THOC3

THO complex subunit 3, the group of WD repeat domain containing|THO complex

Basic information

Region (hg38): 5:175917873-176034680

Links

ENSG00000051596 ∙ NCBI:84321 ∙ OMIM:606929 ∙ HGNC:19072 ∙ Uniprot:Q96J01 ∙ 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 THOC3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the THOC3 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						0
missense			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	0	0

Variants in THOC3

This is a list of pathogenic ClinVar variants found in the THOC3 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-175961361-T-C		not specified	Uncertain significance (Jun 07, 2024)
5-175964993-A-C		not specified	Uncertain significance (Oct 06, 2021)
5-175965068-T-C		not specified	Uncertain significance (Apr 25, 2022)
5-175965122-C-T		not specified	Uncertain significance (Feb 22, 2023)
5-175967185-G-A		not specified	Uncertain significance (Aug 17, 2022)
5-175968018-C-T		not specified	Uncertain significance (Apr 12, 2024)
5-175968045-C-T		not specified	Uncertain significance (Sep 16, 2021)
5-175968091-C-T		not specified	Uncertain significance (Jan 24, 2024)
5-175968117-G-A		not specified	Uncertain significance (Feb 14, 2023)
5-175968118-G-T		not specified	Uncertain significance (Mar 16, 2022)
5-175968168-C-T		not specified	Uncertain significance (Oct 12, 2021)
5-175968199-G-A		not specified	Uncertain significance (Feb 21, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
THOC3	protein_coding	protein_coding	ENST00000265097	6	116808

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0287	0.928	125651	0	24	125675	0.0000955

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.05	86	158	0.543	0.00000788	2269
Missense in Polyphen		17	31.981	0.53156		494
Synonymous	1.02	53	63.3	0.837	0.00000339	624
Loss of Function	1.74	4	9.90	0.404	4.22e-7	155

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000809	0.0000619
Ashkenazi Jewish	0.00	0.00
East Asian	0.000994	0.000979
Finnish	0.00	0.00
European (Non-Finnish)	0.0000278	0.0000264
Middle Eastern	0.000994	0.000979
South Asian	0.0000335	0.0000327
Other	0.000169	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for efficient export of polyadenylated RNA and spliced mRNA. 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. {ECO:0000269|PubMed:11979277, ECO:0000269|PubMed:15833825, ECO:0000269|PubMed:15998806, ECO:0000269|PubMed:17190602, ECO:0000269|PubMed:18974867}.
• Pathway: RNA transport - Homo sapiens (human);Spliceosome - 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: 0.122

Haploinsufficiency Scores

• pHI: 0.146
• ghis: 0.473

Essentials

• essential_gene_CRISPR: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.973

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Thoc3

Gene ontology

• Biological process: RNA export from nucleus;mRNA export from nucleus;RNA splicing;mRNA 3'-end processing;viral mRNA export from host cell nucleus
• Cellular component: transcription export complex;THO complex part of transcription export complex;nuclear chromosome, telomeric region;nucleoplasm;nuclear speck
• Molecular function: RNA binding