SFXN3

protein-coding

sideroflexin 3, the group of Solute carrier family 56, sideroflexins

Gene summary

Enables L-serine transmembrane transporter activity. Involved in serine import into mitochondrion. Located in mitochondrion. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_030971.6

Inheritance

—

ClinVar variants

U:50B:1

Top phenotype

Neurodevelopmental disorder

gnomAD constraint

pLI —, LoF o/e 0.76

Max pathogenic AF

—

Genomic locus

chr10:101,031,234-101,041,241

External References & Databases

Ensembl (ENSG00000107819)

Transcript & Mutation Effects

hg38 • Region Span ~10.0 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 SFXN3 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 41

not providedTotal: 3

Neurodevelopmental disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_030971.6. 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			43 clinvar	1 clinvar		44
nonsense			1 clinvar			1
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	50	1	0	51

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 48 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_030971.6	RefSeq	NP_112233.3	10	MANE Select
ENST00000393459.6	Ensembl	ENSP00000377103.1	10	MANE Select
NM_001388027.1	RefSeq	NP_001374956.1	11	Standard
NM_001388028.1	RefSeq	NP_001374957.1	11	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Urea cycle and metabolism of arginine, proline, glutamate, aspartate and asparagine
Validated targets of C-MYC transcriptional repression

Biological Process

ion transmembrane transport
iron ion homeostasis

Molecular Function

ion transmembrane transporter activity

Cellular Component

mitochondrion
integral component of membrane
mitochondrial membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000224807
Coding exons: 11
Length: 10008
Individuals with no LoFs: 125007
Homozygous LoFs: 3
Heterozygous LoFs: 738
Defined: 125748
p: 0.00295

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.436	173	190	0.911	0.0000104	2098
Missense (PolyPhen)		47	49.712	0.94544		550
Synonymous	-0.0911	78	77.0	1.01	0.00000449	672
Loss of Function	0.947	14	18.4	0.762	8.57e-7	201

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00087	0.00086	rare
Latino/Admixed American	0.0038	0.0038	notable
Ashkenazi Jewish	0.0034	0.0034	notable
East Asian	0.00071	0.00071	rare
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.0044	0.0044	notable
South Asian	0.00059	0.00056	rare
Other	0.0049	0.0049	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Potential iron transporter.;

Recessive Scores

pRec: 0.0883

Intolerance Scores

LoFtool: 0.871
RVIS EVS: 0.33
RVIS percentile EVS: 73.41

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.273

Gene Damage Prediction

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