Human Gene CLN6 (ENST00000249806.11_8) from GENCODE V47lift37
  Description: CLN6 transmembrane ER protein (from RefSeq NM_017882.3)
Gencode Transcript: ENST00000249806.11_8
Gencode Gene: ENSG00000128973.13_16
Transcript (Including UTRs)
   Position: hg19 chr15:68,499,330-68,522,066 Size: 22,737 Total Exon Count: 7 Strand: -
Coding Region
   Position: hg19 chr15:68,500,478-68,521,922 Size: 21,445 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesGeneReviewsModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr15:68,499,330-68,522,066)mRNA (may differ from genome)Protein (311 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CLN6_HUMAN
DESCRIPTION: RecName: Full=Ceroid-lipofuscinosis neuronal protein 6; Short=Protein CLN6;
SUBUNIT: Interacts with CRMP2.
SUBCELLULAR LOCATION: Endoplasmic reticulum membrane; Multi-pass membrane protein.
DISEASE: Defects in CLN6 are the cause of neuronal ceroid lipofuscinosis type 6 (CLN6) [MIM:601780]. A form of neuronal ceroid lipofuscinosis. Neuronal ceroid lipofuscinoses are progressive neurodegenerative, lysosomal storage diseases characterized by intracellular accumulation of autofluorescent liposomal material, and clinically by seizures, dementia, visual loss, and/or cerebral atrophy. The lipopigment patterns observed most often in neuronal ceroid lipofuscinosis type 6 comprise mixed combinations of granular, curvilinear, and fingerprint profiles.
DISEASE: Defects in CLN6 are the cause of neuronal ceroid lipofuscinosis type 4A (CLN4A) [MIM:204300]. An adult-onset neuronal ceroid lipofuscinosis. Neuronal ceroid lipofuscinoses are progressive neurodegenerative, lysosomal storage diseases characterized by intracellular accumulation of autofluorescent liposomal material, and clinically by seizures, dementia, visual loss, and/or cerebral atrophy. CLN4A has no visual involvement and is characterized by progressive myoclonic epilepsy.
WEB RESOURCE: Name=NCL CLN6; Note=Neural Ceroid Lipofuscinoses mutation db; URL="http://www.ucl.ac.uk/ncl/cln6.shtml";
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/CLN6";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: CLN6
Diseases sorted by gene-association score: ceroid lipofuscinosis, neuronal, 6* (1704), ceroid lipofuscinosis, neuronal, kufs type, adult onset* (1550), adult neuronal ceroid lipofuscinosis* (400), cln4 disease* (400), neuronal ceroid lipofuscinosis* (311), neuronal ceroid-lipofuscinoses* (88), ceroid lipofuscinosis, neuronal, 2 (24), cerebral atrophy (13), ceroid lipofuscinosis, neuronal, 9 (12), ceroid lipofuscinosis, neuronal, 7 (11), ceroid lipofuscinosis, neuronal, 10 (9), ceroid lipofuscinosis, neuronal, 1 (8), ceroid lipofuscinosis, neuronal, 8, northern epilepsy variant (8), ceroid lipofuscinosis, neuronal, 13, kufs type (7), ceroid lipofuscinosis, neuronal, 11 (7), progressive myoclonus epilepsy (7), ceroid lipofuscinosis, neuronal, 3 (6), visual cortex disease (5), visual pathway disease (5), visual epilepsy (3), lipid storage disease (2)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 19.69 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 407.52 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -73.20144-0.508 Picture PostScript Text
3' UTR -488.501148-0.426 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  Pfam Domains:
PF15156 - Ceroid-lipofuscinosis neuronal protein 6

ModBase Predicted Comparative 3D Structure on Q9NWW5
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0042803 protein homodimerization activity

Biological Process:
GO:0001573 ganglioside metabolic process
GO:0007040 lysosome organization
GO:0007042 lysosomal lumen acidification
GO:0007601 visual perception
GO:0008203 cholesterol metabolic process
GO:0030163 protein catabolic process
GO:0030203 glycosaminoglycan metabolic process
GO:0031987 locomotion involved in locomotory behavior
GO:0044265 cellular macromolecule catabolic process
GO:0045862 positive regulation of proteolysis

