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DLEC1 DLEC1 cilia and flagella associated protein [ Homo sapiens (human) ]

Gene ID: 9940, updated on 3-Apr-2024

Summary

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Official Symbol
DLEC1provided by HGNC
Official Full Name
DLEC1 cilia and flagella associated proteinprovided by HGNC
Primary source
HGNC:HGNC:2899
See related
Ensembl:ENSG00000008226 MIM:604050; AllianceGenome:HGNC:2899
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
F56; DLC1; DLC-1; FAP81; CFAP81
Summary
The cytogenetic location of this gene is 3p21.3, and it is located in a region that is commonly deleted in a variety of malignancies. Down-regulation of this gene has been observed in several human cancers including lung, esophageal, renal tumors, and head and neck squamous cell carcinoma. In some cases, reduced expression of this gene in tumor cells is a result of aberrant promoter methylation. Several alternatively spliced transcripts have been observed that contain disrupted coding regions and likely encode nonfunctional proteins.[provided by RefSeq, Mar 2016]
Expression
Biased expression in testis (RPKM 8.8), lung (RPKM 3.8) and 2 other tissues See more
Orthologs
mouse all
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Genomic context

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See DLEC1 in Genome Data Viewer
Location:
3p22.2
Exon count:
38
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (38039208..38124025)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (38043402..38129694)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (38080699..38165516)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 12639 Neighboring gene Sharpr-MPRA regulatory region 7921 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:38035775-38036392 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:38039104-38039674 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14200 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14201 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:38047479-38047979 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:38050723-38051473 Neighboring gene villin like Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14202 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14203 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14204 Neighboring gene phospholipase C delta 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19675 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19676 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:38094034-38094878 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19677 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19678 Neighboring gene protein phosphatase 2 regulatory subunit Bdelta pseudogene 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:38124731-38125295 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:38139347-38139846 Neighboring gene uncharacterized LOC105377033 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:38152870-38153688 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:38158759-38159717 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:38179733-38180676 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19680 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19681 Neighboring gene acetyl-CoA acyltransferase 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:38196601-38197102 Neighboring gene uncharacterized LOC101928234 Neighboring gene MYD88 innate immune signal transduction adaptor Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:38205703-38206902 Neighboring gene oxidative stress responsive kinase 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. PM(2.5) exposure and DLEC1 promoter methylation in Taiwan Biobank participants. Chou YH, et al. Environ Health Prev Med, 2020 Nov 5. PMID 33153431, Free PMC Article
  2. DLEC1 methylation is associated with a better clinical outcome in patients with intrahepatic cholangiocarcinoma of the small duct subtype. Kim Y, et al. Virchows Arch, 2019 Jul. PMID 30610381
  3. DLEC1 is not silenced solely by promoter methylation in head and neck squamous cell carcinoma. Seven D, et al. Gene, 2015 May 25. PMID 25746324
  4. DLEC1, a 3p tumor suppressor, represses NF-κB signaling and is methylated in prostate cancer. Zhang L, et al. J Mol Med (Berl), 2015 Jun. PMID 25648635
  5. Methylation of DLEC1 promoter is a predictor for recurrence in Chinese patients with gastric cancer. Ye X, et al. Dis Markers, 2014. PMID 25574068, Free PMC Article

See all (33) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Dlec1 is required for spermatogenesis and male fertility in mice.
    Title: Dlec1 is required for spermatogenesis and male fertility in mice.
  2. PM2.5 exposure and DLEC1 promoter methylation in Taiwan Biobank participants.
    Title: PM(2.5) exposure and DLEC1 promoter methylation in Taiwan Biobank participants.
  3. Compared with negative methylation (Nm), DLEC1-positive methylation (Pm) was associated with increased GC risk in PS (OR 2.083, 95% CI 1.220-3.558, P = 0.007), but PBX3 Pm was not associated with GC risk.
    Title: Relationship between DLEC1 and PBX3 promoter methylation and the risk and prognosis of gastric cancer in peripheral blood leukocytes.
  4. that the KLF4 and DLEC1 genes can be considered potential methylation biomarkers for uterine leiomyomas
    Title: Different methylation levels in the KLF4, ATF3 and DLEC1 genes in the myometrium and in corpus uteri mesenchymal tumours as assessed by MS-HRM.
  5. DLEC1 methylation can be utilized to identify a subset with a better prognosis in intrahepatic cholangiocarcinomas of the small duct type.
    Title: DLEC1 methylation is associated with a better clinical outcome in patients with intrahepatic cholangiocarcinoma of the small duct subtype.
  6. We found no correlation between the DLEC1, TUSC4 and MLH1 gene expression and NSCLC patient characteristics (gender, age and smoking) or cancer histopathology. No significant differences in the gene expression among NSCLC subtypes indicate the weakness of DLEC1, TUSC4 and MLH1 expression analysis as potential differentiating markers of NSCLC subtypes in the Polish population.
    Title: Small suitability of the DLEC1, MLH1 and TUSC4 mRNA expression analysis as potential prognostic or differentiating markers for NSCLC patients in the Polish population.
  7. the expression levels of DLEC1 and ITGA9 were prominently decreased in lung tumor samples
    Title: Expression level and methylation status of three tumor suppressor genes, DLEC1, ITGA9 and MLH1, in non-small cell lung cancer.
  8. DLEC1 mediates tumor-suppressive activities through NF-kappaB signaling.
    Title: DLEC1, a 3p tumor suppressor, represses NF-κB signaling and is methylated in prostate cancer.
  9. DLEC1 methylation was not associated with the clinicopathological variables of gastric cancer.
    Title: Methylation of DLEC1 promoter is a predictor for recurrence in Chinese patients with gastric cancer.
  10. DLEC1 is down-regulated in head and neck squamous cell tumors and it's promoter methylation is not associated with the clinicopathological parameters.
    Title: DLEC1 is not silenced solely by promoter methylation in head and neck squamous cell carcinoma.
Submit: New GeneRIF Correction See all GeneRIFs (24)

