RTCA

RNA 3'-terminal phosphate cyclase, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 1:100266216-100292769

Previous symbols: [ "RTCD1" ]

Links

ENSG00000137996 ∙ NCBI:8634 ∙ OMIM:611286 ∙ HGNC:17981 ∙ Uniprot:O00442 ∙ 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 RTCA gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RTCA 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					1	1
missense			25	2		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	2	1

Variants in RTCA

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

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

Position	Type	Phenotype	Significance	ClinVar
1-100266406-A-G		not specified	Likely benign (May 13, 2022)
1-100266584-G-A		not specified	Uncertain significance (Jun 16, 2023)
1-100266617-G-T		not specified	Uncertain significance (Feb 27, 2023)
1-100268164-A-C		not specified	Uncertain significance (Dec 03, 2021)
1-100268257-C-G		not specified	Uncertain significance (Jan 23, 2023)
1-100268272-C-A		not specified	Uncertain significance (Nov 12, 2021)
1-100270579-G-T		not specified	Uncertain significance (Nov 10, 2022)
1-100270580-T-A		not specified	Uncertain significance (Feb 28, 2023)
1-100270653-G-A		not specified	Uncertain significance (Apr 22, 2022)
1-100273401-A-G		not specified	Uncertain significance (Jun 26, 2023)
1-100274841-G-C		not specified	Uncertain significance (May 05, 2022)
1-100274856-T-C		not specified	Uncertain significance (May 26, 2023)
1-100274862-G-A		not specified	Uncertain significance (Jun 22, 2021)
1-100274907-G-T		not specified	Uncertain significance (Mar 20, 2023)
1-100274913-G-A		not specified	Uncertain significance (Dec 14, 2021)
1-100274924-A-G		not specified	Uncertain significance (Mar 13, 2023)
1-100274929-T-C			Benign (Jun 20, 2018)
1-100274951-G-A		not specified	Uncertain significance (Sep 27, 2021)
1-100275602-G-A		not specified	Uncertain significance (Jun 13, 2024)
1-100275612-T-C		not specified	Uncertain significance (May 15, 2024)
1-100275720-T-G		not specified	Uncertain significance (Dec 09, 2023)
1-100277266-C-A		not specified	Uncertain significance (Jan 09, 2023)
1-100285236-G-A		not specified	Uncertain significance (Aug 17, 2022)
1-100285288-A-G		not specified	Uncertain significance (Oct 12, 2021)
1-100285317-G-C		not specified	Uncertain significance (Aug 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RTCA	protein_coding	protein_coding	ENST00000260563	12	26563

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.09e-9	0.512	125711	0	36	125747	0.000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.303	195	207	0.941	0.0000104	2445
Missense in Polyphen		41	49.911	0.82146		557
Synonymous	-0.317	77	73.5	1.05	0.00000393	738
Loss of Function	1.10	16	21.5	0.744	0.00000113	266

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000448	0.000448
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000116	0.000114
Middle Eastern	0.000109	0.000109
South Asian	0.000197	0.000196
Other	0.000166	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the conversion of 3'-phosphate to a 2',3'- cyclic phosphodiester at the end of RNA. The mechanism of action of the enzyme occurs in 3 steps: (A) adenylation of the enzyme by ATP; (B) transfer of adenylate to an RNA-N3'P to produce RNA- N3'PP5'A; (C) and attack of the adjacent 2'-hydroxyl on the 3'- phosphorus in the diester linkage to produce the cyclic end product. The biological role of this enzyme is unknown but it is likely to function in some aspects of cellular RNA processing.

Recessive Scores

• pRec: 0.269

Intolerance Scores

• rvis_EVS: 0.37
• rvis_percentile_EVS: 75.29

Haploinsufficiency Scores

• pHI: 0.161
• hipred: N
• hipred_score: 0.397
• ghis: 0.527

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rtca
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: RNA processing
• Cellular component: nucleus;nucleoplasm
• Molecular function: RNA binding;RNA-3'-phosphate cyclase activity;ATP binding