SFXN4

gene
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Also known as SLC56A4

Summary

SFXN4 (sideroflexin 4, HGNC:16088) is a protein-coding gene on chromosome 10q26.11, encoding Sideroflexin-4 (Q6P4A7). Mitochondrial amino-acid transporter.

This gene encodes a member of the sideroflexin family. The encoded protein is a transmembrane protein of the inner mitochondrial membrane, and is required for mitochondrial respiratory homeostasis and erythropoiesis. Mutations in this gene are associated with mitochondriopathy and macrocytic anemia. Alternatively spliced transcript variants have been found in this gene.

Source: NCBI Gene 119559 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): mitochondrial disease (Definitive, ClinGen) — +1 more curated relationship
  • GWAS associations: 3
  • Clinical variants (ClinVar): 208 total — 6 pathogenic, 5 likely-pathogenic
  • Phenotypes (HPO): 20
  • MANE Select transcript: NM_213649

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:16088
Approved symbolSFXN4
Namesideroflexin 4
Location10q26.11
Locus typegene with protein product
StatusApproved
AliasesSLC56A4
Ensembl geneENSG00000183605
Ensembl biotypeprotein_coding
OMIM615564
Entrez119559

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 4 protein_coding, 4 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000355697, ENST00000369131, ENST00000419372, ENST00000461438, ENST00000462913, ENST00000466218, ENST00000484960, ENST00000490417, ENST00000955059

RefSeq mRNA: 1 — MANE Select: NM_213649 NM_213649

CCDS: CCDS7610

Canonical transcript exons

ENST00000355697 — 14 exons

ExonStartEnd
ENSE00001381725119165537119165714
ENSE00003465290119158009119158062
ENSE00003518084119160915119160969
ENSE00003527894119146236119146353
ENSE00003540082119147775119147860
ENSE00003557921119161055119161081
ENSE00003576053119157871119157927
ENSE00003581833119164131119164196
ENSE00003582633119156678119156756
ENSE00003611443119162340119162414
ENSE00003614459119140767119141319
ENSE00003620095119159728119159753
ENSE00003691536119157668119157733
ENSE00003691862119155062119155177

Expression profiles

Bgee: expression breadth ubiquitous, 254 present calls, max score 96.99.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 11.9300 / max 85.0433, expressed in 1775 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
1116779.73201754
1116762.1752970
1116750.022813

Top tissues by expression

256 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
apex of heartUBERON:000209896.99gold quality
adrenal tissueUBERON:001830395.43gold quality
tibialis anteriorUBERON:000138595.14gold quality
right adrenal gland cortexUBERON:003582794.96gold quality
body of pancreasUBERON:000115094.68gold quality
right adrenal glandUBERON:000123394.42gold quality
hindlimb stylopod muscleUBERON:000425294.35gold quality
mucosa of transverse colonUBERON:000499194.30gold quality
right uterine tubeUBERON:000130293.95gold quality
gastrocnemiusUBERON:000138893.72gold quality
left adrenal glandUBERON:000123493.60gold quality
deltoidUBERON:000147693.55gold quality
heart left ventricleUBERON:000208493.49gold quality
left adrenal gland cortexUBERON:003582593.49gold quality
muscle of legUBERON:000138393.44gold quality
cardiac ventricleUBERON:000208293.17gold quality
spermCL:000001993.12gold quality
adrenal glandUBERON:000236993.12gold quality
rectumUBERON:000105293.05gold quality
adrenal cortexUBERON:000123592.89gold quality
right lobe of liverUBERON:000111492.69gold quality
right lobe of thyroid glandUBERON:000111992.69gold quality
right atrium auricular regionUBERON:000663192.51gold quality
left lobe of thyroid glandUBERON:000112092.44gold quality
pancreasUBERON:000126492.17gold quality
left ventricle myocardiumUBERON:000656692.00gold quality
thyroid glandUBERON:000204691.96gold quality
cardiac atriumUBERON:000208191.89gold quality
skeletal muscle tissueUBERON:000113491.82gold quality
transverse colonUBERON:000115791.76gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes8.71