Cellular Component:
GO:0005783 endoplasmic reticulum
GO:0005788 endoplasmic reticulum lumen
GO:0005789 endoplasmic reticulum membrane
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  BC013130 - Homo sapiens ceroid-lipofuscinosis, neuronal 6, late infantile, variant, mRNA (cDNA clone MGC:21605 IMAGE:4517748), complete cds.
BC010849 - Homo sapiens ceroid-lipofuscinosis, neuronal 6, late infantile, variant, mRNA (cDNA clone MGC:8851 IMAGE:3878776), complete cds.
AK000568 - Homo sapiens cDNA FLJ20561 fis, clone KAT11961.
AK074753 - Homo sapiens cDNA FLJ90272 fis, clone NT2RP1000050, highly similar to Ceroid-lipofuscinosis neuronal protein 6.
AK027604 - Homo sapiens cDNA FLJ14698 fis, clone NT2RP2006069.
JD376239 - Sequence 357263 from Patent EP1572962.
JD317848 - Sequence 298872 from Patent EP1572962.
JD372584 - Sequence 353608 from Patent EP1572962.
JD073976 - Sequence 55000 from Patent EP1572962.
JD515303 - Sequence 496327 from Patent EP1572962.
JD317040 - Sequence 298064 from Patent EP1572962.
JD228019 - Sequence 209043 from Patent EP1572962.
JD503706 - Sequence 484730 from Patent EP1572962.
JD167423 - Sequence 148447 from Patent EP1572962.
JD078331 - Sequence 59355 from Patent EP1572962.
JD269143 - Sequence 250167 from Patent EP1572962.
JD271610 - Sequence 252634 from Patent EP1572962.
JD527641 - Sequence 508665 from Patent EP1572962.
JD258299 - Sequence 239323 from Patent EP1572962.
JD360963 - Sequence 341987 from Patent EP1572962.
LF208538 - JP 2014500723-A/16041: Polycomb-Associated Non-Coding RNAs.
JD439685 - Sequence 420709 from Patent EP1572962.
JD388734 - Sequence 369758 from Patent EP1572962.
LF377444 - JP 2014500723-A/184947: Polycomb-Associated Non-Coding RNAs.
AK291175 - Homo sapiens cDNA FLJ78017 complete cds, highly similar to Homo sapiens ceroid-lipofuscinosis, neuronal 6, late infantile, variant, mRNA.
JD492321 - Sequence 473345 from Patent EP1572962.
JD546644 - Sequence 527668 from Patent EP1572962.
JD535677 - Sequence 516701 from Patent EP1572962.
JD120494 - Sequence 101518 from Patent EP1572962.
JD507798 - Sequence 488822 from Patent EP1572962.
JD239139 - Sequence 220163 from Patent EP1572962.
JD545074 - Sequence 526098 from Patent EP1572962.
JD426648 - Sequence 407672 from Patent EP1572962.
JD372943 - Sequence 353967 from Patent EP1572962.
JD217905 - Sequence 198929 from Patent EP1572962.
JD520664 - Sequence 501688 from Patent EP1572962.
JD563416 - Sequence 544440 from Patent EP1572962.
JD291338 - Sequence 272362 from Patent EP1572962.
JD081855 - Sequence 62879 from Patent EP1572962.
AK293155 - Homo sapiens cDNA FLJ57253 complete cds, highly similar to Ceroid-lipofuscinosis neuronal protein 6.
AK293197 - Homo sapiens cDNA FLJ57025 complete cds, highly similar to Ceroid-lipofuscinosis neuronal protein 6.
JD220570 - Sequence 201594 from Patent EP1572962.
JD220551 - Sequence 201575 from Patent EP1572962.
JD140563 - Sequence 121587 from Patent EP1572962.
KJ904788 - Synthetic construct Homo sapiens clone ccsbBroadEn_14182 CLN6-like gene, encodes complete protein.
DQ891480 - Synthetic construct clone IMAGE:100004110; FLH177352.01X; RZPDo839G08124D ceroid-lipofuscinosis, neuronal 6, late infantile, variant (CLN6) gene, encodes complete protein.
EU176598 - Synthetic construct Homo sapiens clone IMAGE:100011403; FLH177351.01L; RZPDo839H03254D ceroid-lipofuscinosis, neuronal 6, late infantile, variant (CLN6) gene, encodes complete protein.
KU178671 - Homo sapiens ceroid-lipofuscinosis neuronal 6 late infantile variant isoform 1 (CLN6) mRNA, partial cds.
KU178672 - Homo sapiens ceroid-lipofuscinosis neuronal 6 late infantile variant isoform 2 (CLN6) mRNA, complete cds, alternatively spliced.
KU178673 - Homo sapiens ceroid-lipofuscinosis neuronal 6 late infantile variant isoform 4 (CLN6) mRNA, partial cds, alternatively spliced.
KU178674 - Homo sapiens ceroid-lipofuscinosis neuronal 6 late infantile variant isoform 5 (CLN6) mRNA, partial cds, alternatively spliced.
CR457244 - Homo sapiens full open reading frame cDNA clone RZPDo834F0912D for gene CLN6, ceroid-lipofuscinosis, neuronal 6, late infantile, variant; complete cds, incl. stopcodon.
AK124013 - Homo sapiens cDNA FLJ42019 fis, clone SPLEN2034081.
JD074980 - Sequence 56004 from Patent EP1572962.
JD169968 - Sequence 150992 from Patent EP1572962.
MA444115 - JP 2018138019-A/16041: Polycomb-Associated Non-Coding RNAs.
MA613021 - JP 2018138019-A/184947: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: A8K560, B4DDH6, CLN6_HUMAN, ENST00000249806.1, ENST00000249806.10, ENST00000249806.2, ENST00000249806.3, ENST00000249806.4, ENST00000249806.5, ENST00000249806.6, ENST00000249806.7, ENST00000249806.8, ENST00000249806.9, NM_017882, Q6IAB1, Q96SR0, Q9NWW5, uc317fae.1, uc317fae.2
UCSC ID: ENST00000249806.11_8
RefSeq Accession: NM_017882.3
Protein: Q9NWW5 (aka CLN6_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene CLN6:
dystonia-ov (Hereditary Dystonia Overview)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.