MTREX

Mtr4 exosome RNA helicase, the group of Nuclear exosome targeting complex|Ski2 like RNA helicases

Basic information

Region (hg38): 5:55307989-55425579

Previous symbols: [ "KIAA0052", "SKIV2L2" ]

Links

ENSG00000039123 ∙ NCBI:23517 ∙ OMIM:618122 ∙ HGNC:18734 ∙ Uniprot:P42285 ∙ 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 MTREX gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MTREX 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				2	2	4
missense			62	2		64
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			5			5
Total	0	0	67	4	2

Variants in MTREX

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

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

Position	Type	Phenotype	Significance	ClinVar
5-55308034-T-G		not specified	Uncertain significance (Oct 30, 2024)
5-55308045-G-A		not specified	Uncertain significance (Jun 12, 2023)
5-55308048-T-C		not specified	Uncertain significance (Dec 10, 2024)
5-55308056-G-A		not specified	Likely benign (Feb 07, 2023)
5-55308070-T-G			Benign (Apr 04, 2018)
5-55308122-C-A		not specified	Uncertain significance (Jan 04, 2024)
5-55308132-C-T		not specified	Uncertain significance (Jun 27, 2023)
5-55308146-G-C		not specified	Uncertain significance (Mar 16, 2024)
5-55322332-G-A		not specified	Likely benign (Nov 15, 2024)
5-55322355-G-A		not specified	Uncertain significance (Jul 31, 2024)
5-55322361-A-G		not specified	Uncertain significance (Sep 15, 2021)
5-55322364-A-C		not specified	Uncertain significance (Jul 12, 2023)
5-55322388-G-A		not specified	Uncertain significance (Jun 13, 2024)
5-55322388-G-T		not specified	Uncertain significance (Oct 01, 2024)
5-55322431-C-T		not specified	Uncertain significance (Feb 08, 2023)
5-55324136-G-A		not specified	Uncertain significance (Dec 19, 2023)
5-55324140-A-G		not specified	Uncertain significance (May 18, 2023)
5-55324170-T-G		not specified	Uncertain significance (Dec 14, 2022)
5-55327717-T-C		not specified	Uncertain significance (Sep 30, 2024)
5-55327759-G-A		not specified	Uncertain significance (Jan 07, 2025)
5-55341729-G-C		not specified	Uncertain significance (Dec 08, 2023)
5-55343359-T-G		not specified	Uncertain significance (Aug 28, 2024)
5-55343382-A-G		not specified	Uncertain significance (Oct 29, 2024)
5-55343384-T-C		not specified	Uncertain significance (Feb 20, 2025)
5-55343405-A-G		not specified	Uncertain significance (Jan 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MTREX	protein_coding	protein_coding	ENST00000230640	27	117822

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.861	0.139	125713	0	33	125746	0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.06	345	546	0.632	0.0000281	6890
Missense in Polyphen		87	216.29	0.40224		2637
Synonymous	-1.25	198	177	1.12	0.00000894	1878
Loss of Function	5.69	12	59.3	0.202	0.00000318	766

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000217	0.000217
Ashkenazi Jewish	0.000104	0.0000992
East Asian	0.000274	0.000272
Finnish	0.000186	0.000185
European (Non-Finnish)	0.0000803	0.0000791
Middle Eastern	0.000274	0.000272
South Asian	0.000238	0.000229
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of exosome targeting complexes. Subunit of the trimeric nuclear exosome targeting (NEXT) complex, a complex that directs a subset of non-coding short-lived RNAs for exosomal degradation. Subunit of the trimeric poly(A) tail exosome targeting (PAXT) complex, a complex that directs a subset of long and polyadenylated poly(A) RNAs for exosomal degradation. The RNA exosome is fundamental for the degradation of RNA in eukaryotic nuclei. Substrate targeting is facilitated by its cofactor MTREX, which links to RNA-binding protein adapters (PubMed:27871484). Associated with the RNA exosome complex and involved in the 3'- processing of the 7S pre-RNA to the mature 5.8S rRNA (PubMed:17412707, PubMed:29107693). May be involved in pre-mRNA splicing. {ECO:0000269|PubMed:17412707, ECO:0000269|PubMed:27871484, ECO:0000269|PubMed:29107693}.
• Pathway: RNA degradation - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.156

Intolerance Scores

• rvis_EVS: -1.15
• rvis_percentile_EVS: 6.23

Haploinsufficiency Scores

• pHI: 0.580
• hipred: Y
• hipred_score: 0.625
• ghis: 0.690

Essentials

• essential_gene_gene_trap: E

Mouse Genome Informatics

• Gene name: Mtrex

Zebrafish Information Network

• Gene name: mtrex
• Affected structure: eye
• Phenotype tag: abnormal
• Phenotype quality: decreased size

Gene ontology

• Biological process: mRNA splicing, via spliceosome;maturation of 5.8S rRNA;rRNA processing;RNA catabolic process
• Cellular component: nuclear exosome (RNase complex);exosome (RNase complex);nucleus;nucleoplasm;nucleolus;TRAMP complex;catalytic step 2 spliceosome
• Molecular function: RNA binding;ATP-dependent RNA helicase activity;protein binding;ATP binding