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See other C4A CNV Assays ›
Gene Symbol
C4A
Assay Reference Genome
Location

Chr.6:31952462 on build GRCh38
Cytoband
6p21.33
Assay ID Hs07226351_cn
Size
Availability Made To Order
Catalog # 4400291
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Assay Details

Target Gene Details

Entrez Gene ID:

 720

Gene Name:

 complement component 4A (Rodgers blood group)

Gene Aliases:

 C4, C4A2, C4A3, C4A4, C4A6, C4AD, C4S, CO4, CPAMD2, RG

Location:

 Chr.6:31982057-32002680 on Build GRCh38

Assay Gene Location:

 Overlaps Intron 9 - Intron 11
Gene Symbol Transcript Accession Exon Location Assay Transcript Location Protein ID
C4A NM_001252204.1 NP_001239133.1
NM_007293.2 NP_009224.2
AB209989.1
AK293191.1
BC063289.1 AAH63289.1
BC144546.1
BC146673.1
BC146849.1
BC151204.1
BC171786.1
BX452374.2
K02403.1 AAB59537.1

Target Gene Details

Entrez Gene ID:

 100302242

Gene Name:

 microRNA 1236

Gene Aliases:

 MIRN1236, hsa-mir-1236

Location:

 Chr.6:31956839-31956940 on Build GRCh38

Assay Gene Location:
Gene Symbol Transcript Accession Exon Location Assay Transcript Location Protein ID
MIR1236 NR_031601.1

Target Gene Details

Entrez Gene ID:

 7936

Gene Name:

 negative elongation factor complex member E

Gene Aliases:

 D6S45, NELF-E, RD, RDBP, RDP

Location:

 Chr.6:31952087-31959087 on Build GRCh38

Assay Gene Location:

 Overlaps Intron 1 - Intron 10
Gene Symbol Transcript Accession Exon Location Assay Transcript Location Protein ID
NELFE NM_002904.5 NP_002895.3
XM_006715205.3 XP_006715268.1
XM_011514913.2 XP_011513215.1
XM_017011299.1 XP_016866788.1
AK300717.1
AK300898.1
AK302652.1
AK303152.1
BC025235.1 AAH25235.1
BC050617.2 AAH50617.1
CD579634.2
JQ313904.1
L03411.1 AAC37523.1
X16105.1 CAA34231.1

Target Gene Details

Entrez Gene ID:

 6499

Gene Name:

 Ski2 like RNA helicase

Gene Aliases:

 170A, DDX13, HLP, SKI2, SKI2W, SKIV2, SKIV2L1, THES2

Location:

 Chr.6:31958804-31969852 on Build GRCh38

Assay Gene Location:

 Overlaps - Exon 1
Gene Symbol Transcript Accession Exon Location Assay Transcript Location Protein ID
SKIV2L NM_006929.4 NP_008860.4

Target Copy Number Variation Details

DGV Version:

