MTX3

metaxin 3, the group of Metaxins

Basic information

Region (hg38): 5:79976716-79991262

Links

ENSG00000177034 ∙ NCBI:345778 ∙ OMIM:619336 ∙ HGNC:24812 ∙ Uniprot:Q5HYI7 ∙ 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 MTX3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MTX3 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			15			15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	0	0

Variants in MTX3

This is a list of pathogenic ClinVar variants found in the MTX3 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-79985590-T-C		not specified	Uncertain significance (Aug 02, 2021)
5-79985633-C-T		not specified	Uncertain significance (May 11, 2022)
5-79985644-C-T		not specified	Uncertain significance (Oct 05, 2021)
5-79986955-A-G		not specified	Uncertain significance (Dec 14, 2023)
5-79986958-C-T		not specified	Uncertain significance (May 29, 2024)
5-79987097-A-C		not specified	Uncertain significance (Dec 13, 2023)
5-79987106-G-A		not specified	Uncertain significance (Dec 09, 2023)
5-79988242-T-G		not specified	Uncertain significance (Nov 01, 2022)
5-79988273-T-C		not specified	Uncertain significance (Jun 16, 2024)
5-79988305-T-A		not specified	Uncertain significance (Jan 27, 2022)
5-79988473-C-T		not specified	Uncertain significance (Aug 12, 2021)
5-79988485-G-A		not specified	Uncertain significance (Dec 02, 2022)
5-79988560-A-C		not specified	Uncertain significance (Jul 15, 2021)
5-79988591-C-A		not specified	Uncertain significance (Mar 18, 2024)
5-79989166-G-A		not specified	Uncertain significance (May 23, 2023)
5-79989216-G-C		not specified	Uncertain significance (Jun 30, 2022)
5-79989217-C-T		not specified	Uncertain significance (Dec 16, 2023)
5-79989235-C-T		not specified	Uncertain significance (Dec 08, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MTX3	protein_coding	protein_coding	ENST00000512560	7	11499

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000165	0.890	124610	0	25	124635	0.000100

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.124	118	122	0.968	0.00000617	1618
Missense in Polyphen		40	49.693	0.80494		695
Synonymous	0.325	42	44.8	0.938	0.00000215	493
Loss of Function	1.46	8	13.8	0.578	7.50e-7	165

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000472	0.000472
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000139	0.000139
European (Non-Finnish)	0.0000890	0.0000885
Middle Eastern	0.00	0.00
South Asian	0.0000683	0.0000654
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Could function in transport of proteins into the mitochondrion. {ECO:0000250}.

Recessive Scores

• pRec: 0.103

Intolerance Scores

• loftool: 0.877
• rvis_EVS: 0.51
• rvis_percentile_EVS: 80.01

Haploinsufficiency Scores

• pHI: 0.306
• hipred: N
• hipred_score: 0.239
• ghis: 0.467

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00903

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mtx3

Gene ontology

• Biological process: protein transport
• Cellular component: mitochondrial sorting and assembly machinery complex