DCP2
decapping mRNA 2, the group of Nudix hydrolase family
Basic information
Region (hg38): 5:112976702-113022195
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the DCP2 gene is commonly pathogenic or not.
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.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 17 | 17 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 18 | 0 | 0 |
Variants in DCP2
This is a list of pathogenic ClinVar variants found in the DCP2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 5-112976958-C-T | not specified | Uncertain significance (Dec 21, 2022) | ||
| 5-112985865-AAG-A | Uncertain significance (Feb 20, 2020) | |||
| 5-112985935-C-A | not specified | Uncertain significance (Dec 21, 2022) | ||
| 5-112985938-A-T | not specified | Uncertain significance (Mar 29, 2023) | ||
| 5-112992136-C-T | not specified | Uncertain significance (Dec 06, 2022) | ||
| 5-112992151-A-C | not specified | Uncertain significance (Feb 22, 2023) | ||
| 5-113001442-A-G | not specified | Uncertain significance (Jun 30, 2023) | ||
| 5-113001569-C-T | not specified | Uncertain significance (Dec 07, 2023) | ||
| 5-113001590-G-A | not specified | Uncertain significance (Jan 12, 2024) | ||
| 5-113001644-C-T | not specified | Uncertain significance (Mar 16, 2022) | ||
| 5-113003955-C-T | not specified | Uncertain significance (Feb 13, 2024) | ||
| 5-113003982-G-A | not specified | Uncertain significance (Sep 23, 2023) | ||
| 5-113004003-G-T | not specified | Uncertain significance (Mar 04, 2024) | ||
| 5-113008022-A-C | not specified | Uncertain significance (Feb 10, 2022) | ||
| 5-113008032-A-G | not specified | Uncertain significance (May 30, 2024) | ||
| 5-113010789-C-G | not specified | Uncertain significance (Feb 28, 2023) | ||
| 5-113013350-G-A | not specified | Uncertain significance (Nov 21, 2023) | ||
| 5-113013363-T-C | not specified | Uncertain significance (Apr 07, 2022) | ||
| 5-113013386-G-A | not specified | Uncertain significance (Mar 24, 2023) | ||
| 5-113013390-C-A | not specified | Uncertain significance (May 20, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| DCP2 | protein_coding | protein_coding | ENST00000389063 | 11 | 44269 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.664 | 0.336 | 125734 | 0 | 11 | 125745 | 0.0000437 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.531 | 202 | 224 | 0.900 | 0.0000111 | 2807 |
| Missense in Polyphen | 51 | 90.239 | 0.56517 | 1150 | ||
| Synonymous | -1.65 | 94 | 75.8 | 1.24 | 0.00000389 | 723 |
| Loss of Function | 3.75 | 5 | 25.4 | 0.197 | 0.00000145 | 294 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000289 | 0.0000289 |
| Ashkenazi Jewish | 0.000199 | 0.000198 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000513 | 0.0000462 |
| European (Non-Finnish) | 0.0000352 | 0.0000352 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000654 | 0.0000653 |
| Other | 0.000164 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Decapping metalloenzyme that catalyzes the cleavage of the cap structure on mRNAs (PubMed:12417715, PubMed:12218187, PubMed:12923261, PubMed:21070968). Removes the 7-methyl guanine cap structure from mRNA molecules, yielding a 5'-phosphorylated mRNA fragment and 7m-GDP (PubMed:12486012, PubMed:12923261, PubMed:21070968). Necessary for the degradation of mRNAs, both in normal mRNA turnover and in nonsense-mediated mRNA decay (PubMed:14527413). Plays a role in replication-dependent histone mRNA degradation (PubMed:18172165). Has higher activity towards mRNAs that lack a poly(A) tail (PubMed:21070968). Has no activity towards a cap structure lacking an RNA moiety (PubMed:21070968). Blocks autophagy in nutrient-rich conditions by repressing the expression of ATG-related genes through degration of their transcripts (PubMed:26098573). {ECO:0000269|PubMed:12218187, ECO:0000269|PubMed:12417715, ECO:0000269|PubMed:12486012, ECO:0000269|PubMed:12923261, ECO:0000269|PubMed:14527413, ECO:0000269|PubMed:18172165, ECO:0000269|PubMed:21070968, ECO:0000269|PubMed:26098573}.;
- Pathway
- RNA degradation - Homo sapiens (human);Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA;KSRP (KHSRP) binds and destabilizes mRNA;Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA;Metabolism of RNA;Regulation of mRNA stability by proteins that bind AU-rich elements;mRNA decay by 5, to 3, exoribonuclease;Deadenylation-dependent mRNA decay
(Consensus)
Recessive Scores
- pRec
- 0.108
Intolerance Scores
- loftool
- 0.437
- rvis_EVS
- -0.89
- rvis_percentile_EVS
- 10.3
Haploinsufficiency Scores
- pHI
- 0.480
- hipred
- Y
- hipred_score
- 0.777
- ghis
- 0.643
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.636
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Dcp2
- Phenotype
- pigmentation phenotype; normal phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span);
Gene ontology
- Biological process
- nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;deadenylation-dependent decapping of nuclear-transcribed mRNA;mRNA catabolic process;negative regulation of telomere maintenance via telomerase;regulation of mRNA stability;exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay;histone mRNA catabolic process;RNA phosphodiester bond hydrolysis, exonucleolytic;regulation of telomerase RNA localization to Cajal body
- Cellular component
- P-body;nucleoplasm;cytoplasm;cytosol;RISC complex;cell junction;cytoplasmic ribonucleoprotein granule
- Molecular function
- 5'-3' exoribonuclease activity;protein binding;exoribonuclease activity, producing 5'-phosphomonoesters;manganese ion binding;m7G(5')pppN diphosphatase activity;telomerase RNA binding