DLEC1
Basic information
Region (hg38): 3:38039205-38124025
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (272 variants)
- not_provided (29 variants)
- Malignant_tumor_of_esophagus (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the DLEC1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000007335.4. Only rare variants are included in the table.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 17 | |||||
missense | 245 | 29 | 279 | |||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 248 | 37 | 11 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
DLEC1 | protein_coding | protein_coding | ENST00000308059 | 37 | 84821 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
2.13e-35 | 0.0848 | 123852 | 4 | 1022 | 124878 | 0.00412 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -0.499 | 1044 | 1.00e+3 | 1.04 | 0.0000560 | 11433 |
Missense in Polyphen | 264 | 257.76 | 1.0242 | 2980 | ||
Synonymous | -0.656 | 422 | 405 | 1.04 | 0.0000233 | 3520 |
Loss of Function | 2.26 | 67 | 90.1 | 0.744 | 0.00000465 | 997 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00469 | 0.00461 |
Ashkenazi Jewish | 0.00335 | 0.00328 |
East Asian | 0.000723 | 0.000723 |
Finnish | 0.00167 | 0.00167 |
European (Non-Finnish) | 0.00677 | 0.00674 |
Middle Eastern | 0.000723 | 0.000723 |
South Asian | 0.00167 | 0.00164 |
Other | 0.00398 | 0.00379 |
dbNSFP
Source:
- Function
- FUNCTION: May act as a tumor suppressor by inhibiting cell proliferation. {ECO:0000269|PubMed:10213508}.;
- Disease
- DISEASE: Lung cancer (LNCR) [MIM:211980]: A common malignancy affecting tissues of the lung. The most common form of lung cancer is non-small cell lung cancer (NSCLC) that can be divided into 3 major histologic subtypes: squamous cell carcinoma, adenocarcinoma, and large cell lung cancer. NSCLC is often diagnosed at an advanced stage and has a poor prognosis. Note=The gene represented in this entry may be involved in disease pathogenesis. DLEC1 silencing due to promoter methylation and aberrant transcription are implicated in the development of lung cancer.; DISEASE: Esophageal cancer (ESCR) [MIM:133239]: A malignancy of the esophagus. The most common types are esophageal squamous cell carcinoma and adenocarcinoma. Cancer of the esophagus remains a devastating disease because it is usually not detected until it has progressed to an advanced incurable stage. {ECO:0000269|PubMed:10213508}. Note=The gene represented in this entry may be involved in disease pathogenesis. DLEC1 silencing due to promoter methylation and aberrant transcription may be implicated in the development of esophageal cancer.;
Recessive Scores
- pRec
- 0.109
Intolerance Scores
- loftool
- 0.935
- rvis_EVS
- 0.16
- rvis_percentile_EVS
- 64.93
Haploinsufficiency Scores
- pHI
- 0.982
- hipred
- N
- hipred_score
- 0.233
- ghis
- 0.489
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.112
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | High |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Dlec1
- Phenotype
- reproductive system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);
Gene ontology
- Biological process
- negative regulation of cell population proliferation
- Cellular component
- cytoplasm;cytosol
- Molecular function
- molecular_function