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CCDC88C coiled-coil domain containing 88C [ Homo sapiens (human) ]

Gene ID: 440193, updated on 3-Nov-2024

Summary

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Official Symbol
CCDC88Cprovided by HGNC
Official Full Name
coiled-coil domain containing 88Cprovided by HGNC
Primary source
HGNC:HGNC:19967
See related
Ensembl:ENSG00000015133 MIM:611204; AllianceGenome:HGNC:19967
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
HYC1; DAPLE; HKRP2; SCA40; KIAA1509
Summary
This gene encodes a ubiquitously expressed coiled-coil domain-containing protein that interacts with the dishevelled protein and is a negative regulator of the Wnt signalling pathway. The protein encoded by this gene has a PDZ-domain binding motif in its C-terminus with which it interacts with the dishevelled protein. Dishevelled is a scaffold protein involved in the regulation of the Wnt signaling pathway. The Wnt signaling pathway plays an important role in embryonic development, tissue maintenance, and cancer progression. Mutations in this gene cause autosomal recessive, primary non-syndromic congenital hydrocephalus; a condition characterized by excessive accumulation of cerebrospinal fluid in the ventricles of the brain. [provided by RefSeq, Jan 2013]
Expression
Broad expression in lymph node (RPKM 9.5), spleen (RPKM 8.3) and 24 other tissues See more
Orthologs
mouse all
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Genomic context

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See CCDC88C in Genome Data Viewer
Location:
14q32.11-q32.12
Exon count:
34
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (91271323..91417820, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (85496797..85643060, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (91737667..91884164, complement)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene D-glutamate cyclase Neighboring gene Sharpr-MPRA regulatory region 15407 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8893 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8894 Neighboring gene small nucleolar RNA, H/ACA box 11B Neighboring gene ReSE screen-validated silencer GRCh37_chr14:91619068-91619346 Neighboring gene Sharpr-MPRA regulatory region 3148 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8895 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8896 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8897 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8898 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8899 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8900 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:91710745-91711246 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6019 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:91719939-91720470 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:91720471-91721002 Neighboring gene CRISPRi-validated cis-regulatory element chr14.1904 Neighboring gene Sharpr-MPRA regulatory region 4292 Neighboring gene CRISPRi-validated cis-regulatory element chr14.1906 Neighboring gene G protein-coupled receptor 68 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:91749514-91749720 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6022 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6023 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:91771631-91772466 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:91772467-91773300 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8902 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8903 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8904 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8905 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8906 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:91818809-91819780 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:91821242-91821752 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:91826469-91826970 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:91826971-91827470 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8907 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6024 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8908 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8909 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8910 Neighboring gene uncharacterized LOC107984673 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:91838097-91838709 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8911 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr14:91841845-91842517 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8912 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:91843867-91844540 Neighboring gene uncharacterized LOC105370624 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6025 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:91848585-91849375 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:91849376-91850165 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:91853480-91854308 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:91854309-91855135 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8913 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:91864835-91865466 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8914 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:91866728-91867357 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8916 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8917 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8918 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8919 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8920 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6026 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:91884645-91885289 Neighboring gene COX assembly mitochondrial protein homolog Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8921 Neighboring gene CCDC88C divergent transcript Neighboring gene uncharacterized LOC124903361

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. CCDC88C variants are associated with focal epilepsy and genotype-phenotype correlation.
    Title: CCDC88C variants are associated with focal epilepsy and genotype-phenotype correlation.
  2. A Novel c.3636-4 A>G Mutation in the CCDC88C Plays a Causative Role in Familial Spinocerebellar Ataxia.
    Title: A Novel c.3636-4 A>G Mutation in the CCDC88C Plays a Causative Role in Familial Spinocerebellar Ataxia.
  3. Confirmation of the Pathogenetic Role of the CCDC88C Gene in Early-Onset Pure Spastic Paraplegia.
    Title: Confirmation of the Pathogenetic Role of the CCDC88C Gene in Early-Onset Pure Spastic Paraplegia.
  4. Spinocerebellar Ataxia in a Hungarian Female Patient with a Novel Variant of Unknown Significance in the CCDC88C Gene.
    Title: Spinocerebellar Ataxia in a Hungarian Female Patient with a Novel Variant of Unknown Significance in the CCDC88C Gene.
  5. Neuropathological hallmarks of fetal hydrocephalus linked to CCDC88C pathogenic variants.
    Title: Neuropathological hallmarks of fetal hydrocephalus linked to CCDC88C pathogenic variants.
  6. The Daple-CK1epsilon complex regulates Dvl2 phosphorylation and canonical Wnt signaling.
    Title: The Daple-CK1ε complex regulates Dvl2 phosphorylation and canonical Wnt signaling.
  7. DAPLE protein inhibits nucleotide exchange on Galphas and Galphaq via the same motif that activates Galphai.
    Title: DAPLE protein inhibits nucleotide exchange on Gα(s) and Gα(q) via the same motif that activates Gαi.
  8. Two Isoforms of the Guanine Nucleotide Exchange Factor, Daple/CCDC88C Cooperate as Tumor Suppressors.
    Title: Two Isoforms of the Guanine Nucleotide Exchange Factor, Daple/CCDC88C Cooperate as Tumor Suppressors.
  9. Fusion driven JMML: a novel CCDC88C-FLT3 fusion responsive to sorafenib identified by RNA sequencing.
    Title: Fusion driven JMML: a novel CCDC88C-FLT3 fusion responsive to sorafenib identified by RNA sequencing.
  10. DAPLE and MPDZ function as cooperative partners at apical junctions.
    Title: DAPLE and MPDZ bind to each other and cooperate to promote apical cell constriction.
Submit: New GeneRIF Correction See all GeneRIFs (20)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Hydrocephalus, nonsyndromic, autosomal recessive 1
MedGen: C3887608 OMIM: 236600 GeneReviews: Not available
not available
Spinocerebellar ataxia type 40
MedGen: C4518336 OMIM: 616053 GeneReviews: Not available
not available

