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Category Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21

GIFtS
-

CLVS2 Gene

protein-coding GIFtS: 43
GCID: GC06P123360

clavesin 2

(Previous names: chromosome 6 open reading frame 212, chromosome 6 open...)
(Previous symbols: C6orf212, C6orf213, RLBP1L2)

Explore 1 disease affiliated with
CLVS2 via

MalaCards

our new
Human Malady Compendium

(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc, ⁷Ensembl, ⁸DME, ⁹miRBase, and/or ¹⁰fRNAdb)
About This Section

Aliases
Clavesin 2¹ ²		Retinaldehyde Binding Protein 1-Like 2¹ ²
C6orf212¹ ² ³		Retinaldehyde-Binding Protein 1-Like 2² ³
C6orf213¹ ² ³		Chromosome 6 Open Reading Frame 212¹
RLBP1L2¹ ² ³		Chromosome 6 Open Reading Frame 213¹
BA160A10.4¹		Clavesin-2¹

External Ids:	HGNC: 23046¹	Entrez Gene: 134829²	Ensembl: ENSG00000146352⁷	UniProtKB: Q5SYC1³

Export aliases for CLVS2 gene to outside databases

Previous GC identifer: GC06P120894

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

UniProtKB/Swiss-Prot: CLVS2_HUMAN, Q5SYC1

Function: Required for normal morphology of late endosomes and/or lysosomes in neurons (By similarity). Binds

phosphatidylinositol 3,5-bisphosphate (PtdIns(3,5)P2)

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section

RefSeq DNA sequence:

NC_000006.11 NC_018917.1 NT_025741.15

Regulatory elements:

Search SABiosciences Regulatory transcription factor binding sites for CLVS2
Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids

Search SABiosciences Chromatin IP Primers for CLVS2

Epigenetics:

QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat CLVS2

Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 6q22.31 Ensembl cytogenetic band: 6q22.31 HGNC cytogenetic band: 6q22.31

CLVS2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CLVS2 gene location

GeneLoc information about chromosome 6 GeneLoc Exon Structure

GeneLoc location for GC06P123360: view genomic region (about GC identifiers)

Start:	123,317,116 bp from pter	End:	123,385,612 bp from pter
Size:	68,497 bases	Orientation:	plus strand

(According to ¹UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to ²PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
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About This Section

UniProtKB/Swiss-Prot: CLVS2_HUMAN, Q5SYC1 (See protein sequence)

Recommended Name: Clavesin-2

Size: 327 amino acids; 38000 Da

Subunit: Forms a complex with clathrin heavy chain and gamma-adaptin

Subcellular location: Golgi apparatus, trans-Golgi network membrane; Peripheral membrane protein (By similarity).

Cytoplasmic vesicle, clathrin-coated vesicle (By similarity). Early endosome membrane; Peripheral membrane protein

Miscellaneous: Binding to PtdIns(3,5)P2 is not required for localization (By similarity)

Secondary accessions: B3KTG5 B4DHL0 C8UZT4 Q5SYC0

Alternative splicing: 2 isoforms: Q5SYC1-1 Q5SYC1-2 (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for CLVS2: NX_Q5SYC1

Post-translational modifications:

View modification sites using PhosphoSitePlus²

View neXtProt modification sites for NX_Q5SYC1

CLVS2 Protein expression data from MOPED and PaxDb: About this image

REFSEQ proteins: NP_001010852.2

ENSEMBL proteins:

ENSP00000275162 ENSP00000357423

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	Uscn Proteins for CLVS2

Gene Ontology (GO): 5 cellular component terms (GO ID links to tree view): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005768	endosome	IDA	19651769
GO:0005794	Golgi apparatus	IEA	--
GO:0005802	trans-Golgi network	ISS	--
GO:0030136	clathrin-coated vesicle	ISS	--
GO:0031901	early endosome membrane	IEA	--

CLVS2 for ontologies About GeneDecksing

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(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section

CLVS2 for domains About GeneDecksing

3 InterPro domains/families:

IPR001071 CRAL-bd_toc_tran

IPR001251 CRAL-TRIO_dom

IPR011074 CRAL/TRIO_N_dom

Graphical View of Domain Structure for InterPro Entry Q5SYC1

ProtoNet protein and cluster: Q5SYC1

2 Blocks protein families:

IPB001071 Cellular retinaldehyde-binding protein signature

IPB001251 Cellular retinaldehyde-binding (CRAL)/Triple function domain (TRIO)

UniProtKB/Swiss-Prot: CLVS2_HUMAN, Q5SYC1

Domain: The CRAL-TRIO domain is required for targeting to the membrane and for binding PtdIns(3,5)P2

