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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 STK19 PBX2 LTA NOTCH4 C6orf25 HLA-DMB LY6G6D DDX39B MIR6721 MIR219A1 NELFE CFB LOC102725068 EGFL8 C2 CUTA C6orf48 HSPA1B PFDN6 C4B HLA-DQB1-AS1 HCP5 CYP21A1P MIR6873 PPT2 LOC100507547 ZBTB9 AGPAT1 PSMB8-AS1 PRRC2A KIFC1 LY6G6F SNORD117 APOM DAXX LY6G6C MIR6833 MSH5 TNF HLA-DQA2 HLA-DOA NCR3 PRRT1 CYP21A2 CLIC1 AGER B3GALT4 FKBPL ATP6V1G2-DDX39B PSMB8 MIR6832 HSPA1A PHF1 DXO LY6G6E GPSM3 SNORD48 LST1 MIR6834 PPP1R2P1 ABHD16A VWA7 RING1 CSNK2B MIR4646 HCG23 NFKBIL1 TNXA SLC44A4 GPANK1 SNORA38 RXRB MICB HLA-DQB1 COL11A2 VPS52 HCG24 EHMT2 SYNGAP1 TNXB HLA-DRA C4A DDX39B-AS1 WDR46 MIR1236 RGL2 SLC39A7 LSM2 BRD2 LOC100287329 TAP1 RNF5 HLA-DQB2 HLA-DQA1 HSPA1L LOC101929163 HLA-DRB6 RPS18 TAP2 SNORD52 SAPCD1-AS1 HLA-DRB5 HSD17B8 HCG26 LY6G5C TAPBP BAG6 HCG25 HLA-DMA SKIV2L SNORD84 HLA-DPA1 DDAH2 C6orf10 VARS SAPCD1 BTNL2 HLA-DPB2 LY6G5B AIF1 MIR5004 MSH5-SAPCD1 MIR3135B PSMB9 ATF6B MCCD1 C6orf47 C2-AS1 PPT2-EGFL8 ZBTB12 LTB HLA-DOB ZBTB22 ATP6V1G2 NEU1 HLA-DPB1 LOC100294145 HLA-DRB1
dgv10404n54 Chr.6:31312550 - 32516591 on Build GRCh38 Loss MICB STK19 PBX2 LTA NOTCH4 C6orf25 LY6G6D DDX39B MIR6721 NELFE CFB EHMT2 LOC102725068 EGFL8 C2 TNXB HLA-DRA C4A C6orf48 HSPA1B DDX39B-AS1 MIR1236 C4B HCP5 CYP21A1P PPT2 HLA-B LOC100507547 LSM2 AGPAT1 PRRC2A LOC100287329 LY6G6F RNF5 SNORD117 APOM HSPA1L LY6G6C MIR6833 MSH5 TNF LOC101929163 NCR3 PRRT1 CYP21A2 CLIC1 AGER SNORD52 MICA SAPCD1-AS1 FKBPL ATP6V1G2-DDX39B HCG26 MIR6832 LY6G5C BAG6 HSPA1A SKIV2L SNORD84 DXO DDAH2 C6orf10 VARS SAPCD1 LY6G6E BTNL2 LY6G5B GPSM3 AIF1 SNORD48 LST1 MIR6891 MSH5-SAPCD1 ABHD16A ATF6B VWA7 MCCD1 C6orf47 C2-AS1 PPT2-EGFL8 CSNK2B ZBTB12 MIR4646 HCG23 NFKBIL1 LTB ATP6V1G2 TNXA NEU1 SLC44A4 GPANK1 SNORA38
nsv515035 Chr.6:31985264 - 31990776 on Build GRCh38 Gain+Loss C4A
esv3890827 Chr.6:31981575 - 32043703 on Build GRCh38 Gain+Loss CYP21A1P CYP21A2 TNXA TNXB C4A C4B
nsv5247 Chr.6:31957962 - 32055439 on Build GRCh38 Deletion CYP21A1P NELFE CYP21A2 STK19 TNXA SKIV2L TNXB DXO C4A C4B
esv3340418 Chr.6:31990996 - 31993094 on Build GRCh38 Duplication C4A
dgv10467n54 Chr.6:31982489 - 31991703 on Build GRCh38 Loss C4A
