SFXN5

protein-coding

sideroflexin 5, the group of Solute carrier family 56, sideroflexins

Gene summary

Predicted to enable citrate transmembrane transporter activity. Predicted to be involved in citrate transport and mitochondrial transmembrane transport. Located in mitochondrion. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_144579.3

Inheritance

—

ClinVar variants

U:77B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.45

Max pathogenic AF

—

Genomic locus

chr2:72,942,036-73,075,619

External References & Databases

Ensembl (ENSG00000144040)

Transcript & Mutation Effects

hg38 • Region Span ~133.6 kb

Loading mutation effect viewer...

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 SFXN5 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 69

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_144579.3. 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			1 clinvar			1
missense			73 clinvar	1 clinvar		74
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	77	1	0	78

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 71 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_144579.3	RefSeq	NP_653180.1	14	MANE Select
ENST00000272433.7	Ensembl	ENSP00000272433.2	14	MANE Select
NM_001330400.2	RefSeq	NP_001317329.1	15	Standard
NM_001330401.2	RefSeq	NP_001317330.1	12	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

citrate transport
ion transmembrane transport
iron ion homeostasis

Molecular Function

citrate transmembrane transporter activity

Cellular Component

integral component of membrane
mitochondrial membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000272433
Coding exons: 14
Length: 133583
Individuals with no LoFs: 125699
Homozygous LoFs: 1
Heterozygous LoFs: 48
Defined: 125748
p: 0.000195

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.892	168	204	0.824	0.0000121	2159
Missense (PolyPhen)		57	82.501	0.6909		821
Synonymous	-1.23	102	87.4	1.17	0.00000540	701
Loss of Function	2.38	10	22.1	0.453	0.00000120	234

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00018	rare
Latino/Admixed American	0.00020	0.00020	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.00011	0.00011	rare
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.00025	0.00024	rare
South Asian	0.00026	0.00023	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Transports citrate. Potential iron transporter (By similarity). {ECO:0000250}.;

Recessive Scores

pRec: 0.114

Intolerance Scores

LoFtool: 0.699
RVIS EVS: -0.78
RVIS percentile EVS: 12.88

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.302

Gene Damage Prediction

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