MX2

MX dynamin like GTPase 2

Basic information

Region (hg38): 21:41361998-41409393

Links

ENSG00000183486 ∙ NCBI:4600 ∙ OMIM:147890 ∙ HGNC:7533 ∙ Uniprot:P20592 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Tourette syndrome (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MX2 gene.

• Inborn genetic diseases (38 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MX2 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			36	4		40
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	36	5	1

Variants in MX2

This is a list of pathogenic ClinVar variants found in the MX2 region.

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

Position	Type	Phenotype	Significance	ClinVar
21-41370109-C-A			Benign (Feb 24, 2021)
21-41376940-A-G		not specified	Uncertain significance (Oct 25, 2023)
21-41376981-A-C		not specified	Uncertain significance (Mar 24, 2023)
21-41377001-A-T		not specified	Uncertain significance (Jan 24, 2023)
21-41377150-G-A		not specified	Uncertain significance (May 31, 2023)
21-41377790-G-A		not specified	Uncertain significance (Jun 30, 2023)
21-41377831-C-T		not specified	Uncertain significance (Jul 12, 2023)
21-41377886-T-A		not specified	Uncertain significance (Sep 20, 2023)
21-41377906-G-A		not specified	Uncertain significance (Aug 11, 2021)
21-41377912-G-A		not specified	Uncertain significance (Jan 17, 2024)
21-41380067-G-A		not specified	Likely benign (Jul 10, 2023)
21-41380130-G-T		not specified	Uncertain significance (Jul 25, 2023)
21-41382437-G-A		not specified	Uncertain significance (Jul 12, 2022)
21-41382442-A-G		not specified	Uncertain significance (Oct 29, 2021)
21-41382469-A-G		not specified	Uncertain significance (Feb 28, 2023)
21-41382497-C-T		not specified	Uncertain significance (Apr 27, 2023)
21-41382514-G-A		not specified	Uncertain significance (Jun 06, 2023)
21-41382525-G-T		not specified	Uncertain significance (Apr 10, 2023)
21-41382556-G-A		not specified	Uncertain significance (Jun 30, 2022)
21-41382560-T-A		not specified	Uncertain significance (Jul 09, 2021)
21-41390574-C-G		not specified	Uncertain significance (Nov 10, 2021)
21-41390601-C-A		not specified	Uncertain significance (Aug 12, 2021)
21-41390634-G-A		not specified	Uncertain significance (Dec 13, 2022)
21-41390683-C-T		not specified	Uncertain significance (May 17, 2023)
21-41395682-A-G		not specified	Uncertain significance (Jan 17, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MX2	protein_coding	protein_coding	ENST00000330714	13	47448

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.48e-9	0.993	125672	0	76	125748	0.000302

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.582	393	427	0.921	0.0000251	4759
Missense in Polyphen		124	162.61	0.76256		1731
Synonymous	-0.256	175	171	1.02	0.0000113	1343
Loss of Function	2.50	19	34.9	0.544	0.00000188	372

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00120	0.00119
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000326	0.000325
Middle Eastern	0.00	0.00
South Asian	0.000229	0.000229
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Interferon-induced dynamin-like GTPase with potent antiviral activity against human immunodeficiency virus type 1 (HIV-1). Acts by targeting the viral capsid and affects the nuclear uptake and/or stability of the HIV-1 replication complex and the subsequent chromosomal integration of the proviral DNA. Exhibits antiviral activity also against simian immunodeficiency virus (SIV-mnd). May play a role in regulating nucleocytoplasmic transport and cell-cycle progression. {ECO:0000269|PubMed:15184662, ECO:0000269|PubMed:24048477, ECO:0000269|PubMed:24055605, ECO:0000269|PubMed:24121441}.
• Pathway: Vitamin D Receptor Pathway;Cytokine Signaling in Immune system;Immune System;Interferon alpha/beta signaling;ISG15 antiviral mechanism;Antiviral mechanism by IFN-stimulated genes;Interferon Signaling (Consensus)

Intolerance Scores

• loftool: 0.260
• rvis_EVS: -0.35
• rvis_percentile_EVS: 29.56

Haploinsufficiency Scores

• pHI: 0.0374
• hipred: N
• hipred_score: 0.172
• ghis: 0.534

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.472

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mx2

Gene ontology

• Biological process: mitochondrial fission;dynamin family protein polymerization involved in mitochondrial fission;defense response;response to virus;protein transport;response to interferon-alpha;innate immune response;regulation of nucleocytoplasmic transport;mRNA transport;defense response to virus;regulation of cell cycle;type I interferon signaling pathway;membrane fusion
• Cellular component: nucleus;nuclear pore;cytoplasm;cytosol;membrane;mitochondrial membrane
• Molecular function: GTPase activity;protein binding;GTP binding;microtubule binding