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    CCM2L CCM2 like scaffold protein [ Homo sapiens (human) ]

    Gene ID: 140706, updated on 10-Dec-2024

    Summary

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    Official Symbol
    CCM2Lprovided by HGNC
    Official Full Name
    CCM2 like scaffold proteinprovided by HGNC
    Primary source
    HGNC:HGNC:16153
    See related
    Ensembl:ENSG00000101331 AllianceGenome:HGNC:16153
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    C20orf160; dJ310O13.5
    Summary
    Predicted to be involved in heart morphogenesis. Predicted to act upstream of or within several processes, including heart development; negative regulation of homotypic cell-cell adhesion; and positive regulation of fibroblast growth factor production. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in spleen (RPKM 38.8), fat (RPKM 5.9) and 2 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See CCM2L in Genome Data Viewer
    Location:
    20q11.21
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (32010438..32032180)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (33735070..33756812)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (30598241..30619983)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene ReSE screen-validated silencer GRCh37_chr20:30556227-30556404 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:30559879-30560380 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:30560381-30560880 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:30564043-30564544 Neighboring gene XK related 7 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:30575890-30576724 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:30576725-30577558 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:30598063-30598590 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:30599501-30600092 Neighboring gene RNA, 5S ribosomal pseudogene 481 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12771 Neighboring gene NANOG hESC enhancer GRCh37_chr20:30611787-30612288 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:30619014-30619541 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17705 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17706 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12773 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12774 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:30641518-30641717 Neighboring gene RNA, 5S ribosomal pseudogene 482 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17707 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17708 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17709 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12775 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12776 Neighboring gene HCK proto-oncogene, Src family tyrosine kinase Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:30659475-30659975 Neighboring gene MPRA-validated peak4189 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:30672211-30672710 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:30678826-30679621 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:30688747-30689248

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Dynamic regulation of the cerebral cavernous malformation pathway controls vascular stability and growth. Zheng X, et al. Dev Cell, 2012 Aug 14. PMID 22898778, Free PMC Article
    2. The DNA sequence and comparative analysis of human chromosome 20. Deloukas P, et al. Nature, 2001 Dec 20-27. PMID 11780052
    3. New genetic associations detected in a host response study to hepatitis B vaccine. Davila S, et al. Genes Immun, 2010 Apr. PMID 20237496
    4. Cross-linking mass spectrometry discovers, evaluates, and corroborates structures and protein-protein interactions in the human cell. Bartolec TK, et al. Proc Natl Acad Sci U S A, 2023 Apr 25. PMID 37071682, Free PMC Article
    5. PLEKHA4/kramer Attenuates Dishevelled Ubiquitination to Modulate Wnt and Planar Cell Polarity Signaling. Shami Shah A, et al. Cell Rep, 2019 May 14. PMID 31091453, Free PMC Article

    See all (12) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Observational study of gene-disease association. (HuGE Navigator)
      Title: New genetic associations detected in a host response study to hepatitis B vaccine.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ43600

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables molecular_function ND
    No biological Data available
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    involved_in heart morphogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cellular_component ND
    No biological Data available
    more info
    		  

    General protein information

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    Preferred Names
    cerebral cavernous malformations 2 protein-like
    Names
    CCM2 like scaffolding protein
    CCM2-like
    cerebral cavernous malformation 2-like

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001365692.1 → NP_001352621.1  cerebral cavernous malformations 2 protein-like isoform 1

      Status: VALIDATED

      Source sequence(s)
      AL031658
      Consensus CDS
      CCDS93028.1
      UniProtKB/Swiss-Prot
      Q5JYR9, Q8N5F1, Q8N6G8, Q96MD5, Q9NUG4
      Related
      ENSP00000392448.2, ENST00000452892.3
      Conserved Domains (2) summary
      cd13166
      Location:41 → 345
      PTB_CCM2; Cerebral cavernous malformation 2 FERM domain C-lobe
      pfam16545
      Location:403 → 493
      CCM2_C; Cerebral cavernous malformation protein, harmonin-homology

    2. NM_080625.4 → NP_542192.2  cerebral cavernous malformations 2 protein-like isoform 2

      See identical proteins and their annotated locations for NP_542192.2

      Status: VALIDATED

      Source sequence(s)
      AL031658, BC030254, CA406781, DA936380, DB331650
      Consensus CDS
      CCDS13195.1
      UniProtKB/Swiss-Prot
      Q9NUG4
      Related
      ENSP00000262659.8, ENST00000262659.12
      Conserved Domains (1) summary
      cd13166
      Location:41 → 345
      PTB_CCM2; Cerebral cavernous malformation 2 FERM domain C-lobe

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000020.11 Reference GRCh38.p14 Primary Assembly

      Range
      32010438..32032180
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011528568.4 → XP_011526870.1  cerebral cavernous malformations 2 protein-like isoform X3

      Conserved Domains (2) summary
      cd13166
      Location:33 → 337
      PTB_CCM2; Cerebral cavernous malformation 2 FERM domain C-lobe
      pfam16545
      Location:395 → 511
      CCM2_C; Cerebral cavernous malformation protein, harmonin-homology

    2. XM_011528566.3 → XP_011526868.1  cerebral cavernous malformations 2 protein-like isoform X1

      Conserved Domains (2) summary
      cd13166
      Location:41 → 345
      PTB_CCM2; Cerebral cavernous malformation 2 FERM domain C-lobe
      pfam16545
      Location:403 → 519
      CCM2_C; Cerebral cavernous malformation protein, harmonin-homology

    3. XM_011528567.4 → XP_011526869.1  cerebral cavernous malformations 2 protein-like isoform X2

      Conserved Domains (2) summary
      cd13166
      Location:34 → 338
      PTB_CCM2; Cerebral cavernous malformation 2 FERM domain C-lobe
      pfam16545
      Location:396 → 512
      CCM2_C; Cerebral cavernous malformation protein, harmonin-homology

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060944.1 Alternate T2T-CHM13v2.0

      Range
      33735070..33756812
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054323010.1 → XP_054178985.1  cerebral cavernous malformations 2 protein-like isoform X3

    2. XM_054323008.1 → XP_054178983.1  cerebral cavernous malformations 2 protein-like isoform X1

    3. XM_054323009.1 → XP_054178984.1  cerebral cavernous malformations 2 protein-like isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NUG4.3 GenPept UniProtKB/Swiss-Prot:Q9NUG4

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