EBI GWAS Catalog

Description
Large-scale genotyping identifies 41 new loci associated with breast cancer risk.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ00354, KIAA1509

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables G-protein alpha-subunit binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables PDZ domain binding ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
enables dynein light intermediate chain binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables frizzled binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables guanyl-nucleotide exchange factor activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables identical protein binding ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
enables microtubule binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein dimerization activity IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in Wnt signaling pathway, planar cell polarity pathway IEA
Inferred from Electronic Annotation
more info
  
involved_in apical constriction IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in cilium organization IEA
Inferred from Electronic Annotation
more info
  
involved_in cytoplasmic microtubule organization IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in cytoskeleton-dependent intracellular transport IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in microtubule bundle formation IEA
Inferred from Electronic Annotation
more info
  
involved_in mucociliary clearance IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of canonical Wnt signaling pathway IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of microtubule depolymerization IEA
Inferred from Electronic Annotation
more info
  
involved_in non-canonical Wnt signaling pathway IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within_positive_effect positive regulation of JNK cascade IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in protein destabilization ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
involved_in respiratory basal cell differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in small GTPase-mediated signal transduction IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
located_in apical junction complex IEA
Inferred from Electronic Annotation
more info
  
located_in cell junction IDA
Inferred from Direct Assay
more info
  
located_in cell junction IMP
Inferred from Mutant Phenotype
more info
 PubMed 
is_active_in centrosome IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in extracellular region IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
protein Daple
Names
Dvl-associating protein with a high frequency of leucine residues
hook-related protein 2
spinocerebellar ataxia 40

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.

Genomic

  1. NG_033118.2 RefSeqGene

    Range
    5025..151522
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001080414.4 → NP_001073883.2  protein Daple

    See identical proteins and their annotated locations for NP_001073883.2

    Status: REVIEWED

    Source sequence(s)
    AB040942, AK302839, AL133153, AL135818, AL137353, BX283171, DR006516
    Consensus CDS
    CCDS45151.1
    UniProtKB/Swiss-Prot
    Q69YK1, Q7L1M2, Q86SX7, Q8IYG8, Q9P219
    Related
    ENSP00000374507.6, ENST00000389857.11
    Conserved Domains (4) summary
    pfam01576
    Location:329 → 1319
    Myosin_tail_1; Myosin tail
    pfam05622
    Location:17 → 633
    HOOK; HOOK protein
    cl23720
    Location:489 → 601
    RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)
    cl24005
    Location:664 → 741
    DUF2570; Protein of unknown function (DUF2570)

RNA

  1. NR_189158.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL133153, AL135818

  2. NR_189159.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL133153, AL135818

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_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    91271323..91417820 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011536796.3 → XP_011535098.1  protein Daple isoform X1

    Conserved Domains (3) summary
    pfam01576
    Location:293 → 1283
    Myosin_tail_1; Myosin tail
    cl23720
    Location:453 → 565
    RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)
    cl24005
    Location:628 → 705
    DUF2570; Protein of unknown function (DUF2570)

  2. XM_047431418.1 → XP_047287374.1  protein Daple isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    85496797..85643060 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054376141.1 → XP_054232116.1  protein Daple isoform X1

  2. XM_054376142.1 → XP_054232117.1  protein Daple isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9P219.3 GenPept UniProtKB/Swiss-Prot:Q9P219

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Chemical Information
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Tools
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