Similarity: Contains 1 CRAL-TRIO domain

(According to ¹UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or ²DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
About This Section

Function Summary:

UniProtKB/Swiss-Prot: CLVS2_HUMAN, Q5SYC1

Function: Required for normal morphology of late endosomes and/or lysosomes in neurons (By similarity). Binds

phosphatidylinositol 3,5-bisphosphate (PtdIns(3,5)P2)

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Gene Ontology (GO): 2 molecular function terms (GO ID links to tree view): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005215	transporter activity	IEA	--
GO:0080025	phosphatidylinositol-3,5-bisphosphate binding	IDA	19651769

CLVS2 for ontologies About GeneDecksing

1 GenomeRNAi human phenotype for CLVS2:

Increased gamma-H2AX phosphory

(Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to ¹UniProtKB, ²MINT, ³I2D, and/or ⁴STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
About This Section

Interactions:

Search SABiosciences Gene Network Central^TM Interacting Genes and Proteins Networks for CLVS2

Gene Ontology (GO): 1 biological process term (GO ID links to tree view): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0007040	lysosome organization	ISS	--

CLVS2 for ontologies About GeneDecksing

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section

Browse Small Molecules at EMD Millipore

Browse drugs & compounds from Enzo Life Sciences

Browse Tocris compounds for CLVS2
Search CenterWatch for drugs/clinical trials and news about CLVS2

(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
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About This Section

REFSEQ mRNAs for CLVS2 gene:

NM_001010852.2

Unigene Cluster for CLVS2:

Clavesin 2

Hs.486361 [show with all ESTs]

Unigene Representative Sequence: AK095527

2 Ensembl transcripts including schematic representations, and UCSC links where relevant:

ENST00000275162(uc003pzi.1) ENST00000368438

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Additional cDNA sequence:

AK095527.1 AK295158.1 BC101376.1 BC101377.2

1 DOTS entry:

DT.99936993

3 AceView cDNA sequences:

AK095527 BE796967 BG899217

GeneLoc Exon Structure

(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section

CLVS2 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: TTAATGTAGC

About this image

CLVS2 expression in embryonic tissues and stem cells

Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine About this table

Stem Cell Differentiation: 1 LifeMap Cell

Name

Category

Definitive endoderm-like cells (A scalable, suspensi...)

Expression:

Positive

Negative

Selective marker

Experimental details:

Curated

Microarrays

In-situ hybridization

See CLVS2 Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for CLVS2

SOURCE GeneReport for Unigene cluster: Hs.486361

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In Situ
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(Orthologs according to ^1,2HomoloGene (²older version, for species not in ¹newer version), ³euGenes, ⁴SGD , ⁵MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or ⁶Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
About This Section

This gene was present in the common ancestor of animals.

Orthologs for CLVS2 gene from 4/16 species (see all 16) About this table

Organism	Taxonomic classification	Gene	Description	Human Similarity	Orthology Type	Details
chicken (Gallus gallus)	Aves	CLVS2¹	clavesin 2	86.44(n) 97.25(a)		428616 XM_426173.3 XP_426173.3
lizard (Anolis carolinensis)	Reptilia	CLVS2⁶	--	91(a)	1 ↔ 1	1(182100662-182156308)
zebrafish (Danio rerio)	Actinopterygii	clvs2¹	clavesin 2	78.7(n) 89.3(a)		566769 NM_001025545.2 NP_001020716.1
fruit fly (Drosophila melanogaster)	Insecta	CG33966⁶ CG31636⁶ (see all 18)	--	25(a) 25(a) (see all 18)	possible ortholog possible ortholog (see all 18)	3L(1234130-1235420) 2L(6656459-6657879)

ENSEMBL Gene Tree for CLVS2 (if available)
TreeFam Gene Tree for CLVS2 (if available)

(Paralogs according to ¹HomoloGene,
²Ensembl, and ³SIMAP, Pseudogenes according to ⁴Pseudogene.org Build 68)
About This Section

Paralogs for CLVS2 gene

RLBP1² TTPAL² CLVS1² TTPA²

5 SIMAP similar genes for CLVS2 using alignment to 1 protein entry: CLVS2_HUMAN:

CLVS1 RLBP1 DKFZp686E0870 TTPA TTPAL

CLVS2 for paralogs About GeneDecksing

(SNPs/Variants according to the ¹NCBI SNP Database, ²Ensembl, ³PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section

