RNGTT
Basic information
Region (hg38): 6:88609896-88963618
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 RNGTT 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 | 14 | 14 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 14 | 0 | 0 |
Variants in RNGTT
This is a list of pathogenic ClinVar variants found in the RNGTT region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
6-88612765-T-C | not specified | Uncertain significance (Sep 29, 2023) | ||
6-88612787-G-A | not specified | Uncertain significance (Jan 03, 2022) | ||
6-88612788-T-A | not specified | Uncertain significance (Apr 07, 2023) | ||
6-88614329-C-T | not specified | Uncertain significance (Mar 31, 2024) | ||
6-88801569-T-C | not specified | Uncertain significance (Oct 03, 2023) | ||
6-88801608-C-G | not specified | Uncertain significance (Aug 05, 2023) | ||
6-88844398-C-T | not specified | Uncertain significance (May 27, 2022) | ||
6-88844418-T-C | not specified | Uncertain significance (Dec 19, 2022) | ||
6-88844460-A-G | not specified | Uncertain significance (May 20, 2024) | ||
6-88891840-G-C | not specified | Uncertain significance (Apr 12, 2022) | ||
6-88904726-G-A | not specified | Uncertain significance (May 02, 2024) | ||
6-88904782-C-T | not specified | Uncertain significance (Nov 10, 2022) | ||
6-88904783-C-T | not specified | Uncertain significance (May 10, 2024) | ||
6-88904839-G-A | not specified | Uncertain significance (Mar 07, 2024) | ||
6-88904876-G-A | not specified | Uncertain significance (Jun 21, 2022) | ||
6-88929007-T-G | not specified | Uncertain significance (Jan 29, 2024) | ||
6-88929017-C-T | not specified | Uncertain significance (Mar 26, 2024) | ||
6-88941078-C-A | not specified | Uncertain significance (Oct 12, 2021) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
RNGTT | protein_coding | protein_coding | ENST00000369485 | 16 | 353364 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.374 | 0.626 | 125731 | 0 | 17 | 125748 | 0.0000676 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 3.00 | 174 | 326 | 0.533 | 0.0000170 | 3943 |
Missense in Polyphen | 37 | 110.82 | 0.33388 | 1386 | ||
Synonymous | 0.555 | 99 | 106 | 0.932 | 0.00000536 | 1061 |
Loss of Function | 4.27 | 8 | 35.4 | 0.226 | 0.00000200 | 430 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000187 | 0.000185 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000118 | 0.000109 |
Finnish | 0.0000462 | 0.0000462 |
European (Non-Finnish) | 0.0000641 | 0.0000615 |
Middle Eastern | 0.000118 | 0.000109 |
South Asian | 0.000131 | 0.000131 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Bifunctional mRNA-capping enzyme exhibiting RNA 5'- triphosphatase activity in the N-terminal part and mRNA guanylyltransferase activity in the C-terminal part. Catalyzes the first two steps of cap formation: by removing the gamma-phosphate from the 5'-triphosphate end of nascent mRNA to yield a diphosphate end, and by transferring the gmp moiety of GTP to the 5'-diphosphate terminus. {ECO:0000269|PubMed:21636784, ECO:0000269|PubMed:9473487, ECO:0000269|PubMed:9512541}.;
- Pathway
- mRNA surveillance pathway - Homo sapiens (human);mRNA Processing;Disease;RNA Pol II CTD phosphorylation and interaction with CE during HIV infection;Gene expression (Transcription);Transcription of the HIV genome;Late Phase of HIV Life Cycle;HIV Life Cycle;HIV Infection;RNA Pol II CTD phosphorylation and interaction with CE;RNA Polymerase II Transcription;Metabolism of RNA;Infectious disease;mRNA capping;mRNA Capping
(Consensus)
Recessive Scores
- pRec
- 0.197
Intolerance Scores
- loftool
- 0.263
- rvis_EVS
- -0.56
- rvis_percentile_EVS
- 19.54
Haploinsufficiency Scores
- pHI
- 0.841
- hipred
- Y
- hipred_score
- 0.693
- ghis
- 0.637
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.988
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rngtt
- Phenotype
Zebrafish Information Network
- Gene name
- rngtt
- Affected structure
- anatomical system
- Phenotype tag
- abnormal
- Phenotype quality
- quality
Gene ontology
- Biological process
- transcription by RNA polymerase II;7-methylguanosine mRNA capping;RNA processing;viral process;peptidyl-tyrosine dephosphorylation;polynucleotide 5' dephosphorylation
- Cellular component
- nucleus;nucleoplasm
- Molecular function
- mRNA guanylyltransferase activity;polynucleotide 5'-phosphatase activity;protein tyrosine phosphatase activity;protein binding;GTP binding;protein tyrosine/serine/threonine phosphatase activity;RNA guanylyltransferase activity;triphosphatase activity