 Release date: 2016-05-15, GRCh GRCh38
Target
Variation		 Location CNV
Subtype		 Genes
dgv10473n54 Chr.6:31985858 - 31990466 on Build GRCh38 Loss C4A
nsv1112900 Chr.6:31455323 - 33480423 on Build GRCh38 Deletion EGFL8 GPSM3 CSNK2B HSPA1L RNF5 LY6G5C PSMB8-AS1 FKBPL HLA-DMA AGPAT1 LY6G6D LOC100287329 TNXB SLC39A7 HLA-DPA1 HLA-DPB1 MIR3135B MIR6721 RGL2 PHF1 VPS52 ATF6B LST1 SYNGAP1 SNORD52 HCP5 NCR3 MSH5-SAPCD1 NELFE LY6G5B MIR219A1 ZBTB22 RING1 B3GALT4 HCG25 HLA-DRB5 HLA-DRB6 VARS LY6G6E DDX39B SNORA38 C6orf48 ATP6V1G2 C4B HLA-DQA1 MIR6832 LSM2 C4A HSPA1A PBX2 HLA-DQB2 TAP1 CUTA BRD2 TNXA WDR46 APOM COL11A2 LTB NEU1 PRRC2A TNF C6orf25 HLA-DQA2 AIF1 HSPA1B PSMB8 MIR5004 HSD17B8 DXO MCCD1 EHMT2 TAPBP SNORD84 CFB HCG24 MIR1236 HLA-DOB C6orf10 CLIC1 SNORD48 HLA-DRA LY6G6F BAG6 ZBTB9 C2 KIFC1 LY6G6C LOC100507547 PPT2-EGFL8 PPT2 LOC100294145 PSMB9 STK19 LTA CYP21A1P SKIV2L DDX39B-AS1 RXRB VWA7 MIR6833 HLA-DQB1-AS1 HLA-DPB2 SAPCD1-AS1 ABHD16A PRRT1 HLA-DQB1 TAP2 NFKBIL1 SLC44A4 SAPCD1 HCG23 PPP1R2P1 MIR6873 DAXX RPS18 C2-AS1 BTNL2 CYP21A2 HCG26 DDAH2 C6orf47 MIR6834 HLA-DRB1 GPANK1 HLA-DOA MSH5 HLA-DMB LOC101929163 PFDN6 ZBTB12 SNORD117 NOTCH4 AGER MICB ATP6V1G2-DDX39B LOC102725068 MIR4646
dgv10404n54 Chr.6:31312550 - 32516591 on Build GRCh38 Loss EGFL8 GPSM3 CSNK2B HSPA1L HLA-B DXO RNF5 LY6G5C MCCD1 EHMT2 FKBPL AGPAT1 SNORD84 CFB LY6G6D LOC100287329 TNXB MIR1236 C6orf10 CLIC1 SNORD48 HLA-DRA LY6G6F BAG6 C2 LY6G6C LOC100507547 PPT2-EGFL8 MIR6721 PPT2 ATF6B LST1 STK19 SNORD52 HCP5 LTA NCR3 CYP21A1P MSH5-SAPCD1 SKIV2L NELFE LY6G5B DDX39B-AS1 VWA7 MIR6833 SAPCD1-AS1 ABHD16A PRRT1 VARS LY6G6E NFKBIL1 SLC44A4 DDX39B SAPCD1 SNORA38 HCG23 C6orf48 ATP6V1G2 C2-AS1 C4B BTNL2 CYP21A2 MIR6832 HCG26 LSM2 DDAH2 C4A HSPA1A C6orf47 GPANK1 PBX2 MSH5 LOC101929163 MICA MIR6891 TNXA ZBTB12 APOM SNORD117 NOTCH4 AGER LTB MICB NEU1 PRRC2A TNF C6orf25 ATP6V1G2-DDX39B LOC102725068 MIR4646 AIF1 HSPA1B
esv3890827 Chr.6:31981575 - 32043703 on Build GRCh38 Gain+Loss C4B CYP21A2 TNXB CYP21A1P C4A TNXA
nsv515035 Chr.6:31985264 - 31990776 on Build GRCh38 Gain+Loss C4A
nsv284 Chr.6:31957962 - 32028944 on Build GRCh38 Deletion STK19 C4B DXO CYP21A1P C4A SKIV2L NELFE TNXA
esv3333985 Chr.6:31990996 - 32007795 on Build GRCh38 Duplication CYP21A1P C4A
dgv10467n54 Chr.6:31982489 - 31991703 on Build GRCh38 Loss C4A
nsv601971 Chr.6:31971488 - 32046679 on Build GRCh38 Gain STK19 C4B CYP21A2 TNXB DXO CYP21A1P C4A TNXA
