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CDIP1 cell death inducing p53 target 1 [ Homo sapiens (human) ]

Gene ID: 29965, updated on 5-Mar-2024

Summary

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Official Symbol
CDIP1provided by HGNC
Official Full Name
cell death inducing p53 target 1provided by HGNC
Primary source
HGNC:HGNC:13234
See related
Ensembl:ENSG00000089486 MIM:610503; AllianceGenome:HGNC:13234
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
I1; CDIP; LITAFL; C16orf5
Summary
Predicted to enable metal ion binding activity. Acts upstream of or within intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator and tumor necrosis factor-mediated signaling pathway. Located in cytoplasmic side of late endosome membrane; cytoplasmic side of lysosomal membrane; and nucleus. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in brain (RPKM 37.0), kidney (RPKM 18.1) and 24 other tissues See more
Orthologs
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Genomic context

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Location:
16p13.3
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (4510669..4538773, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (4540144..4568234, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (4560670..4588774, complement)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:4516031-4516532 Neighboring gene NmrA like redox sensor 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:4526195-4526696 Neighboring gene uncharacterized LOC124903636 Neighboring gene heme oxygenase 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:4543888-4544077 Neighboring gene Sharpr-MPRA regulatory region 9698 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:4563218-4563745 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:4563746-4564272 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:4564273-4564800 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:4571909-4572773 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:4579080-4579732 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:4579733-4580384 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10340 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7152 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7153 Neighboring gene chromosome 16 open reading frame 96 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:4604203-4604813 Neighboring gene SUB1 pseudogene 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:4635152-4635652 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:4642470-4643270 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:4644073-4644872 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:4661103-4661738 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7154 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7155 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7156 Neighboring gene UBA like domain containing 1

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. The Novel ALG-2 Target Protein CDIP1 Promotes Cell Death by Interacting with ESCRT-I and VAPA/B. Inukai R, et al. Int J Mol Sci, 2021 Jan 25. PMID 33503978, Free PMC Article
  2. C16orf5, a novel proline-rich gene at 16p13.3, is highly expressed in the brain. Bhalla K, et al. J Hum Genet, 1999. PMID 10570909
  3. Expression of the p53 target CDIP correlates with sensitivity to TNFα-induced apoptosis in cancer cells. Brown-Endres L, et al. Cancer Res, 2012 May 1. PMID 22549949, Free PMC Article
  4. Sequential CRISPR-Based Screens Identify LITAF and CDIP1 as the Bacillus cereus Hemolysin BL Toxin Host Receptors. Liu J, et al. Cell Host Microbe, 2020 Sep 9. PMID 32544461, Free PMC Article
  5. The Charcot Marie Tooth disease protein LITAF is a zinc-binding monotopic membrane protein. Qin W, et al. Biochem J, 2016 Nov 1. PMID 27582497, Free PMC Article

See all (20) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Role of ELK1 in regulating colorectal cancer progression: miR-31-5p/CDIP1 axis in CRC pathogenesis.
    Title: Role of ELK1 in regulating colorectal cancer progression: miR-31-5p/CDIP1 axis in CRC pathogenesis.
  2. The Novel ALG-2 Target Protein CDIP1 Promotes Cell Death by Interacting with ESCRT-I and VAPA/B.
    Title: The Novel ALG-2 Target Protein CDIP1 Promotes Cell Death by Interacting with ESCRT-I and VAPA/B.
  3. Study conclude that LITAF is a monotopic membrane protein whose membrane integration is stabilised by a zinc finger. The related human protein, CDIP1 (cell death involved p53 target 1), displays identical membrane topology, suggesting that this mode of membrane integration is conserved in LITAF family proteins.
    Title: The Charcot Marie Tooth disease protein LITAF is a zinc-binding monotopic membrane protein.
  4. CDIP expression correlates with sensitivity of cancer cells with TNFalpha, and CDIP seems to be a regulator of the p53-mediated death versus survival response of cells to TNFalpha.
    Title: Expression of the p53 target CDIP correlates with sensitivity to TNFα-induced apoptosis in cancer cells.
  5. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
  6. These findings support a novel p53 --> CDIP --> TNF-alpha apoptotic pathway that directs apoptosis after exposure of cells to genotoxic stress.
    Title: CDIP, a novel pro-apoptotic gene, regulates TNFalpha-mediated apoptosis in a p53-dependent manner.
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)

