RO60

Ro60, Y RNA binding protein

Basic information

Region (hg38): 1:193059454-193091777

Previous symbols: [ "SSA2", "TROVE2" ]

Links

ENSG00000116747 ∙ NCBI:6738 ∙ OMIM:600063 ∙ HGNC:11313 ∙ Uniprot:P10155 ∙ 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 RO60 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RO60 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			52			52
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	52	0	1

Variants in RO60

This is a list of pathogenic ClinVar variants found in the RO60 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-193069078-G-A		not specified	Uncertain significance (Feb 23, 2023)
1-193069139-G-C		not specified	Uncertain significance (Dec 28, 2023)
1-193069140-A-T		not specified	Uncertain significance (Dec 28, 2023)
1-193069188-C-T		not specified	Uncertain significance (Jan 23, 2024)
1-193069211-T-A		not specified	Uncertain significance (Dec 30, 2023)
1-193069322-G-C		not specified	Uncertain significance (Mar 27, 2024)
1-193069364-G-A		not specified	Uncertain significance (Dec 13, 2022)
1-193069427-C-G		not specified	Uncertain significance (Jan 24, 2023)
1-193069456-T-G		not specified	Uncertain significance (May 03, 2023)
1-193069496-C-T		not specified	Uncertain significance (Aug 19, 2024)
1-193069512-C-T		not specified	Uncertain significance (Dec 04, 2024)
1-193069520-T-A		not specified	Uncertain significance (Aug 14, 2024)
1-193069616-C-A		not specified	Uncertain significance (May 20, 2024)
1-193069622-C-G		not specified	Uncertain significance (Dec 04, 2024)
1-193069625-T-G		not specified	Uncertain significance (Mar 15, 2024)
1-193075828-A-G		not specified	Uncertain significance (Aug 02, 2023)
1-193075835-C-A		not specified	Uncertain significance (Aug 27, 2024)
1-193075849-A-G		not specified	Uncertain significance (Apr 29, 2024)
1-193075883-A-C		not specified	Uncertain significance (Dec 14, 2023)
1-193075949-G-T		not specified	Uncertain significance (Aug 26, 2022)
1-193075954-A-G		not specified	Uncertain significance (Nov 28, 2024)
1-193075985-A-G		not specified	Uncertain significance (Dec 15, 2023)
1-193075998-A-C		not specified	Uncertain significance (Apr 07, 2023)
1-193076020-A-C		not specified	Uncertain significance (Mar 19, 2024)
1-193076509-G-A			Benign (May 09, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RO60	protein_coding	protein_coding	ENST00000367446	8	32356

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.583	0.417	124750	0	33	124783	0.000132

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.05	240	290	0.827	0.0000147	3533
Missense in Polyphen		63	99.805	0.63123		1205
Synonymous	0.763	88	97.6	0.902	0.00000480	1018
Loss of Function	3.65	5	24.5	0.204	0.00000126	320

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000732	0.000732
Ashkenazi Jewish	0.00	0.00
East Asian	0.000281	0.000278
Finnish	0.00	0.00
European (Non-Finnish)	0.0000531	0.0000353
Middle Eastern	0.000281	0.000278
South Asian	0.0000337	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: RNA-binding protein that binds to misfolded non-coding RNAs, pre-5S rRNA, and several small cytoplasmic RNA molecules known as Y RNAs. May stabilize some of these RNAs and protect them from degradation. {ECO:0000269|PubMed:18056422}.
• Pathway: Systemic lupus erythematosus - Homo sapiens (human) (Consensus)

Intolerance Scores

• loftool: 0.264
• rvis_EVS: -0.34
• rvis_percentile_EVS: 30.56

Haploinsufficiency Scores

• pHI: 0.0999
• hipred: Y
• hipred_score: 0.756
• ghis: 0.641

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.978

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Trove2
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); cellular phenotype; hematopoietic system 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); renal/urinary system phenotype; immune system phenotype

Gene ontology

• Biological process: immune system development;transcription by RNA polymerase III;smoothened signaling pathway;response to UV;cilium assembly
• Cellular component: nucleoplasm;cytosol;ribonucleoprotein complex
• Molecular function: RNA binding;U2 snRNA binding;metal ion binding