RTCB

RNA 2',3'-cyclic phosphate and 5'-OH ligase, the group of tRNA splicing ligase complex

Basic information

Region (hg38): 22:32387582-32412248

Previous symbols: [ "C22orf28" ]

Links

ENSG00000100220 ∙ NCBI:51493 ∙ OMIM:613901 ∙ HGNC:26935 ∙ Uniprot:Q9Y3I0 ∙ 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 RTCB gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RTCB 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					2	2
missense			18			18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	18	0	2

Variants in RTCB

This is a list of pathogenic ClinVar variants found in the RTCB region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
22-32388040-G-C		not specified	Uncertain significance (Sep 27, 2022)
22-32392286-A-G		not specified	Uncertain significance (Aug 30, 2021)
22-32393947-A-G		not specified	Uncertain significance (Sep 29, 2023)
22-32395072-G-A		not specified	Uncertain significance (Oct 25, 2023)
22-32395091-C-T		not specified	Uncertain significance (Mar 01, 2023)
22-32395103-G-A		not specified	Uncertain significance (Jun 29, 2022)
22-32395126-T-C		not specified	Uncertain significance (Mar 20, 2023)
22-32395164-C-G			Benign (Dec 18, 2017)
22-32395172-G-T		not specified	Uncertain significance (May 11, 2022)
22-32395208-C-A		not specified	Uncertain significance (Jun 22, 2024)
22-32395208-C-T		not specified	Uncertain significance (Nov 17, 2022)
22-32396088-A-G		not specified	Uncertain significance (Dec 19, 2022)
22-32396165-G-A		not specified	Uncertain significance (Sep 20, 2023)
22-32396178-C-T		not specified	Uncertain significance (Jun 17, 2024)
22-32396183-G-A		not specified	Uncertain significance (Mar 26, 2024)
22-32396205-T-C		not specified	Uncertain significance (Sep 01, 2021)
22-32396236-A-G			Benign (Jul 13, 2018)
22-32398033-T-C		not specified	Uncertain significance (Jan 04, 2024)
22-32398100-A-G		not specified	Likely benign (Mar 12, 2024)
22-32399623-T-C		not specified	Uncertain significance (Jan 20, 2023)
22-32399686-C-G		not specified	Uncertain significance (Jun 30, 2023)
22-32401757-T-C		not specified	Uncertain significance (Sep 20, 2023)
22-32401866-C-G		not specified	Uncertain significance (Dec 15, 2022)
22-32406701-C-T		not specified	Uncertain significance (Apr 15, 2024)
22-32406709-T-C		not specified	Uncertain significance (Apr 24, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RTCB	protein_coding	protein_coding	ENST00000216038	12	24674

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00521	0.995	125711	0	36	125747	0.000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.57	218	294	0.742	0.0000153	3324
Missense in Polyphen		63	121.71	0.51763		1371
Synonymous	-1.02	115	102	1.13	0.00000526	956
Loss of Function	3.23	9	27.2	0.331	0.00000152	305

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000148	0.000148
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.000163	0.000163
Finnish	0.000185	0.000185
European (Non-Finnish)	0.000185	0.000176
Middle Eastern	0.000163	0.000163
South Asian	0.0000327	0.0000327
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalytic subunit of the tRNA-splicing ligase complex that acts by directly joining spliced tRNA halves to mature-sized tRNAs by incorporating the precursor-derived splice junction phosphate into the mature tRNA as a canonical 3',5'- phosphodiester. May act as an RNA ligase with broad substrate specificity, and may function toward other RNAs. {ECO:0000269|PubMed:21311021, ECO:0000269|PubMed:24870230}.
• Pathway: tRNA processing;Metabolism of RNA;tRNA processing in the nucleus (Consensus)

Recessive Scores

• pRec: 0.182

Intolerance Scores

• rvis_EVS: -0.8
• rvis_percentile_EVS: 12.24

Haploinsufficiency Scores

• pHI: 0.137
• hipred: Y
• hipred_score: 0.756
• ghis: 0.642

Essentials

• essential_gene_CRISPR: E
• essential_gene_gene_trap: E

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rtcb
• Phenotype: immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: tRNA exon ligation utilizing 2',3' cyclic phosphate of 5'-exon as source of linkage phosphate;in utero embryonic development;placenta development;tRNA splicing, via endonucleolytic cleavage and ligation
• Cellular component: nucleus;nuclear envelope;nucleoplasm;cytoplasm;endoplasmic reticulum membrane;cytosol;intracellular membrane-bounded organelle;tRNA-splicing ligase complex
• Molecular function: RNA binding;RNA ligase (ATP) activity;protein binding;ATP binding;vinculin binding;metal ion binding