nsv428141 Chr.6:31903735 - 32125066 on Build GRCh38 Gain+Loss C2 DXO TNXA CFB ATF6B STK19 C2-AS1 C4B CYP21A2 TNXB CYP21A1P MIR1236 C4A SKIV2L NELFE
nsv602004 Chr.6:31984717 - 31990466 on Build GRCh38 Gain+Loss C4A
dgv10403n54 Chr.6:31312324 - 32049763 on Build GRCh38 Loss CSNK2B HSPA1L HLA-B DXO LY6G5C MCCD1 EHMT2 SNORD84 CFB LY6G6D LOC100287329 TNXB MIR1236 CLIC1 SNORD48 LY6G6F BAG6 C2 LY6G6C LST1 STK19 SNORD52 HCP5 LTA NCR3 CYP21A1P MSH5-SAPCD1 SKIV2L NELFE LY6G5B DDX39B-AS1 VWA7 SAPCD1-AS1 ABHD16A VARS LY6G6E NFKBIL1 SLC44A4 DDX39B SAPCD1 SNORA38 C6orf48 ATP6V1G2 C2-AS1 C4B CYP21A2 MIR6832 HCG26 LSM2 DDAH2 C4A HSPA1A C6orf47 GPANK1 MSH5 MICA MIR6891 TNXA ZBTB12 APOM SNORD117 LTB MICB NEU1 PRRC2A TNF C6orf25 ATP6V1G2-DDX39B LOC102725068 MIR4646 AIF1 HSPA1B
dgv10469n54 Chr.6:31984179 - 31988083 on Build GRCh38 Loss C4A
nsv602034 Chr.6:31991487 - 32002199 on Build GRCh38 Loss C4A
nsv821566 Chr.6:31984670 - 31991249 on Build GRCh38 Deletion C4A
nsv10824 Chr.6:31980357 - 32046247 on Build GRCh38 Gain+Loss STK19 C4B CYP21A2 TNXB CYP21A1P C4A TNXA
dgv20n31 Chr.6:31990245 - 32046126 on Build GRCh38 Gain C4B CYP21A2 TNXB CYP21A1P C4A TNXA
dgv10468n54 Chr.6:31983430 - 32045574 on Build GRCh38 Loss C4B CYP21A2 TNXB CYP21A1P C4A TNXA
esv28110 Chr.6:31980130 - 32048749 on Build GRCh38 Gain+Loss STK19 C4B CYP21A2 TNXB CYP21A1P C4A TNXA
dgv10466n54 Chr.6:31980320 - 32029165 on Build GRCh38 Loss STK19 C4B CYP21A1P C4A TNXA
dgv10463n54 Chr.6:31817661 - 32683279 on Build GRCh38 Loss EGFL8 GPSM3 DXO RNF5 EHMT2 FKBPL AGPAT1 CFB TNXB MIR1236 C6orf10 SNORD48 HLA-DRA C2 LOC100507547 PPT2-EGFL8 MIR6721 PPT2 ATF6B STK19 SNORD52 CYP21A1P SKIV2L NELFE MIR6833 HLA-DQB1-AS1 PRRT1 HLA-DRB5 HLA-DRB6 HLA-DQB1 SLC44A4 HCG23 C6orf48 C2-AS1 C4B BTNL2 CYP21A2 HLA-DQA1 C4A HSPA1A HLA-DRB1 PBX2 LOC101929163 TNXA ZBTB12 NOTCH4 AGER NEU1 HSPA1B
dgv10471n54 Chr.6:31985690 - 31993863 on Build GRCh38 Loss C4A
nsv1126749 Chr.6:31457323 - 32594423 on Build GRCh38 Deletion EGFL8 GPSM3 CSNK2B HSPA1L DXO RNF5 LY6G5C MCCD1 EHMT2 FKBPL AGPAT1 SNORD84 CFB LY6G6D LOC100287329 TNXB MIR1236 C6orf10 CLIC1 SNORD48 HLA-DRA LY6G6F BAG6 C2 LY6G6C LOC100507547 PPT2-EGFL8 MIR6721 PPT2 ATF6B LST1 STK19 SNORD52 HCP5 LTA NCR3 CYP21A1P MSH5-SAPCD1 SKIV2L NELFE LY6G5B DDX39B-AS1 VWA7 MIR6833 SAPCD1-AS1 ABHD16A PRRT1 HLA-DRB5 HLA-DRB6 VARS LY6G6E NFKBIL1 SLC44A4 DDX39B SAPCD1 SNORA38 HCG23 C6orf48 ATP6V1G2 C2-AS1 C4B BTNL2 CYP21A2 MIR6832 HCG26 LSM2 DDAH2 C4A HSPA1A C6orf47 HLA-DRB1 GPANK1 PBX2 MSH5 LOC101929163 TNXA ZBTB12 APOM SNORD117 NOTCH4 AGER LTB MICB NEU1 PRRC2A TNF C6orf25 ATP6V1G2-DDX39B LOC102725068 MIR4646 AIF1 HSPA1B