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 alpha-tubulin binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables beta-tubulin binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables molecular_function ND
No biological Data available
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables tubulin binding IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in cell differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in defense response to tumor cell IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of cell population proliferation IEA
Inferred from Electronic Annotation
more info
  
involved_in spermatogenesis ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
is_active_in cilium 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 cytosol IDA
Inferred from Direct Assay
more info
  

General protein information

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Preferred Names
deleted in lung and esophageal cancer protein 1
Names
DLEC, cilia and flagella associated protein
cilia and flagella associated protein 81
deleted in lung and esophageal cancer 1

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_023237.1 RefSeqGene

    Range
    5004..89821
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001321153.2 → NP_001308082.1  deleted in lung and esophageal cancer protein 1 isoform 3

    Status: REVIEWED

    Source sequence(s)
    AB020522, AB425198, AP006309, CB243860
    UniProtKB/TrEMBL
    B1B5Y4

  2. NM_007335.4 → NP_031361.2  deleted in lung and esophageal cancer protein 1 isoform DLEC1-N1

    See identical proteins and their annotated locations for NP_031361.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (DLEC1-N1) encodes the shortest isoform.
    Source sequence(s)
    AB020522, AL137706, AP006309, CB243860
    Consensus CDS
    CCDS2672.2
    UniProtKB/Swiss-Prot
    Q9NSW0, Q9NTG5, Q9Y238
    UniProtKB/TrEMBL
    B7ZW06
    Related
    ENSP00000308597.6, ENST00000308059.11

  3. NM_007337.4 → NP_031363.2  deleted in lung and esophageal cancer protein 1 isoform DLEC1-S3

    See identical proteins and their annotated locations for NP_031363.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (DLEC1-S3) lacks an exon in the 3' coding region that results in a frameshift and use of a downstream stop codon, compared to variant DLEC1-N1. The encoded isoform (DLEC1-S3) has a longer, distinct C-terminus compared to the DLEC1-N1 isoform. There are currently no publicly available full-length transcripts supporting this variant, but it is supported by data in PMID:10213508.
    Source sequence(s)
    AB020522, AL137706, AP006309, CB243860
    UniProtKB/TrEMBL
    B7ZW06
    Related
    ENSP00000315914.5, ENST00000346219.7

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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    38039208..38124025
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011534317.3 → XP_011532619.1  deleted in lung and esophageal cancer protein 1 isoform X1

    UniProtKB/TrEMBL
    B1B5Y4

  2. XM_006713438.4 → XP_006713501.1  deleted in lung and esophageal cancer protein 1 isoform X2

    UniProtKB/TrEMBL
    B1B5Y4

  3. XM_011534318.3 → XP_011532620.1  deleted in lung and esophageal cancer protein 1 isoform X3

    UniProtKB/TrEMBL
    B1B5Y4

  4. XM_006713439.4 → XP_006713502.1  deleted in lung and esophageal cancer protein 1 isoform X4

    UniProtKB/TrEMBL
    B1B5Y4

  5. XM_006713440.4 → XP_006713503.1  deleted in lung and esophageal cancer protein 1 isoform X5

    UniProtKB/TrEMBL
    B1B5Y4

  6. XM_047449369.1 → XP_047305325.1  deleted in lung and esophageal cancer protein 1 isoform X6

  7. XM_047449370.1 → XP_047305326.1  deleted in lung and esophageal cancer protein 1 isoform X7

RNA

  1. XR_940527.3 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    38043402..38129694
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054348647.1 → XP_054204622.1  deleted in lung and esophageal cancer protein 1 isoform X1

  2. XM_054348648.1 → XP_054204623.1  deleted in lung and esophageal cancer protein 1 isoform X2

  3. XM_054348649.1 → XP_054204624.1  deleted in lung and esophageal cancer protein 1 isoform X3

  4. XM_054348650.1 → XP_054204625.1  deleted in lung and esophageal cancer protein 1 isoform X4

  5. XM_054348651.1 → XP_054204626.1  deleted in lung and esophageal cancer protein 1 isoform X5

  6. XM_054348652.1 → XP_054204627.1  deleted in lung and esophageal cancer protein 1 isoform X6

  7. XM_054348653.1 → XP_054204628.1  deleted in lung and esophageal cancer protein 1 isoform X7

RNA

  1. XR_008486873.1 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_007336.1: Suppressed sequence

    Description
    NM_007336.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.

  2. NM_007338.2: Suppressed sequence

    Description
    NM_007338.2: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9Y238.2 GenPept UniProtKB/Swiss-Prot:Q9Y238

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