THOC5

THO complex subunit 5, the group of THO complex

Basic information

Region (hg38): 22:29505878-29555216

Previous symbols: [ "C22orf19" ]

Links

ENSG00000100296 ∙ NCBI:8563 ∙ OMIM:612733 ∙ HGNC:19074 ∙ Uniprot:Q13769 ∙ 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 THOC5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the THOC5 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			20		1	21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	0	2

Variants in THOC5

This is a list of pathogenic ClinVar variants found in the THOC5 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-29508512-C-T		not specified	Uncertain significance (Aug 02, 2021)
22-29512036-G-A			Benign (Dec 31, 2019)
22-29512048-T-A		not specified	Uncertain significance (Feb 21, 2024)
22-29517068-T-C		not specified	Uncertain significance (Apr 19, 2023)
22-29517289-C-T			Benign (Jul 19, 2018)
22-29517303-C-T		not specified	Uncertain significance (May 24, 2024)
22-29519039-G-A		not specified	Uncertain significance (Jan 23, 2024)
22-29519069-T-C		not specified	Uncertain significance (Mar 12, 2024)
22-29519086-C-A		not specified	Uncertain significance (Dec 06, 2021)
22-29519098-G-A		not specified	Uncertain significance (Nov 04, 2022)
22-29520058-A-T		not specified	Uncertain significance (Jul 14, 2023)
22-29525841-G-A		not specified	Uncertain significance (Jun 22, 2021)
22-29525859-A-G		not specified	Uncertain significance (Apr 17, 2023)
22-29525897-G-C		not specified	Uncertain significance (Aug 17, 2022)
22-29528090-G-C		not specified	Uncertain significance (Jun 01, 2023)
22-29528129-C-G		not specified	Uncertain significance (Mar 28, 2023)
22-29528446-C-G		not specified	Uncertain significance (Aug 04, 2023)
22-29529216-C-T		not specified	Uncertain significance (Jun 08, 2022)
22-29531878-G-A		not specified	Uncertain significance (Oct 05, 2023)
22-29531914-T-C		not specified	Uncertain significance (Mar 21, 2023)
22-29531918-C-T		not specified	Uncertain significance (Feb 28, 2023)
22-29531929-G-A		not specified	Uncertain significance (Mar 31, 2024)
22-29539391-T-C		not specified	Uncertain significance (May 03, 2023)
22-29539455-A-T		not specified	Uncertain significance (Apr 28, 2023)
22-29549113-T-C		not specified	Uncertain significance (May 24, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
THOC5	protein_coding	protein_coding	ENST00000490103	19	49338

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0453	0.955	125725	0	23	125748	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.73	296	393	0.754	0.0000220	4512
Missense in Polyphen		45	61.81	0.72804		808
Synonymous	0.879	140	154	0.910	0.00000880	1260
Loss of Function	4.42	11	41.9	0.263	0.00000210	491

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000177	0.000177
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000472	0.0000462
European (Non-Finnish)	0.000124	0.000123
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as component of the THO subcomplex of the TREX complex which is thought to couple mRNA transcription, processing and nuclear export, and which specifically associates with spliced mRNA and not with unspliced pre-mRNA. TREX is recruited to spliced mRNAs by a transcription-independent mechanism, binds to mRNA upstream of the exon-junction complex (EJC) and is recruited in a splicing- and cap-dependent manner to a region near the 5' end of the mRNA where it functions in mRNA export to the cytoplasm via the TAP/NFX1 pathway. The TREX complex is essential for the export of Kaposi's sarcoma-associated herpesvirus (KSHV) intronless mRNAs and infectious virus production. THOC5 in conjunction with ALYREF/THOC4 functions in NXF1-NXT1 mediated nuclear export of HSP70 mRNA; both proteins enhance the RNA binding activity of NXF1 and are required for NXF1 localization to the nuclear rim. Involved in transcription elongation and genome stability. Involved in alternative polyadenylation site choice by recruiting CPSF6 to 5' region of target genes; probably mediates association of the TREX and CFIm complexes.
• Pathway: RNA transport - Homo sapiens (human);Gene expression (Transcription);RNA Polymerase II Transcription;Metabolism of RNA;Cleavage of Growing Transcript in the Termination Region ;RNA Polymerase II Transcription Termination;Transport of Mature mRNA derived from an Intron-Containing Transcript;mRNA 3,-end processing;Transport of Mature Transcript to Cytoplasm;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.0985

Intolerance Scores

• loftool: 0.676
• rvis_EVS: 0.22
• rvis_percentile_EVS: 68.38

Haploinsufficiency Scores

• pHI: 0.0808
• hipred: Y
• hipred_score: 0.637
• ghis: 0.473

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.554

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Thoc5
• 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); hematopoietic system phenotype; liver/biliary system phenotype; immune system phenotype

Gene ontology

• Biological process: RNA export from nucleus;mRNA export from nucleus;RNA splicing;monocyte differentiation;mRNA 3'-end processing;positive regulation of DNA-templated transcription, elongation;viral mRNA export from host cell nucleus;primitive hemopoiesis;negative regulation of DNA damage checkpoint
• Cellular component: nuclear chromosome;transcription export complex;THO complex;THO complex part of transcription export complex;nuclear chromosome, telomeric region;nucleus;nucleoplasm;cytoplasm
• Molecular function: mRNA binding;protein binding