Hs03001962_cn

• Gene Symbol: LSM2
• Assay Reference Genome Location: Chr.6:31806977 on build GRCh38
• Cytoband: 6p21.33

Target Gene Details

• Entrez Gene ID: 57819
• Gene Name: LSM2 homolog, U6 small nuclear RNA and mRNA degradation associated
• Gene Aliases: C6orf28, G7B, YBL026W, snRNP
• Location: Chr.6:31797392-31806984 on Build GRCh38
• Assay Gene Location: Overlaps - Exon 1

Gene Symbol	Transcript Accession	Exon Location	Assay Transcript Location	Protein ID
LSM2	NM_021177.4			NP_067000.1
	AF136977.1			AAG49438.1
	AF196468.1			AAG33023.1
	AJ245416.1			CAB52190.1
	BC009192.2			AAH09192.1
	BP203102.1
	BU189898.1

Target Copy Number Variation Details

• DGV Version: Release date: 2016-05-15, GRCh GRCh38

Target Variation	Location	CNV Subtype	Genes
nsv1126749	Chr.6:31457323 - 32594423 on Build GRCh38	Deletion	SAPCD1-AS1 HLA-DRA LOC100507547 SNORD48 TNXA HSPA1A BAG6 HCG26 LY6G5C NCR3 TNXB LOC100287329 SNORD117 GPSM3 AIF1 LY6G6C LY6G5B NELFE C6orf25 CFB PRRC2A EHMT2 LOC102725068 HCG23 HSPA1L HSPA1B DDX39B-AS1 ABHD16A MICB HLA-DRB6 HCP5 CSNK2B MIR6721 LSM2 ATF6B ATP6V1G2-DDX39B EGFL8 C6orf47 LTB C2-AS1 VWA7 STK19 VARS SNORA38 LY6G6E ATP6V1G2 MIR6833 SNORD52 C4B PRRT1 C4A ZBTB12 CYP21A1P MSH5-SAPCD1 SNORD84 PBX2 PPT2 NEU1 C2 C6orf48 C6orf10 FKBPL GPANK1 HLA-DRB5 DDX39B CYP21A2 HLA-DRB1 DDAH2 APOM AGER DXO LOC101929163 MIR4646 PPT2-EGFL8 LTA AGPAT1 RNF5 MIR1236 SKIV2L MIR6832 CLIC1 SLC44A4 MSH5 LY6G6F NOTCH4 NFKBIL1 LST1 MCCD1 TNF SAPCD1 LY6G6D BTNL2
nsv1073969	Chr.6:31456422 - 33480523 on Build GRCh38	Deletion	HLA-DRA SNORD48 WDR46 BAG6 TNXB HLA-DQB1 HLA-DPA1 LY6G6C HLA-DQB2 TAP1 PRRC2A EHMT2 LOC102725068 MIR3135B DDX39B-AS1 HLA-DRB6 VPS52 PPP1R2P1 RGL2 LSM2 MIR5004 KIFC1 ATF6B B3GALT4 VWA7 VARS HLA-DOA SNORA38 ATP6V1G2 MIR6833 SNORD52 PHF1 C4B HCG24 PPT2 NEU1 HLA-DQB1-AS1 C2 C6orf10 FKBPL GPANK1 HLA-DRB5 DDX39B PSMB8 ZBTB9 HLA-DRB1 AGER DXO PPT2-EGFL8 PSMB9 LTA HLA-DMA TAPBP DAXX CLIC1 SLC44A4 SLC39A7 MSH5 LY6G6F RPS18 NFKBIL1 LST1 MIR6834 SAPCD1 LY6G6D BTNL2 SAPCD1-AS1 HLA-DMB LOC100507547 TNXA HSPA1A HLA-DPB1 HCG26 LY6G5C NCR3 LOC100287329 PSMB8-AS1 SNORD117 GPSM3 AIF1 SYNGAP1 LY6G5B NELFE C6orf25 LOC100294145 CFB MIR6873 HCG23 HSPA1L HSPA1B ABHD16A MICB CUTA HCP5 MIR219A1 CSNK2B MIR6721 ATP6V1G2-DDX39B EGFL8 C6orf47 LTB C2-AS1 HSD17B8 STK19 LY6G6E RXRB PRRT1 C4A ZBTB12 CYP21A1P MSH5-SAPCD1 SNORD84 PBX2 C6orf48 CYP21A2 HLA-DQA2 DDAH2 APOM BRD2 HLA-DPB2 LOC101929163 MIR4646 AGPAT1 RNF5 RING1 PFDN6 MIR1236 HCG25 TAP2 SKIV2L MIR6832 HLA-DQA1 NOTCH4 ZBTB22 HLA-DOB MCCD1 TNF COL11A2
