DCP1B
Basic information
Region (hg38): 12:1946053-2004535
Links
Phenotypes
GenCC
Source:
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 DCP1B 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 | 3 | |||||
missense | 33 | 38 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 33 | 5 | 3 |
Variants in DCP1B
This is a list of pathogenic ClinVar variants found in the DCP1B region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
12-1946226-C-T | not specified | Uncertain significance (Oct 04, 2022) | ||
12-1946235-T-A | not specified | Uncertain significance (Dec 19, 2023) | ||
12-1946267-T-G | not specified | Uncertain significance (Mar 24, 2023) | ||
12-1949153-G-A | not specified | Uncertain significance (Jul 13, 2021) | ||
12-1949158-C-T | Benign (Dec 31, 2019) | |||
12-1949229-C-T | not specified | Uncertain significance (Jan 17, 2024) | ||
12-1949230-G-A | Likely benign (Dec 31, 2019) | |||
12-1949253-C-T | not specified | Uncertain significance (Aug 14, 2023) | ||
12-1949259-T-G | not specified | Uncertain significance (Sep 25, 2023) | ||
12-1949318-C-T | not specified | Uncertain significance (Mar 15, 2024) | ||
12-1952483-G-A | not specified | Uncertain significance (Dec 02, 2022) | ||
12-1952486-C-G | not specified | Uncertain significance (Apr 07, 2023) | ||
12-1952531-C-T | not specified | Uncertain significance (Dec 20, 2023) | ||
12-1952561-T-C | not specified | Uncertain significance (Aug 19, 2023) | ||
12-1952574-G-A | not specified | Uncertain significance (Oct 22, 2021) | ||
12-1952734-C-G | not specified | Uncertain significance (Jun 30, 2022) | ||
12-1952763-G-A | not specified | Uncertain significance (Dec 22, 2023) | ||
12-1952780-G-A | not specified | Uncertain significance (Apr 07, 2022) | ||
12-1952785-G-C | not specified | Uncertain significance (Apr 25, 2023) | ||
12-1952789-C-T | Benign (Dec 31, 2019) | |||
12-1952829-G-A | not specified | Uncertain significance (Jul 13, 2021) | ||
12-1952860-C-G | not specified | Uncertain significance (Dec 13, 2022) | ||
12-1952883-G-T | not specified | Uncertain significance (Nov 07, 2023) | ||
12-1952910-G-A | not specified | Uncertain significance (Dec 07, 2021) | ||
12-1952924-T-A | not specified | Uncertain significance (Oct 07, 2022) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
DCP1B | protein_coding | protein_coding | ENST00000280665 | 9 | 58482 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.60e-10 | 0.594 | 125677 | 0 | 71 | 125748 | 0.000282 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.532 | 308 | 335 | 0.918 | 0.0000167 | 4011 |
Missense in Polyphen | 50 | 75.01 | 0.66658 | 996 | ||
Synonymous | -0.273 | 133 | 129 | 1.03 | 0.00000675 | 1258 |
Loss of Function | 1.34 | 19 | 26.4 | 0.719 | 0.00000122 | 313 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00104 | 0.00104 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000662 | 0.000653 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.000231 | 0.000229 |
Middle Eastern | 0.000662 | 0.000653 |
South Asian | 0.000116 | 0.0000980 |
Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: May play a role in the degradation of mRNAs, both in normal mRNA turnover and in nonsense-mediated mRNA decay. May remove the 7-methyl guanine cap structure from mRNA molecules, yielding a 5'-phosphorylated mRNA fragment and 7m-GDP (By similarity). {ECO:0000250}.;
- Pathway
- RNA degradation - Homo sapiens (human);Metabolism of RNA;p73 transcription factor network;mRNA decay by 5, to 3, exoribonuclease;Deadenylation-dependent mRNA decay
(Consensus)
Recessive Scores
- pRec
- 0.0845
Intolerance Scores
- loftool
- 0.833
- rvis_EVS
- 0.71
- rvis_percentile_EVS
- 85.76
Haploinsufficiency Scores
- pHI
- 0.0877
- hipred
- N
- hipred_score
- 0.379
- ghis
- 0.465
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.841
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Dcp1b
- Phenotype
Gene ontology
- Biological process
- nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;deadenylation-dependent decapping of nuclear-transcribed mRNA;deadenylation-independent decapping of nuclear-transcribed mRNA;positive regulation of catalytic activity;exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay
- Cellular component
- P-body;nucleus;cytosol;membrane;intracellular membrane-bounded organelle
- Molecular function
- protein binding;enzyme activator activity;hydrolase activity