Genotypes

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 molecular_function ND
No biological Data available
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables zinc ion binding IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
is_active_in cytoplasmic side of late endosome membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytoplasmic side of late endosome membrane IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in cytoplasmic side of lysosomal membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytoplasmic side of lysosomal membrane IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleus NAS
Non-traceable Author Statement
more info
 PubMed 

General protein information

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Preferred Names
cell death-inducing p53-target protein 1
Names
LITAF-like protein
cell death inducing protein
cell death involved p53-target
lipopolysaccharide-induced tumor necrosis factor-alpha-like protein
transmembrane protein I1

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_001199054.2 → NP_001185983.1  cell death-inducing p53-target protein 1 isoform a

    See identical proteins and their annotated locations for NP_001185983.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a). Variants 1 and 2 both encode the same isoform (a).
    Source sequence(s)
    AC007606, AL833853
    Consensus CDS
    CCDS42114.1
    UniProtKB/Swiss-Prot
    A8K7M1, B4DFU1, B4DY75, D3DUD6, Q96ID8, Q9H0Q4, Q9H305, Q9P112
    Related
    ENSP00000454994.1, ENST00000563332.6
    Conserved Domains (1) summary
    pfam10601
    Location:137 → 203
    zf-LITAF-like; LITAF-like zinc ribbon domain

  2. NM_001199055.2 → NP_001185984.1  cell death-inducing p53-target protein 1 isoform b

    See identical proteins and their annotated locations for NP_001185984.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and uses an alternate in-frame splice junction at the 5' end of an exon compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a.
    Source sequence(s)
    AC007606, AK294257
    Consensus CDS
    CCDS58419.1
    UniProtKB/Swiss-Prot
    Q9H305
    Related
    ENSP00000455462.1, ENST00000563507.5
    Conserved Domains (1) summary
    pfam10601
    Location:98 → 166
    zf-LITAF-like; LITAF-like zinc ribbon domain

  3. NM_001199056.2 → NP_001185985.1  cell death-inducing p53-target protein 1 isoform c

    See identical proteins and their annotated locations for NP_001185985.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR and lacks an alternate internal segemnt compared to variant 1. The resulting isoform (c) has the same N- and C-termini but is shorter compared to isoform a.
    Source sequence(s)
    AC007606, AK302297
    Consensus CDS
    CCDS58420.1
    UniProtKB/Swiss-Prot
    Q9H305
    Related
    ENSP00000455050.1, ENST00000562334.5
    Conserved Domains (1) summary
    pfam10601
    Location:58 → 126
    zf-LITAF-like; LITAF-like zinc ribbon domain

  4. NM_013399.3 → NP_037531.2  cell death-inducing p53-target protein 1 isoform a

    See identical proteins and their annotated locations for NP_037531.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 both encode the same isoform (a).
    Source sequence(s)
    AC007606, BC002882, DA055704
    Consensus CDS
    CCDS42114.1
    UniProtKB/Swiss-Prot
    A8K7M1, B4DFU1, B4DY75, D3DUD6, Q96ID8, Q9H0Q4, Q9H305, Q9P112
    Related
    ENSP00000457877.1, ENST00000567695.6
    Conserved Domains (1) summary
    pfam10601
    Location:137 → 203
    zf-LITAF-like; LITAF-like zinc ribbon domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    4510669..4538773 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047434044.1 → XP_047290000.1  cell death-inducing p53-target protein 1 isoform X1

    UniProtKB/Swiss-Prot
    A8K7M1, B4DFU1, B4DY75, D3DUD6, Q96ID8, Q9H0Q4, Q9H305, Q9P112

  2. XM_047434043.1 → XP_047289999.1  cell death-inducing p53-target protein 1 isoform X1

    UniProtKB/Swiss-Prot
    A8K7M1, B4DFU1, B4DY75, D3DUD6, Q96ID8, Q9H0Q4, Q9H305, Q9P112

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NT_187608.1 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    212992..216989 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    4540144..4568234 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054380198.1 → XP_054236173.1  cell death-inducing p53-target protein 1 isoform X1

    UniProtKB/Swiss-Prot
    A8K7M1, B4DFU1, B4DY75, D3DUD6, Q96ID8, Q9H0Q4, Q9H305, Q9P112

  2. XM_054380197.1 → XP_054236172.1  cell death-inducing p53-target protein 1 isoform X1

    UniProtKB/Swiss-Prot
    A8K7M1, B4DFU1, B4DY75, D3DUD6, Q96ID8, Q9H0Q4, Q9H305, Q9P112
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9H305.1 GenPept UniProtKB/Swiss-Prot:Q9H305

Gene LinkOut

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