SNP ID	Valid	Clinical significance	Chr 6 pos	Sequence	#	AA Chg	Type	More	#	Allele freq	Pop	Total sample	More
Genomic Data					Transcription Related Data				Allele Frequencies
				--	--	--		--	--
rs147076471^1,2		--	123315629(+)	`ACAGAA/TAGCTA`	1	--	us2k¹		0	--	--	--	--
rs114810925^1,2	F,	--	123315861(+)	`GGGCAA/GTTAGT`	1	--	us2k¹		1		WA	118
rs6925717^1,2	C,F,A,	--	123315965(+)	`CGAAAC/TATAAA`	1	--	us2k¹		6		NA WA CSA EA	364
rs7762170^1,2	C,F,A,H,	--	123316097(+)	`TCCTAG/AAAGGA`	1	--	us2k¹		8		WA NA CSA EA	368
rs117123942^1,2	F,	--	123316101(+)	`AGAAGG/AACCTT`	1	--	us2k¹		1		EA	120
rs150700420^1,2		--	123316203(+)	`ATGAC-/TGTGTG TGTGT`	1	--	us2k¹		0	--	--	--	--
rs72020924^1,2	C,	--	123316204(+)	`ATGAC-/TGTGTGT`	1	--	us2k¹		0	--	--	--	--
rs183769403^1,2		--	123316266(+)	`AATTTA/GCATTA`	1	--	us2k¹		0	--	--	--	--
rs187958576^1,2		--	123316273(+)	`ATTAAC/TTTAAT`	1	--	us2k¹		0	--	--	--	--
rs191273408^1,2		--	123316501(+)	`CCACAA/CCTCGT`	1	--	us2k¹		0	--	--	--	--

HapMap Linkage Disequilibrium report for CLVS2 (123317116 - 123385612 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV): 2 variations for CLVS2
2 Indels: 81573 93994

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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
About This Section

CLVS2 for disorders About GeneDecksing

1 disease for CLVS2: About MalaCards

neuronitis

Export disorders for CLVS2 gene to outside databases

(in PubMed. Associations of this gene to articles via ¹Entrez Gene, ²UniProtKB/Swiss-Prot, ³HGNC, ⁴GAD, ⁵PharmGKB, ⁶HMDB, ⁷DrugBank, ⁸UniProtKB/TrEMBL, ⁹ Novoseek, and/or ¹⁰fRNAdb)
About This Section

PubMed articles for CLVS2 gene integrated from 9 sources:
(articles sorted by number of sources associating them with CLVS2)

Utopia: connect your pdf to the dynamic
world of online information

The clavesin family: neuron-specific lipid- and clathrin-binding Sec14 proteins regulating lysosomal morphology. (PubMed id 19651769)^{1, 2, 3} Katoh Y....McPherson P.S. (2009)
Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)^{1, 2} Ota T.... Sugano S. (2004)
A genome-wide search for loci interacting with known p rostate cancer risk-associated genetic variants. (PubMed id 22219177)¹ Tao S....Sun J. (2012)
The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)² Gerhard D.S....Malek J. (2004)
The DNA sequence and analysis of human chromosome 6. (PubMed id 14574404)² Mungall A.J.... Beck S. (2003)
Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)¹ Strausberg R.L....Marra M.A. (2002)

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section

		AND	OR
Aliases
Free Text

Query String		PubMed OMIM NCBI Bookshelf
	(Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
About This Section

Entrez Gene: 134829	HGNC: 23046	AceView: C6orf213	Ensembl:ENSG00000146352	euGenes: HUgn134829
ECgene: CLVS2	H-InvDB: CLVS2

(According to HUGE)
About This Section

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section

Name	Description
PharmGKB entry for CLVS2	Pharmacogenomics, SNPs, Pathways

Intellectual Property for CLVS2 gene
(Patent information from GeneIP, Licensable technologies from WIS Yeda, Salk, Tufts, IP news from LifeMap Sciences, Inc.)

About This Section

Patent Information for CLVS2 gene:
Search GeneIP for patents involving CLVS2

GeneCards and IP:
Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search

(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences),
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About This Section


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GeneCards Homepage - Last full update: 19 Mar 2013 - Incrementals: 21 Mar 2013 , 15 Apr 2013 , 26 Apr 2013

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Category			VWF (GIFTS: 73) von Willebrand factor
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The GeneCards human gene database gene index: 1 3 5 6 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

The GeneCards Human Gene Database

Developed at the Crown Human Genome Center, Department of Molecular Genetics, the Weizmann Institute of Science

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CLVS2 Gene

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CLVS2 Gene

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Aliasesfor CLVS2 gene

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for CLVS2 gene

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for CLVS2 gene

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for CLVS2 gene

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for CLVS2 gene

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for CLVS2 gene

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for CLVS2 gene

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for CLVS2 gene

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for CLVS2 gene

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for CLVS2 gene

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for CLVS2 gene

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for CLVS2 gene

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for CLVS2 gene

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for CLVS2 gene

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