MMGT1

membrane magnesium transporter 1, the group of ER membrane protein complex subunits

Basic information

Region (hg38): X:135960588-135974029

Previous symbols: [ "TMEM32" ]

Links

ENSG00000169446 ∙ NCBI:93380 ∙ OMIM:301098 ∙ HGNC:28100 ∙ Uniprot:Q8N4V1 ∙ 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 MMGT1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MMGT1 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			5			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					4	4
Total	0	0	5	1	4

Variants in MMGT1

This is a list of pathogenic ClinVar variants found in the MMGT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-135965029-G-A		not specified	Uncertain significance (Nov 17, 2023)
X-135965031-C-T		not specified	Uncertain significance (Apr 22, 2024)
X-135965032-G-A		not specified	Uncertain significance (Nov 17, 2022)
X-135965059-A-G			Likely benign (Sep 01, 2022)
X-135965068-T-G		not specified	Uncertain significance (Dec 21, 2023)
X-135965115-C-T		not specified	Uncertain significance (Jun 21, 2022)
X-135967168-G-A			Benign (May 14, 2021)
X-135967453-T-C		not specified	Uncertain significance (Feb 17, 2024)
X-135970904-G-C			Benign (May 13, 2021)
X-135973535-T-C			Benign (May 13, 2021)
X-135973974-C-T			Benign (May 13, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MMGT1	protein_coding	protein_coding	ENST00000305963	4	11994

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.798	0.197	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.22	30	55.6	0.540	0.00000457	827
Missense in Polyphen		5	19.022	0.26285		296
Synonymous	0.521	19	22.1	0.859	0.00000173	278
Loss of Function	2.13	0	5.30	0.00	4.69e-7	73

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mediates Mg(2+) transport. {ECO:0000250|UniProtKB:Q8K273}.
• Pathway: Transport of small molecules;Miscellaneous transport and binding events (Consensus)

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.184
• rvis_EVS: 0.08
• rvis_percentile_EVS: 59.43

Haploinsufficiency Scores

• pHI: 0.453
• hipred: N
• hipred_score: 0.385
• ghis: 0.542

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.136

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mmgt1

Gene ontology

• Biological process: cobalt ion transport;copper ion transport;magnesium ion transport;iron ion transmembrane transport;magnesium ion transmembrane transport
• Cellular component: Golgi membrane;early endosome;Golgi apparatus;plasma membrane;membrane;integral component of membrane;early endosome membrane;ER membrane protein complex
• Molecular function: cobalt ion transmembrane transporter activity;ferrous iron transmembrane transporter activity;magnesium ion transmembrane transporter activity;inorganic cation transmembrane transporter activity