nsv601971 Chr.6:31971488 - 32046679 on Build GRCh38 Gain CYP21A1P CYP21A2 STK19 TNXA TNXB DXO C4A C4B
nsv602004 Chr.6:31984717 - 31990466 on Build GRCh38 Gain+Loss C4A
esv2759415 Chr.6:31903735 - 32241336 on Build GRCh38 Gain+Loss PRRT1 CYP21A2 STK19 AGER PBX2 NOTCH4 FKBPL MIR6721 NELFE CFB EGFL8 SKIV2L C2 TNXB DXO C4A MIR1236 GPSM3 C4B CYP21A1P PPT2 LOC100507547 ATF6B AGPAT1 C2-AS1 PPT2-EGFL8 RNF5 TNXA MIR6833
nsv602034 Chr.6:31991487 - 32002199 on Build GRCh38 Loss C4A
nsv601990 Chr.6:31984179 - 31990466 on Build GRCh38 Loss C4A
dgv10403n54 Chr.6:31312324 - 32049763 on Build GRCh38 Loss MICB STK19 LTA C6orf25 LY6G6D DDX39B NELFE CFB EHMT2 LOC102725068 C2 TNXB C4A C6orf48 HSPA1B DDX39B-AS1 MIR1236 C4B HCP5 CYP21A1P HLA-B LSM2 PRRC2A LOC100287329 LY6G6F SNORD117 APOM HSPA1L LY6G6C MSH5 TNF NCR3 CYP21A2 CLIC1 SNORD52 MICA SAPCD1-AS1 ATP6V1G2-DDX39B HCG26 MIR6832 LY6G5C BAG6 HSPA1A SKIV2L SNORD84 DXO DDAH2 VARS SAPCD1 LY6G6E LY6G5B AIF1 SNORD48 LST1 MIR6891 MSH5-SAPCD1 ABHD16A VWA7 MCCD1 C6orf47 C2-AS1 CSNK2B ZBTB12 MIR4646 NFKBIL1 LTB ATP6V1G2 TNXA NEU1 SLC44A4 GPANK1 SNORA38
nsv821566 Chr.6:31984670 - 31991249 on Build GRCh38 Deletion C4A
nsv10824 Chr.6:31980357 - 32046247 on Build GRCh38 Gain+Loss CYP21A1P CYP21A2 STK19 TNXA TNXB C4A C4B
dgv20n31 Chr.6:31990245 - 32046126 on Build GRCh38 Gain CYP21A1P CYP21A2 TNXA TNXB C4A C4B
esv3890828 Chr.6:31983430 - 31988647 on Build GRCh38 Loss C4A
dgv10466n54 Chr.6:31980320 - 32029165 on Build GRCh38 Loss CYP21A1P STK19 TNXA C4A C4B
esv28110 Chr.6:31980130 - 32048749 on Build GRCh38 Gain+Loss CYP21A1P CYP21A2 STK19 TNXA TNXB C4A C4B
dgv10472n54 Chr.6:31985690 - 32812026 on Build GRCh38 Loss HLA-DQB1 PRRT1 CYP21A2 AGER PBX2 NOTCH4 FKBPL HLA-DRB5 MIR6721 EGFL8 TNXB HLA-DRA C4A C6orf10 BTNL2 GPSM3 C4B HLA-DQB1-AS1 CYP21A1P PPT2 MIR3135B LOC100507547 ATF6B AGPAT1 PPT2-EGFL8 HCG23 RNF5 HLA-DQB2 HLA-DQA1 TNXA MIR6833 HLA-DRB1 LOC101929163 HLA-DRB6 HLA-DQA2
dgv10463n54 Chr.6:31817661 - 32683279 on Build GRCh38 Loss HLA-DQB1 STK19 PBX2 NOTCH4 MIR6721 NELFE CFB EHMT2 EGFL8 C2 TNXB HLA-DRA C4A C6orf48 HSPA1B MIR1236 C4B HLA-DQB1-AS1 CYP21A1P PPT2 LOC100507547 AGPAT1 RNF5 HLA-DQA1 MIR6833 LOC101929163 HLA-DRB6 PRRT1 CYP21A2 AGER SNORD52 FKBPL HLA-DRB5 HSPA1A SKIV2L DXO C6orf10 BTNL2 GPSM3 SNORD48 ATF6B C2-AS1 PPT2-EGFL8 ZBTB12 HCG23 TNXA NEU1 SLC44A4 HLA-DRB1
