RNGTT

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

Basic information

Region (hg38): 6:88609897-88963618

Links

ENSG00000111880 ∙ NCBI:8732 ∙ OMIM:603512 ∙ HGNC:10073 ∙ Uniprot:O60942 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

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: gnomAD

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: 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

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Rngtt

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