dgv10403n54	Chr.6:31312324 - 32049763 on Build GRCh38	Loss	SAPCD1-AS1 SNORD48 TNXA HSPA1A BAG6 HCG26 LY6G5C NCR3 TNXB LOC100287329 SNORD117 AIF1 LY6G6C LY6G5B NELFE C6orf25 CFB PRRC2A EHMT2 LOC102725068 HSPA1L HSPA1B DDX39B-AS1 ABHD16A HLA-B MICB HCP5 CSNK2B LSM2 ATP6V1G2-DDX39B C6orf47 LTB C2-AS1 VWA7 STK19 VARS SNORA38 LY6G6E ATP6V1G2 SNORD52 C4B C4A ZBTB12 CYP21A1P MSH5-SAPCD1 SNORD84 MICA NEU1 C2 C6orf48 GPANK1 DDX39B CYP21A2 DDAH2 MIR6891 APOM DXO MIR4646 LTA MIR1236 SKIV2L MIR6832 CLIC1 SLC44A4 MSH5 LY6G6F NFKBIL1 LST1 MCCD1 TNF SAPCD1 LY6G6D
nsv1112900	Chr.6:31455323 - 33480423 on Build GRCh38	Deletion	HLA-DRA SNORD48 WDR46 BAG6 TNXB HLA-DQB1 HLA-DPA1 LY6G6C HLA-DQB2 TAP1 PRRC2A EHMT2 LOC102725068 MIR3135B DDX39B-AS1 HLA-DRB6 VPS52 PPP1R2P1 RGL2 LSM2 MIR5004 KIFC1 ATF6B B3GALT4 VWA7 VARS HLA-DOA SNORA38 ATP6V1G2 MIR6833 SNORD52 PHF1 C4B HCG24 PPT2 NEU1 HLA-DQB1-AS1 C2 C6orf10 FKBPL GPANK1 HLA-DRB5 DDX39B PSMB8 ZBTB9 HLA-DRB1 AGER DXO PPT2-EGFL8 PSMB9 LTA HLA-DMA TAPBP DAXX CLIC1 SLC44A4 SLC39A7 MSH5 LY6G6F RPS18 NFKBIL1 LST1 MIR6834 SAPCD1 LY6G6D BTNL2 SAPCD1-AS1 HLA-DMB LOC100507547 TNXA HSPA1A HLA-DPB1 HCG26 LY6G5C NCR3 LOC100287329 PSMB8-AS1 SNORD117 GPSM3 AIF1 SYNGAP1 LY6G5B NELFE C6orf25 LOC100294145 CFB MIR6873 HCG23 HSPA1L HSPA1B ABHD16A MICB CUTA HCP5 MIR219A1 CSNK2B MIR6721 ATP6V1G2-DDX39B EGFL8 C6orf47 LTB C2-AS1 HSD17B8 STK19 LY6G6E RXRB PRRT1 C4A ZBTB12 CYP21A1P MSH5-SAPCD1 SNORD84 PBX2 C6orf48 CYP21A2 HLA-DQA2 DDAH2 APOM BRD2 HLA-DPB2 LOC101929163 MIR4646 AGPAT1 RNF5 RING1 PFDN6 MIR1236 HCG25 TAP2 SKIV2L MIR6832 HLA-DQA1 NOTCH4 ZBTB22 HLA-DOB MCCD1 TNF COL11A2
dgv10404n54	Chr.6:31312550 - 32516591 on Build GRCh38	Loss	SAPCD1-AS1 HLA-DRA LOC100507547 SNORD48 TNXA HSPA1A BAG6 HCG26 LY6G5C NCR3 TNXB LOC100287329 SNORD117 GPSM3 AIF1 LY6G6C LY6G5B NELFE C6orf25 CFB PRRC2A EHMT2 LOC102725068 HCG23 HSPA1L HSPA1B DDX39B-AS1 ABHD16A HLA-B MICB HCP5 CSNK2B MIR6721 LSM2 ATF6B ATP6V1G2-DDX39B EGFL8 C6orf47 LTB C2-AS1 VWA7 STK19 VARS SNORA38 LY6G6E ATP6V1G2 MIR6833 SNORD52 C4B PRRT1 C4A ZBTB12 CYP21A1P MSH5-SAPCD1 SNORD84 PBX2 MICA PPT2 NEU1 C2 C6orf48 C6orf10 FKBPL GPANK1 DDX39B CYP21A2 DDAH2 MIR6891 APOM AGER DXO LOC101929163 MIR4646 PPT2-EGFL8 LTA AGPAT1 RNF5 MIR1236 SKIV2L MIR6832 CLIC1 SLC44A4 MSH5 LY6G6F NOTCH4 NFKBIL1 LST1 MCCD1 TNF SAPCD1 LY6G6D BTNL2

More Information

Additional Information:

For this assay, SNP(s) [rs113065708] are located under a primer or probe sequence. To help evaluate the possible impact of a given SNP on your experiment, please refer to the 1000 Genomes and NCBI dbSNP databases. A higher minor allele frequency in your study population represents a higher risk to assay performance.

• Set Membership: Intragenic, Non-exonic, DGV Variation

Panther Classification:

Molecular Function -

RNA splicing factor

Gene Ontology Categories:

Process(es)

mRNA splicing, via spliceosome
exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay

Function(s)

RNA binding
protein binding
U6 snRNA binding
Ral GTPase binding
poly(A) RNA binding