RTRAF

RNA transcription, translation and transport factor, the group of tRNA splicing ligase complex

Basic information

Region (hg38): 14:51989514-52010694

Previous symbols: [ "C14orf166" ]

Links

ENSG00000087302 ∙ NCBI:51637 ∙ OMIM:610858 ∙ HGNC:23169 ∙ Uniprot:Q9Y224 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 14.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
ENST00000261700.8	ENSP00000261700.3	8	yes	-
ENST00000553362.1	ENSP00000451153.1	5	-	-
ENST00000556760.5	ENSP00000451715.1	8	-	-
ENST00000557553.5	ENSP00000451751.1	3	-	-

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RTRAF gene is commonly pathogenic or not. These statistics are base on transcript: NM_000016039.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			3			3
nonsense			1			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			5			5
Total	0	0	9	0	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RTRAF	protein_coding	protein_coding	ENST00000261700	8	15228

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		125727	0	13	125740	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.353	115	126	0.912	0.00000617	1606
Missense in Polyphen		21	34.678	0.60557		516
Synonymous	0.673	38	43.7	0.870	0.00000214	440
Loss of Function	2.71	4	15.5	0.258	8.12e-7	177

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000120	0.000120
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000554	0.0000527
Middle Eastern	0.000109	0.000109
South Asian	0.0000344	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: RNA-binding protein involved in modulation of mRNA transcription by Polymerase II (PubMed:16950395). Component of the tRNA-splicing ligase complex and is required for tRNA ligation (PubMed:24870230). May be required for RNA transport (PubMed:24608264). {ECO:0000269|PubMed:16950395, ECO:0000269|PubMed:24608264, ECO:0000269|PubMed:24870230}.
• Pathway: tRNA processing;Metabolism of RNA;tRNA processing in the nucleus (Consensus)

Recessive Scores

• pRec: 0.142

Intolerance Scores

• rvis_EVS: -0.32
• rvis_percentile_EVS: 31.46

Essentials

• essential_gene_gene_trap: E

Gene ontology

• Biological process: tRNA splicing, via endonucleolytic cleavage and ligation;negative regulation of protein kinase activity;viral process;positive regulation of transcription by RNA polymerase II;RNA transport
• Cellular component: nucleus;nucleoplasm;cytoplasm;centrosome;cytosol;perinuclear region of cytoplasm;tRNA-splicing ligase complex;mitotic spindle
• Molecular function: RNA polymerase II complex binding;RNA binding;protein binding;identical protein binding