nsv1073969 Chr.6:31456422 - 33480523 on Build GRCh38 Deletion EGFL8 GPSM3 CSNK2B HSPA1L RNF5 LY6G5C PSMB8-AS1 FKBPL HLA-DMA AGPAT1 LY6G6D LOC100287329 TNXB SLC39A7 HLA-DPA1 HLA-DPB1 MIR3135B MIR6721 RGL2 PHF1 VPS52 ATF6B LST1 SYNGAP1 SNORD52 HCP5 NCR3 MSH5-SAPCD1 NELFE LY6G5B MIR219A1 ZBTB22 RING1 B3GALT4 HCG25 HLA-DRB5 HLA-DRB6 VARS LY6G6E DDX39B SNORA38 C6orf48 ATP6V1G2 C4B HLA-DQA1 MIR6832 LSM2 C4A HSPA1A PBX2 HLA-DQB2 TAP1 CUTA BRD2 TNXA WDR46 APOM COL11A2 LTB NEU1 PRRC2A TNF C6orf25 HLA-DQA2 AIF1 HSPA1B PSMB8 MIR5004 HSD17B8 DXO MCCD1 EHMT2 TAPBP SNORD84 CFB HCG24 MIR1236 HLA-DOB C6orf10 CLIC1 SNORD48 HLA-DRA LY6G6F BAG6 ZBTB9 C2 KIFC1 LY6G6C LOC100507547 PPT2-EGFL8 PPT2 LOC100294145 PSMB9 STK19 LTA CYP21A1P SKIV2L DDX39B-AS1 RXRB VWA7 MIR6833 HLA-DQB1-AS1 HLA-DPB2 SAPCD1-AS1 ABHD16A PRRT1 HLA-DQB1 TAP2 NFKBIL1 SLC44A4 SAPCD1 HCG23 PPP1R2P1 MIR6873 DAXX RPS18 C2-AS1 BTNL2 CYP21A2 HCG26 DDAH2 C6orf47 MIR6834 HLA-DRB1 GPANK1 HLA-DOA MSH5 HLA-DMB LOC101929163 PFDN6 ZBTB12 SNORD117 NOTCH4 AGER MICB ATP6V1G2-DDX39B LOC102725068 MIR4646
nsv602030 Chr.6:31988493 - 31990466 on Build GRCh38 Loss C4A
nsv819957 Chr.6:31988273 - 32033484 on Build GRCh38 Loss C4B CYP21A1P C4A TNXA
nsv981129 Chr.6:31980992 - 32057861 on Build GRCh38 Duplication STK19 C4B CYP21A2 TNXB CYP21A1P C4A TNXA

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More Information


Important Information

The Hs07226351_cn assay specifically detects the short form (aka C4S) of the C4 gene family members, C4A and C4B, which encode functionally distinct protein isoforms. Long and short forms of the C4 genes exist due to the presence or absence of a 6.4 kb endogenous HERV-K retrovirus inserted into intron 9. Assay Hs07226352_cn detects the long form (aka C4L) of the C4 genes. Assays are also available that specifically detect each C4 isoform: assay Hs07226349_cn detects the C4A gene and assay Hs07226350_cn detects the C4B gene. Individuals can have deletions or multiple copies of the C4 genes. The number of C4A and C4B genes equals the number of C4 long and C4 short gene forms in an individual.
Hs07226352_cn assay for C4 gene long form (C4L)

Additional Information:

This assay has 2 genomic targets in NCBI build GRCh38

Set Membership:

 Intragenic Intronic Non-exonic DGV Variation Validated

Panther Classification:

Gene Ontology Categories:

Function(s) Process(es)


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