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CDKN1C cyclin dependent kinase inhibitor 1C [ Homo sapiens (human) ]

Gene ID: 1028, updated on 14-Nov-2024

Summary

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Official Symbol
CDKN1Cprovided by HGNC
Official Full Name
cyclin dependent kinase inhibitor 1Cprovided by HGNC
Primary source
HGNC:HGNC:1786
See related
Ensembl:ENSG00000129757 MIM:600856; AllianceGenome:HGNC:1786
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
BWS; WBS; p57; BWCR; KIP2; p57Kip2
Summary
This gene is imprinted, with preferential expression of the maternal allele. The encoded protein is a tight-binding, strong inhibitor of several G1 cyclin/Cdk complexes and a negative regulator of cell proliferation. Mutations in this gene are implicated in sporadic cancers and Beckwith-Wiedemann syndorome, suggesting that this gene is a tumor suppressor candidate. Three transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Oct 2010]
Expression
Biased expression in placenta (RPKM 87.0), fat (RPKM 42.6) and 9 other tissues See more
Orthologs
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Genomic context

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See CDKN1C in Genome Data Viewer
Location:
11p15.4
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (2883218..2885775, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (2972459..2975017, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (2904448..2907005, complement)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene potassium voltage-gated channel subfamily Q member 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:2878979-2879960 Neighboring gene KCNQ1 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:2884189-2884886 Neighboring gene CRISPRi-validated cis-regulatory element chr11.592 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:2890154-2890662 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:2904223-2904722 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:2906831-2907666 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:2905995-2906830 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:2907667-2908502 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:2913065-2913864 Neighboring gene SLC22A18 antisense RNA Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3074 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:2924695-2925196 Neighboring gene KCNQ1 downstream neighbor Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:2933345-2934048 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:2935457-2936158 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:2949927-2950535 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:2950536-2951145 Neighboring gene solute carrier family 22 member 18 Neighboring gene pleckstrin homology like domain family A member 2

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. Expanded phenotype and cancer risk in patients with Beckwith-Wiedemann spectrum caused by CDKN1C variants.
    Title: Expanded phenotype and cancer risk in patients with Beckwith-Wiedemann spectrum caused by CDKN1C variants.
  2. STK40 inhibits trophoblast fusion by mediating COP1 ubiquitination to degrade P57[Kip2].
    Title: STK40 inhibits trophoblast fusion by mediating COP1 ubiquitination to degrade P57(Kip2).
  3. Promoter methylation and enhanced SKP2 are associated with the downregulation of CDKN1C in cervical squamous cell carcinoma.
    Title: Promoter methylation and enhanced SKP2 are associated with the downregulation of CDKN1C in cervical squamous cell carcinoma.
  4. MYOD-SKP2 axis boosts tumorigenesis in fusion negative rhabdomyosarcoma by preventing differentiation through p57[Kip2] targeting.
    Title: MYOD-SKP2 axis boosts tumorigenesis in fusion negative rhabdomyosarcoma by preventing differentiation through p57(Kip2) targeting.
  5. Structure-Function Analysis of p57KIP2 in the Human Pancreatic Beta Cell Reveals a Bipartite Nuclear Localization Signal.
    Title: Structure-Function Analysis of p57KIP2 in the Human Pancreatic Beta Cell Reveals a Bipartite Nuclear Localization Signal.
  6. Exploiting the fibroblast growth factor receptor-1 vulnerability to therapeutically restrict the MYC-EZH2-CDKN1C axis-driven proliferation in Mantle cell lymphoma.
    Title: Exploiting the fibroblast growth factor receptor-1 vulnerability to therapeutically restrict the MYC-EZH2-CDKN1C axis-driven proliferation in Mantle cell lymphoma.
  7. PIK3R3 is upregulated in liver cancer and activates Akt signaling to control cancer growth by regulation of CDKN1C and SMC1A.
    Title: PIK3R3 is upregulated in liver cancer and activates Akt signaling to control cancer growth by regulation of CDKN1C and SMC1A.
  8. Identification and targeting of a HES1-YAP1-CDKN1C functional interaction in fusion-negative rhabdomyosarcoma.
    Title: Identification and targeting of a HES1-YAP1-CDKN1C functional interaction in fusion-negative rhabdomyosarcoma.
  9. High Maternal Serum Estradiol in First Trimester of Multiple Pregnancy Contributes to Small for Gestational Age via DNMT1-Mediated CDKN1C Upregulation.
    Title: High Maternal Serum Estradiol in First Trimester of Multiple Pregnancy Contributes to Small for Gestational Age via DNMT1-Mediated CDKN1C Upregulation.
  10. Loss of p57 Expression in Conceptions Other Than Complete Hydatidiform Mole: A Case Series With Emphasis on the Etiology, Genetics, and Clinical Significance.
    Title: Loss of p57 Expression in Conceptions Other Than Complete Hydatidiform Mole: A Case Series With Emphasis on the Etiology, Genetics, and Clinical Significance.
Submit: New GeneRIF Correction See all GeneRIFs (195)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated 2020-09-25)

ClinGen Genome Curation PagePubMed
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated 2020-09-25)

ClinGen Genome Curation PagePubMed

EBI GWAS Catalog

Description
Common variants in the calcium-sensing receptor gene are associated with total serum calcium levels.
EBI GWAS Catalog