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

14 targeting SFXN4, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-27A-3P99.9872.132955
HSA-MIR-27B-3P99.9872.132955
HSA-MIR-998599.9872.112939
HSA-MIR-806299.8868.43995
HSA-MIR-498-5P99.7669.641807
HSA-MIR-4524A-3P99.7266.852406
HSA-MIR-520F-5P99.3470.401632
HSA-MIR-425499.1165.151315
HSA-MIR-66199.0965.942062
HSA-MIR-6771-3P98.2066.53971
HSA-MIR-4797-3P97.4867.14989
HSA-MIR-6849-3P97.2564.571371
HSA-MIR-3194-5P96.8064.901027
HSA-MIR-1292-5P96.7462.14238

Literature-anchored findings (GeneRIF, showing 6)

  • we isolated a cDNA encoding a novel sideroflexin protein (SFXN4), which showed 59% identity and 71% similarity to mouse sideroflexin4. (PMID:14756423)
  • Our findings establish mutations in SFXN4 as a cause of mitochondriopathy and macrocytic anemia. (PMID:24119684)
  • Prenatal onset of mitochondrial disease is associated with sideroflexin 4 deficiency. (PMID:31059822)
  • Sideroflexin 4 affects Fe-S cluster biogenesis, iron metabolism, mitochondrial respiration and heme biosynthetic enzymes. (PMID:31873120)
  • Sideroflexin 4 is a complex I assembly factor that interacts with the MCIA complex and is required for the assembly of the ND2 module. (PMID:35333655)
  • Comprehensive Analysis of Sideroflexin 4 in Hepatocellular Carcinoma by Bioinformatics and Experiments. (PMID:37786439)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriosfxn4ENSDARG00000069832
mus_musculusSfxn4ENSMUSG00000063698
rattus_norvegicusSfxn4ENSRNOG00000036572

Paralogs (4): SFXN3 (ENSG00000107819), SFXN5 (ENSG00000144040), SFXN2 (ENSG00000156398), SFXN1 (ENSG00000164466)

Protein

Protein identifiers

Sideroflexin-4Q6P4A7 (reviewed: Q6P4A7)

Alternative names: Breast cancer resistance marker 1

All UniProt accessions (3): B1AMV7, B1AMV8, Q6P4A7

UniProt curated annotations — full annotation on UniProt →

Function. Mitochondrial amino-acid transporter. Does not act as a serine transporter: not able to mediate transport of serine into mitochondria.

Subcellular location. Mitochondrion inner membrane.

Disease relevance. Combined oxidative phosphorylation deficiency 18 (COXPD18) [MIM:615578] An autosomal recessive disorder of mitochondrial dysfunction characterized by intrauterine growth retardation, hypotonia, visual impairment, speech delay, and lactic acidosis associated with decreased mitochondrial respiratory chain activity. Affected patients may also show hematologic abnormalities, mainly macrocytic anemia. The disease is caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the sideroflexin family.

Isoforms (3)

UniProt IDNamesCanonical?
Q6P4A7-11yes
Q6P4A7-22
Q6P4A7-33

RefSeq proteins (1): NP_998814* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR004686MtcFamily

Pfam: PF03820

UniProt features (12 total): transmembrane region 5, splice variant 3, modified residue 2, initiator methionine 1, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q6P4A7-F185.330.57

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (2): 2, 197

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

IDPathway
R-HSA-6799198Complex I biogenesis
R-HSA-1428517Aerobic respiration and respiratory electron transport
R-HSA-1430728Metabolism
R-HSA-611105Respiratory electron transport

MSigDB gene sets: 139 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_BRAIN_TUMORAL_MACROPHAGE_DN, WWTAAGGC_UNKNOWN, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GOBP_MITOCHONDRIAL_TRANSPORT, CEBPB_01, GOBP_MITOCHONDRIAL_TRANSMEMBRANE_TRANSPORT, WEI_MYCN_TARGETS_WITH_E_BOX, SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM1, GOBP_AMINO_ACID_TRANSPORT, GOCC_MITOCHONDRIAL_ENVELOPE, IVANOVA_HEMATOPOIESIS_INTERMEDIATE_PROGENITOR, GOBP_TRANSMEMBRANE_TRANSPORT, GOCC_ORGANELLE_INNER_MEMBRANE, VECCHI_GASTRIC_CANCER_EARLY_UP, GOMF_TRANSPORTER_ACTIVITY

