SFXN2

protein-coding

sideroflexin 2, the group of Solute carrier family 56, sideroflexins

Gene summary

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

MANE transcript

NM_178858.6

Inheritance

—

ClinVar variants

U:60B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.43

Max pathogenic AF

—

Genomic locus

chr10:102,714,538-102,743,492

External References & Databases

Ensembl (ENSG00000156398)

Transcript & Mutation Effects

hg38 • Region Span ~29.0 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 SFXN2 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 56

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_178858.6. 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			2 clinvar			2
missense			54 clinvar	3 clinvar		57
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	60	3	0	63

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 69 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_178858.6	RefSeq	NP_849189.1	11	MANE Select
ENST00000369893.10	Ensembl	ENSP00000358909.4	11	MANE Select
NM_001350989.2	RefSeq	NP_001337918.1	11	Standard
ENST00000459894.6	Ensembl	ENSP00000473325.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

ion transmembrane transport
iron ion homeostasis

Molecular Function

ion transmembrane transporter activity

Cellular Component

integral component of membrane
mitochondrial membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000369893
Coding exons: 11
Length: 28955
Individuals with no LoFs: 125102
Homozygous LoFs: 6
Heterozygous LoFs: 639
Defined: 125747
p: 0.00257

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.452	185	203	0.911	0.0000119	2128
Missense (PolyPhen)		76	97.044	0.78315		978
Synonymous	-0.192	80	77.8	1.03	0.00000492	624
Loss of Function	2.27	8	18.5	0.431	8.71e-7	206

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00062	0.00062	rare
Latino/Admixed American	0.0022	0.0022	notable
Ashkenazi Jewish	0.0059	0.0059	notable
East Asian	0	0.0	absent
Finnish	0.0022	0.0022	notable
European (Non-Finnish)	0.0037	0.0036	notable
South Asian	0.00062	0.00062	rare
Other	0.0036	0.0036	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Potential iron transporter.;

Recessive Scores

pRec: 0.102

Intolerance Scores

LoFtool: 0.786
RVIS EVS: -0.42
RVIS percentile EVS: 25.56

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.627

Gene Damage Prediction

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