MMGT1

protein-coding

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

Gene summary

Contributes to membrane insertase activity. Involved in protein insertion into ER membrane by stop-transfer membrane-anchor sequence and tail-anchored membrane protein insertion into ER membrane. Located in endoplasmic reticulum membrane. Part of EMC complex. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

TMEM32

MANE transcript

NM_173470.3

Inheritance

ClinVar variants

U:58B:1

Top phenotype

Hypotonia

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chrX:135,960,588-135,974,029

External References & Databases

Ensembl (ENSG00000169446)

Transcript & Mutation Effects

hg38 • Region Span ~13.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

neurodevelopmental disorderMODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0700092

Submitter: PanelApp Australia

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to MMGT1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 12

not providedTotal: 1

HypotoniaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_173470.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			6 clinvar	1 clinvar		7
missense			35 clinvar			35
nonsense			4 clinvar			4
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			13 clinvar			13
Total	0	0	58	1	0	59

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 14 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_173470.3	RefSeq	NP_775741.1	4	MANE Select
ENST00000305963.3	Ensembl	ENSP00000306220.2	4	MANE Select
NM_001330000.2	RefSeq	NP_001316929.1	4	Standard
ENST00000679621.1	Ensembl	ENSP00000505226.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Transport of small molecules
Miscellaneous transport and binding events

Biological Process

cobalt ion transport
copper ion transport
magnesium ion transport
iron ion transmembrane transport
magnesium ion transmembrane transport

Molecular Function

cobalt ion transmembrane transporter activity
ferrous iron transmembrane transporter activity
magnesium ion transmembrane transporter activity
inorganic cation transmembrane transporter activity

Cellular Component

Golgi membrane
early endosome
Golgi apparatus
plasma membrane
membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000305963
Coding exons: 4
Length: 11994
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.22	30	55.6	0.540	0.00000457	827
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Mediates Mg(2+) transport. {ECO:0000250|UniProtKB:Q8K273}.;

Recessive Scores

pRec: 0.109

Intolerance Scores

LoFtool: 0.184
RVIS EVS: 0.08
RVIS percentile EVS: 59.43

Essentials

Essential (CRISPR): E
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.136

Gene Damage Prediction

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