SMG5
Basic information
Region (hg38): 1:156249224-156282825
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (119 variants)
- not_provided (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SMG5 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000015327.3. 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 | 0 | |||||
| missense | 114 | 120 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 114 | 5 | 1 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SMG5 | protein_coding | protein_coding | ENST00000361813 | 22 | 33606 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0128 | 0.987 | 125721 | 0 | 27 | 125748 | 0.000107 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.13 | 510 | 587 | 0.869 | 0.0000345 | 6627 |
| Missense in Polyphen | 129 | 171.16 | 0.75368 | 1949 | ||
| Synonymous | -0.225 | 229 | 225 | 1.02 | 0.0000123 | 1994 |
| Loss of Function | 5.08 | 15 | 56.1 | 0.268 | 0.00000317 | 614 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000148 | 0.000148 |
| Ashkenazi Jewish | 0.000298 | 0.000298 |
| East Asian | 0.000218 | 0.000217 |
| Finnish | 0.0000924 | 0.0000924 |
| European (Non-Finnish) | 0.0000991 | 0.0000967 |
| Middle Eastern | 0.000218 | 0.000217 |
| South Asian | 0.0000656 | 0.0000653 |
| Other | 0.000165 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Plays a role in nonsense-mediated mRNA decay. Does not have RNase activity by itself. Promotes dephosphorylation of UPF1. Together with SMG7 is thought to provide a link to the mRNA degradation machinery involving exonucleolytic pathways, and to serve as an adapter for UPF1 to protein phosphatase 2A (PP2A), thereby triggering UPF1 dephosphorylation. Necessary for TERT activity. {ECO:0000269|PubMed:17053788}.;
- Pathway
- mRNA surveillance pathway - Homo sapiens (human);Regulation of Telomerase;Signaling events mediated by HDAC Class I
(Consensus)
Recessive Scores
- pRec
- 0.126
Intolerance Scores
- loftool
- 0.506
- rvis_EVS
- -1.02
- rvis_percentile_EVS
- 8.14
Haploinsufficiency Scores
- pHI
- 0.239
- hipred
- Y
- hipred_score
- 0.800
- ghis
- 0.551
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.202
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Smg5
- Phenotype
Zebrafish Information Network
- Gene name
- smg5
- Affected structure
- extension
- Phenotype tag
- abnormal
- Phenotype quality
- decreased thickness
Gene ontology
- Biological process
- nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;mRNA export from nucleus;telomere maintenance via telomerase;regulation of telomere maintenance;regulation of telomere maintenance via telomerase;regulation of dephosphorylation;RNA phosphodiester bond hydrolysis
- Cellular component
- nucleus;telomerase holoenzyme complex;cytoplasm;cytosol
- Molecular function
- protein binding;ubiquitin protein ligase binding;telomeric DNA binding;histone deacetylase binding;protein phosphatase 2A binding;telomerase RNA binding