MRS2

protein-coding

magnesium transporter MRS2

Gene summary

Enables magnesium ion transmembrane transporter activity. Involved in mitochondrial magnesium ion transmembrane transport. Located in mitochondrion. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

MRS2L

MANE transcript

NM_020662.4

Inheritance

—

ClinVar variants

P:1U:70B:1

Top phenotype

Leber-like hereditary optic neuropathy, autosomal recessive

gnomAD constraint

pLI —, LoF o/e 0.64

Max pathogenic AF

—

Genomic locus

chr6:24,402,908-24,426,194

External References & Databases

Ensembl (ENSG00000124532)

Transcript & Mutation Effects

hg38 • Region Span ~23.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to MRS2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 61

Leber-like hereditary optic neuropathy, autosomal recessiveTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020662.4. 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			1 clinvar			1
missense			64 clinvar	1 clinvar		65
nonsense			1 clinvar			1
start loss						0
frameshift	1 clinvar					1
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	1	0	70	1	0	72

Highest pathogenic variant AF is 0.00006160976

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 63 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_020662.4	RefSeq	NP_065713.1	11	MANE Select
ENST00000378386.8	Ensembl	ENSP00000367637.3	11	MANE Select
NM_001286264.2	RefSeq	NP_001273193.1	12	Standard
NM_001286265.2	RefSeq	NP_001273194.1	10	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

magnesium ion transport
mitochondrial magnesium ion transmembrane transport
transmembrane transport

Molecular Function

magnesium ion transmembrane transporter activity

Cellular Component

mitochondrion
mitochondrial inner membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000378386
Coding exons: 11
Length: 22658
Individuals with no LoFs: 125687
Homozygous LoFs: 0
Heterozygous LoFs: 61
Defined: 125748
p: 0.000243

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.703	207	237	0.872	0.0000119	2863
Missense (PolyPhen)		64	77.071	0.8304		1010
Synonymous	-0.415	93	88.1	1.06	0.00000427	872
Loss of Function	1.67	16	25.0	0.640	0.00000134	284

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000064	0.000062	rare
Latino/Admixed American	0.00034	0.00032	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00028	0.00027	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00030	0.00030	rare
South Asian	0.00024	0.00023	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Magnesium transporter that mediates the influx of magnesium into the mitochondrial matrix (PubMed:11401429, PubMed:18384665). Required for normal expression of the mitochondrial respiratory complex I subunits (PubMed:18384665). {ECO:0000269|PubMed:11401429, ECO:0000269|PubMed:18384665}.;

Recessive Scores

pRec: 0.465

Intolerance Scores

LoFtool: 0.884
RVIS EVS: 0.31
RVIS percentile EVS: 72.66

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.102

Gene Damage Prediction

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