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GeneBe

RNGTT

RNA guanylyltransferase and 5'-phosphatase, the group of Atypical dual specificity phosphatases

Basic information

Region (hg38): 6:88609896-88963618

Links

ENSG00000111880NCBI:8732OMIM:603512HGNC:10073Uniprot:O60942AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RNGTT gene.

  • Inborn genetic diseases (10 variants)

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
10
clinvar
10
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 10 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)3155501
6-88612787-G-A not specified Uncertain significance (Jan 03, 2022)2341586
6-88612788-T-A not specified Uncertain significance (Apr 07, 2023)2535014
6-88801569-T-C not specified Uncertain significance (Oct 03, 2023)3155500
6-88801608-C-G not specified Uncertain significance (Aug 05, 2023)2616627
6-88844398-C-T not specified Uncertain significance (May 27, 2022)2370307
6-88844418-T-C not specified Uncertain significance (Dec 19, 2022)2241557
6-88891840-G-C not specified Uncertain significance (Apr 12, 2022)2283114
6-88904782-C-T not specified Uncertain significance (Nov 10, 2022)2341564
6-88904839-G-A not specified Uncertain significance (Mar 07, 2024)3155503
6-88904876-G-A not specified Uncertain significance (Jun 21, 2022)2295944
6-88929007-T-G not specified Uncertain significance (Jan 29, 2024)3155502
6-88929017-C-T Inborn genetic diseases Uncertain significance (Nov 29, 2021)2396714
6-88941078-C-A not specified Uncertain significance (Oct 12, 2021)2254944

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RNGTTprotein_codingprotein_codingENST00000369485 16353364
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.3740.6261257310171257480.0000676
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense3.001743260.5330.00001703943
Missense in Polyphen37110.820.333881386
Synonymous0.555991060.9320.000005361061
Loss of Function4.27835.40.2260.00000200430

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001870.000185
Ashkenazi Jewish0.000.00
East Asian0.0001180.000109
Finnish0.00004620.0000462
European (Non-Finnish)0.00006410.0000615
Middle Eastern0.0001180.000109
South Asian0.0001310.000131
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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