nsv1126749 Chr.6:31457323 - 32594423 on Build GRCh38 Deletion MICB STK19 PBX2 LTA NOTCH4 C6orf25 LY6G6D DDX39B MIR6721 NELFE CFB EHMT2 LOC102725068 EGFL8 C2 TNXB HLA-DRA C4A C6orf48 HSPA1B DDX39B-AS1 MIR1236 C4B HCP5 CYP21A1P PPT2 LOC100507547 LSM2 AGPAT1 PRRC2A LOC100287329 LY6G6F RNF5 SNORD117 APOM HSPA1L LY6G6C MIR6833 MSH5 TNF LOC101929163 HLA-DRB6 NCR3 PRRT1 CYP21A2 CLIC1 AGER SNORD52 SAPCD1-AS1 FKBPL HLA-DRB5 ATP6V1G2-DDX39B HCG26 MIR6832 LY6G5C BAG6 HSPA1A SKIV2L SNORD84 DXO DDAH2 C6orf10 VARS SAPCD1 LY6G6E BTNL2 LY6G5B GPSM3 AIF1 SNORD48 LST1 MSH5-SAPCD1 ABHD16A ATF6B VWA7 MCCD1 C6orf47 C2-AS1 PPT2-EGFL8 CSNK2B ZBTB12 MIR4646 HCG23 NFKBIL1 LTB ATP6V1G2 TNXA NEU1 SLC44A4 HLA-DRB1 GPANK1 SNORA38
nsv602030 Chr.6:31988493 - 31990466 on Build GRCh38 Loss C4A
nsv1073969 Chr.6:31456422 - 33480523 on Build GRCh38 Deletion STK19 PBX2 LTA NOTCH4 C6orf25 HLA-DMB LY6G6D DDX39B MIR6721 MIR219A1 NELFE CFB LOC102725068 EGFL8 C2 CUTA C6orf48 HSPA1B PFDN6 C4B HLA-DQB1-AS1 HCP5 CYP21A1P MIR6873 PPT2 LOC100507547 ZBTB9 AGPAT1 PSMB8-AS1 PRRC2A KIFC1 LY6G6F SNORD117 APOM DAXX LY6G6C MIR6833 MSH5 TNF HLA-DQA2 HLA-DOA NCR3 PRRT1 CYP21A2 CLIC1 AGER B3GALT4 FKBPL ATP6V1G2-DDX39B PSMB8 MIR6832 HSPA1A PHF1 DXO LY6G6E GPSM3 SNORD48 LST1 MIR6834 PPP1R2P1 ABHD16A VWA7 RING1 CSNK2B MIR4646 HCG23 NFKBIL1 TNXA SLC44A4 GPANK1 SNORA38 RXRB MICB HLA-DQB1 COL11A2 VPS52 HCG24 EHMT2 SYNGAP1 TNXB HLA-DRA C4A DDX39B-AS1 WDR46 MIR1236 RGL2 SLC39A7 LSM2 BRD2 LOC100287329 TAP1 RNF5 HLA-DQB2 HLA-DQA1 HSPA1L LOC101929163 HLA-DRB6 RPS18 TAP2 SNORD52 SAPCD1-AS1 HLA-DRB5 HSD17B8 HCG26 LY6G5C TAPBP BAG6 HCG25 HLA-DMA SKIV2L SNORD84 HLA-DPA1 DDAH2 C6orf10 VARS SAPCD1 BTNL2 HLA-DPB2 LY6G5B AIF1 MIR5004 MSH5-SAPCD1 MIR3135B PSMB9 ATF6B MCCD1 C6orf47 C2-AS1 PPT2-EGFL8 ZBTB12 LTB HLA-DOB ZBTB22 ATP6V1G2 NEU1 HLA-DPB1 LOC100294145 HLA-DRB1
nsv819957 Chr.6:31988273 - 32033484 on Build GRCh38 Loss CYP21A1P TNXA C4A C4B
nsv981129 Chr.6:31980992 - 32057861 on Build GRCh38 Duplication CYP21A1P CYP21A2 STK19 TNXA TNXB C4A C4B

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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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