Variation

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See Variation Viewer (GRCh37.p13)

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

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables cyclin-dependent protein serine/threonine kinase inhibitor activity IEA
Inferred from Electronic Annotation
more info
  
enables molecular function inhibitor activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein kinase inhibitor activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables protein-containing complex binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in adrenal gland development IEA
Inferred from Electronic Annotation
more info
  
involved_in camera-type eye development IEA
Inferred from Electronic Annotation
more info
  
involved_in digestive system development IEA
Inferred from Electronic Annotation
more info
  
involved_in embryonic placenta morphogenesis IEA
Inferred from Electronic Annotation
more info
  
involved_in genomic imprinting IEA
Inferred from Electronic Annotation
more info
  
involved_in kidney development IEA
Inferred from Electronic Annotation
more info
  
involved_in multicellular organism growth IEA
Inferred from Electronic Annotation
more info
  
involved_in myeloid cell differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of DNA-templated transcription IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of cyclin-dependent protein kinase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of epithelial cell proliferation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in negative regulation of epithelial cell proliferation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of kinase activity IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of mitotic cell cycle IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in negative regulation of phosphorylation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
  
involved_in neuron maturation IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of DNA-templated transcription IGI
Inferred from Genetic Interaction
more info
 PubMed 
involved_in positive regulation of transforming growth factor beta receptor signaling pathway IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of exit from mitosis IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of lens fiber cell differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in skeletal system development IEA
Inferred from Electronic Annotation
more info
  
involved_in uterus development IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
cyclin-dependent kinase inhibitor 1C
Names
cyclin-dependent kinase inhibitor 1C (p57, Kip2)
cyclin-dependent kinase inhibitor p57

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_008022.1 RefSeqGene

    Range
    5001..7548
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_533

mRNA and Protein(s)

  1. NM_000076.2 → NP_000067.1  cyclin-dependent kinase inhibitor 1C isoform a

    See identical proteins and their annotated locations for NP_000067.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a). Variants 1 and 3 both encode isoform a.
    Source sequence(s)
    AC013791, BC039188, CD676249, U22398
    Consensus CDS
    CCDS7738.1
    UniProtKB/Swiss-Prot
    P49918
    UniProtKB/TrEMBL
    A0A0G2JPX0
    Related
    ENSP00000411552.2, ENST00000430149.3
    Conserved Domains (1) summary
    pfam02234
    Location:32 → 78
    CDI; Cyclin-dependent kinase inhibitor

  2. NM_001122630.2 → NP_001116102.1  cyclin-dependent kinase inhibitor 1C isoform b

    See identical proteins and their annotated locations for NP_001116102.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (b) is shorter at the N-terminus compared to isoform a. Variants 2 and 3 both encode isoform b.
    Source sequence(s)
    AC013791, BC039188, CD676249, U22398
    Consensus CDS
    CCDS44519.1
    UniProtKB/TrEMBL
    B2D1N3
    Related
    ENSP00000411257.2, ENST00000440480.8
    Conserved Domains (1) summary
    pfam02234
    Location:21 → 67
    CDI; Cyclin-dependent kinase inhibitor

  3. NM_001122631.2 → NP_001116103.1  cyclin-dependent kinase inhibitor 1C isoform b

    See identical proteins and their annotated locations for NP_001116103.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence and uses an alternate splice junction in the 3' UTR compared to variant 1. The resulting isoform (b) is shorter at the N-terminus compared to isoform a. Variants 2 and 3 both encode isoform b.
    Source sequence(s)
    AC013791, BC039188, BM673714, CD676249, U22398
    Consensus CDS
    CCDS44519.1
    UniProtKB/TrEMBL
    B2D1N3
    Conserved Domains (1) summary
    pfam02234
    Location:21 → 67
    CDI; Cyclin-dependent kinase inhibitor

  4. NM_001362474.2 → NP_001349403.1  cyclin-dependent kinase inhibitor 1C isoform a

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 3' UTR compared to variant 1. Variants 1 and 3 both encode isoform a.
    Source sequence(s)
    AC013791
    Consensus CDS
    CCDS7738.1
    UniProtKB/Swiss-Prot
    P49918
    UniProtKB/TrEMBL
    A0A0G2JPX0
    Related
    ENSP00000413720.3, ENST00000414822.8
    Conserved Domains (1) summary
    pfam02234
    Location:32 → 78
    CDI; Cyclin-dependent kinase inhibitor

  5. NM_001362475.2 → NP_001349404.1  cyclin-dependent kinase inhibitor 1C isoform c

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR and uses an alternate splice site in the coding region, compared to variant 1, which results in a frameshift. The encoded protein (isoform c) has a shorter and distinct C-terminus, compared to isoform a.
    Source sequence(s)
    AC013791
    Consensus CDS
    CCDS86169.1
    UniProtKB/TrEMBL
    A0A2R8YFP9
    Related
    ENSP00000496631.1, ENST00000647251.1
    Conserved Domains (1) summary
    pfam02234
    Location:22 → 68
    CDI; Cyclin-dependent kinase inhibitor

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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    2883218..2885775 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NT_187585.1 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    115397..117985 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    2972459..2975017 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P49918.1 GenPept UniProtKB/Swiss-Prot:P49918

Gene LinkOut

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