Hs06150780_cn

• Gene Symbol: LSM2
• Assay Reference Genome Location: Chr.6:31803089 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: Within Intron 2

Gene Symbol	Transcript Accession	Exon Location	Assay Transcript Location	Protein ID
LSM2	NM_021177.4			NP_067000.1
	AF136977.1			AAG49438.1
	AF182288.1			AAD56226.1
	AF196468.1			AAG33023.1
	AJ245416.1			CAB52190.1
	BC009192.2			AAH09192.1
	BP203102.1
	BU189898.1
	CR542146.1			CAG46943.1
	CR542157.1			CAG46954.1

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

More Information

Additional Information:

For this assay, SNP(s) [rs114832009] 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, Intronic, 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