SFXN1

protein-coding

sideroflexin 1, the group of Solute carrier family 56, sideroflexins

Gene summary

Enables L-alanine transmembrane transporter activity and L-serine transmembrane transporter activity. Involved in L-alanine transport; L-serine transport; and serine import into mitochondrion. Located in mitochondrial inner membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_022754.7

Inheritance

—

ClinVar variants

U:43B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.44

Max pathogenic AF

—

Genomic locus

chr5:175,477,062-175,529,742

External References & Databases

Ensembl (ENSG00000164466)

Transcript & Mutation Effects

hg38 • Region Span ~52.7 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 SFXN1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 37

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_022754.7. 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 clinvar	1 clinvar	3
missense			40 clinvar		1 clinvar	41
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	43	1	2	46

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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_022754.7	RefSeq	NP_073591.2	10	MANE Select
ENST00000321442.10	Ensembl	ENSP00000316905.5	10	MANE Select
NM_001322977.2	RefSeq	NP_001309906.1	10	Standard
NM_001322978.2	RefSeq	NP_001309907.1	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

miR-targeted genes in leukocytes - TarBase
miR-targeted genes in lymphocytes - TarBase
miR-targeted genes in muscle cell - TarBase

Biological Process

iron ion transport
erythrocyte differentiation
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: ENST00000321442
Coding exons: 10
Length: 52681
Individuals with no LoFs: 125729
Homozygous LoFs: 0
Heterozygous LoFs: 18
Defined: 125747
p: 0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.507	170	190	0.896	0.0000108	2109
Missense (PolyPhen)		37	50.935	0.72642		601
Synonymous	0.636	67	74.0	0.906	0.00000489	627
Loss of Function	2.23	8	18.3	0.437	9.42e-7	204

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000064	0.000062	rare
Latino/Admixed American	0.000087	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00022	0.00022	rare
Finnish	0.000092	0.000092	rare
European (Non-Finnish)	0.000062	0.000062	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Might be involved in the transport of a component required for iron utilization into or out of the mitochondria.;

Recessive Scores

pRec: 0.156

Intolerance Scores

LoFtool: 0.496
RVIS EVS: 0.17
RVIS percentile EVS: 65.96

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.712

Gene Damage Prediction

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