr9:21974848..21974861 [GRCh37]
Chr9:9p21.3		 uncertain significance
GRCh38/hg38 9p24.3-13.3(chr9:204193-33284638)x3 copy number gain See cases [RCV000053707] Chr9:204193..33284638 [GRCh38]
Chr9:204193..33284636 [GRCh37]
Chr9:194193..33274636 [NCBI36]
Chr9:9p24.3-13.3		 pathogenic
NM_000077.5(CDKN2A):c.-17G>T single nucleotide variant Hereditary cancer-predisposing syndrome [RCV000772425]|not provided [RCV004768636] Chr9:21974844 [GRCh38]
Chr9:21974843 [GRCh37]
Chr9:9p21.3		 uncertain significance
NM_000077.5(CDKN2A):c.-8G>A single nucleotide variant Hereditary cancer-predisposing syndrome [RCV000773002]|not specified [RCV004596339] Chr9:21974835 [GRCh38]
Chr9:21974834 [GRCh37]
Chr9:9p21.3		 likely benign|uncertain significance
NM_000077.5(CDKN2A):c.12G>A (p.Ala4=) single nucleotide variant Familial melanoma [RCV001425071] Chr9:21974816 [GRCh38]
Chr9:21974815 [GRCh37]
Chr9:9p21.3		 likely benign
NM_000077.5(CDKN2A):c.-17_7dup (p.Glu2_Pro3insArgAlaAlaGlySerSerMetGlu) duplication Hereditary cancer-predisposing syndrome [RCV003171760] Chr9:21974820..21974821 [GRCh38]
Chr9:21974819..21974820 [GRCh37]
Chr9:9p21.3		 uncertain significance
NM_000077.5(CDKN2A):c.-10G>C single nucleotide variant Hereditary cancer-predisposing syndrome [RCV000582004] Chr9:21974837 [GRCh38]
Chr9:21974836 [GRCh37]
Chr9:9p21.3		 likely benign
Single allele duplication Schizophrenia [RCV000754362] Chr9:20655425..24580688 [GRCh38]
Chr9:9p21.3		 likely pathogenic

QTLs in Region (GRCh38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1643245BW137_HBody weight QTL 137 (human)2.28Body weight9528914931289149Human
2302773MAMTS18_HMammary tumor susceptibility QTL 18 (human)0.039Mammary tumor susceptibility9528914931289149Human
1357299AASTH47_HAllergic/atopic asthma related QTL 47 (human)0.00028Reversible airflow obstruction9528914931289149Human
2315898GLUCO191_HGlucose level QTL 191 (human)1.83Glucose level9528914931289149Human
2293400PRSTS224_HProstate tumor susceptibility QTL 224 (human)1.62Prostate tumor susceptibility9528914931289149Human
2293433PRSTS223_HProstate tumor susceptibility QTL 223 (human)1.6Prostate tumor susceptibility9528914931289149Human


Expression

RNA-SEQ Expression


Sequence



Additional Information

Database Acc Id Source(s)
COSMIC LOC130001603 COSMIC
GTEx LOC130001603 GTEx
Human Proteome Map LOC130001603 Human Proteome Map
NCBI Gene LOC130001603 ENTREZGENE