SLC41A3

protein-coding

solute carrier family 41 member 3, the group of Solute carrier family 41

Gene summary

Enables magnesium:sodium antiporter activity. Involved in mitochondrial magnesium ion transmembrane transport. Located in mitochondrial inner membrane and plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_017836.4

Inheritance

—

ClinVar variants

U:64B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.89

Max pathogenic AF

—

Genomic locus

chr3:126,006,357-126,101,561

External References & Databases

Ensembl (ENSG00000114544)

Transcript & Mutation Effects

hg38 • Region Span ~95.2 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 SLC41A3 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 58

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_017836.4. 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			3 clinvar			3
missense			57 clinvar	6 clinvar		63
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	64	6	0	70

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 73 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_017836.4	RefSeq	NP_060306.4	10	MANE Select
ENST00000360370.9	Ensembl	ENSP00000353533.4	10	MANE Select
NM_001008485.2	RefSeq	NP_001008485.2	11	Standard
NM_001008486.2	RefSeq	NP_001008486.2	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

cation transmembrane transport

Molecular Function

protein binding
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: ENST00000315891
Coding exons: 11
Length: 95207
Individuals with no LoFs: 125694
Homozygous LoFs: 0
Heterozygous LoFs: 54
Defined: 125748
p: 0.000215

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.594	253	281	0.900	0.0000147	3216
Missense (PolyPhen)		91	98.006	0.92852		1165
Synonymous	0.868	108	120	0.899	0.00000686	1093
Loss of Function	0.479	21	23.5	0.893	0.00000128	241

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.00024	0.00023	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00028	0.00027	rare
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.00025	0.00024	rare
South Asian	0.00033	0.00033	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0862

Intolerance Scores

LoFtool: 0.891
RVIS EVS: 0.29
RVIS percentile EVS: 71.57

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.147

Gene Damage Prediction

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