SLC41A2

protein-coding

solute carrier family 41 member 2, the group of Solute carrier family 41

Gene summary

Predicted to enable magnesium ion transmembrane transporter activity. Involved in magnesium ion transport. Located in plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001352171.3

Inheritance

—

ClinVar variants

U:65B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.13

Max pathogenic AF

—

Genomic locus

chr12:104,801,801-104,958,744

External References & Databases

Ensembl (ENSG00000136052)

Transcript & Mutation Effects

hg38 • Region Span ~156.9 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 SLC41A2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 60

not providedTotal: 6

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001352171.3. 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						0
missense			62 clinvar	1 clinvar		63
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	65	1	0	66

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 51 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001352171.3	RefSeq	NP_001339100.1	10	MANE Select
ENST00000258538.8	Ensembl	ENSP00000258538.3	10	MANE Select
NM_001352169.2	RefSeq	NP_001339098.1	10	Standard
NM_001352170.3	RefSeq	NP_001339099.1	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Transport of bile salts and organic acids, metal ions and amine compounds
SLC-mediated transmembrane transport
Transport of small molecules
Metal ion SLC transporters

Biological Process

magnesium ion transmembrane transport

Molecular Function

protein binding
magnesium ion transmembrane transporter activity
divalent inorganic cation transmembrane transporter activity

Cellular Component

plasma membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000258538
Coding exons: 10
Length: 156192
Individuals with no LoFs: 125727
Homozygous LoFs: 0
Heterozygous LoFs: 16
Defined: 125743
p: 0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.78	207	293	0.707	0.0000135	3740
Missense (PolyPhen)		52	98.313	0.52893		1279
Synonymous	1.70	83	105	0.789	0.00000531	1131
Loss of Function	3.94	3	23.7	0.126	0.00000100	325

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000076	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.00011	0.00011	rare
South Asian	0.000066	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Acts as a plasma-membrane magnesium transporter. {ECO:0000269|PubMed:16984228}.;

Recessive Scores

pRec: 0.109

Intolerance Scores

LoFtool: 0.336
RVIS EVS: -0.16
RVIS percentile EVS: 41.64

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.472

Gene Damage Prediction

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