MTX1

metaxin 1, the group of Metaxins

Basic information

Region (hg38): 1:155208694-155213824

Previous symbols: [ "MTX" ]

Links

ENSG00000173171 ∙ NCBI:4580 ∙ OMIM:600605 ∙ HGNC:7504 ∙ Uniprot:Q13505 ∙ 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 MTX1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MTX1 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			14		1	15
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	15	0	1

Variants in MTX1

This is a list of pathogenic ClinVar variants found in the MTX1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-155208864-G-T		not specified	Uncertain significance (Jun 17, 2024)
1-155208917-G-T		not specified	Uncertain significance (Feb 27, 2024)
1-155208962-G-A		not specified	Uncertain significance (Apr 26, 2023)
1-155208991-T-A			Benign (Dec 31, 2019)
1-155209016-C-G		not specified	Uncertain significance (Oct 30, 2023)
1-155209057-C-T		not specified	Uncertain significance (Feb 13, 2023)
1-155209091-G-A		not specified	Uncertain significance (Dec 02, 2022)
1-155209106-G-A		not specified	Uncertain significance (Jan 17, 2024)
1-155209130-C-T		not specified	Uncertain significance (Dec 12, 2023)
1-155209132-C-A		not specified	Uncertain significance (Sep 27, 2021)
1-155209148-G-A		not specified	Uncertain significance (Mar 01, 2024)
1-155209154-T-C		not specified	Uncertain significance (Jul 21, 2021)
1-155209159-G-A		not specified	Uncertain significance (Jan 05, 2022)
1-155209163-C-G		not specified	Uncertain significance (Nov 17, 2022)
1-155209232-C-T		not specified	Uncertain significance (Mar 05, 2024)
1-155209288-G-T		not specified	Uncertain significance (Dec 15, 2023)
1-155209621-C-T		not specified	Uncertain significance (Jan 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MTX1	protein_coding	protein_coding	ENST00000368376	8	5126

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0133	0.981	125734	0	13	125747	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.190	197	190	1.04	0.0000101	2898
Missense in Polyphen		64	63.963	1.0006		1039
Synonymous	-0.902	86	76.0	1.13	0.00000372	1018
Loss of Function	2.40	6	16.5	0.364	9.26e-7	221

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000118	0.000118
Ashkenazi Jewish	0.00	0.00
East Asian	0.000110	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000540	0.0000527
Middle Eastern	0.000110	0.000109
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in transport of proteins into the mitochondrion. Essential for embryonic development (By similarity). {ECO:0000250}.
• Pathway: miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;Metabolism of proteins;Mitochondrial protein import (Consensus)

Recessive Scores

• pRec: 0.0982

Haploinsufficiency Scores

• pHI: 0.298
• hipred: N
• hipred_score: 0.481
• ghis: 0.537

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.603

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mtx1
• Phenotype: homeostasis/metabolism 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)

Gene ontology

• Biological process: lactation;protein transport
• Cellular component: mitochondrial sorting and assembly machinery complex;integral component of membrane