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

Gene ID: 140706, updated on 2-Nov-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, Nov 2024]
Expression
Biased expression in spleen (RPKM 38.8), fat (RPKM 5.9) and 2 other tissues See more
Orthologs
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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 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 Variation Viewer (GRCh37.p13)

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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