GO Biological Process (5): amino acid transport (GO:0006865), mitochondrial transmembrane transport (GO:1990542), monoatomic ion transport (GO:0006811), monoatomic ion transmembrane transport (GO:0034220), transmembrane transport (GO:0055085)

GO Molecular Function (2): monoatomic ion transmembrane transporter activity (GO:0015075), transmembrane transporter activity (GO:0022857)

GO Cellular Component (5): nucleoplasm (GO:0005654), mitochondrion (GO:0005739), mitochondrial inner membrane (GO:0005743), membrane (GO:0016020), mitochondrial membrane (GO:0031966)

Reactome top-level categories

Rollup of top-3 pathways:

CategoryPathways
Respiratory electron transport1
Metabolism1
Aerobic respiration and respiratory electron transport1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
transport3
transmembrane transport3
cellular anatomical structure2
mitochondrial transport1
monoatomic ion transport1
cellular process1
transmembrane transporter activity1
monoatomic ion transmembrane transport1
transporter activity1
nuclear lumen1
cytoplasm1
intracellular membrane-bounded organelle1
organelle inner membrane1
mitochondrial membrane1
mitochondrion1
mitochondrial envelope1
organelle membrane1

Protein interactions and networks

STRING

904 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SFXN4PRADC1Q9BSG0568
SFXN4PRSS37A4D1T9492
SFXN4CCDC18Q5T9S5471
SFXN4COL24A1Q17RW2438
SFXN4FECHP22830423
SFXN4PSME4Q14997421
SFXN4GLRX5Q86SX6420
SFXN4GNALP38405418
SFXN4EBF2Q9HAK2416
SFXN4ZNF490Q9ULM2413
SFXN4CSDE1O75534413
SFXN4NRN1Q9NPD7413
SFXN4MAPK8IP3Q9UPT6410
SFXN4NANOS2P60321406
SFXN4NEGR1Q7Z3B1405

IntAct

61 interactions, top by confidence:

ABTypeScore
CFTRESYT2psi-mi:“MI:2364”(proximity)0.710
IFT27IFT56psi-mi:“MI:0914”(association)0.690
TNFSF8LGALS8psi-mi:“MI:0914”(association)0.530
APLNRSLC33A1psi-mi:“MI:0914”(association)0.530
COX15SLC25A3psi-mi:“MI:0914”(association)0.530
TUBA1ATUBAL3psi-mi:“MI:0914”(association)0.420
FLT4ILVBLpsi-mi:“MI:0914”(association)0.420
RIPK4VWA8psi-mi:“MI:0914”(association)0.350
PB2ESYT2psi-mi:“MI:0914”(association)0.350
HSCBRBP5psi-mi:“MI:0914”(association)0.350
LRRK2psi-mi:“MI:0914”(association)0.350
NMES1NDUFS8psi-mi:“MI:0914”(association)0.350
COQ9NDUFS8psi-mi:“MI:0914”(association)0.350
NDUFA4NUDT19psi-mi:“MI:0914”(association)0.350
NDUFA4NDUFS8psi-mi:“MI:0914”(association)0.350
MAIP1COQ9psi-mi:“MI:0914”(association)0.350
COQ9ACOT7psi-mi:“MI:0914”(association)0.350
BABAM1PYCR3psi-mi:“MI:0914”(association)0.350
Ppsi-mi:“MI:0914”(association)0.350
Mpsi-mi:“MI:0914”(association)0.350
SLC16A11ESYT2psi-mi:“MI:0914”(association)0.350
MAPK4ILVBLpsi-mi:“MI:0914”(association)0.350

BioGRID (118): SFXN4 (Affinity Capture-RNA), SFXN4 (Affinity Capture-RNA), SFXN4 (Affinity Capture-MS), SFXN4 (Affinity Capture-MS), SFXN4 (Affinity Capture-MS), SFXN4 (Affinity Capture-MS), SFXN4 (Affinity Capture-MS), SFXN4 (Affinity Capture-MS), SFXN4 (Affinity Capture-MS), SFXN4 (Affinity Capture-MS), SFXN4 (Affinity Capture-MS), SFXN4 (Affinity Capture-MS), SFXN4 (Affinity Capture-MS), SFXN4 (Affinity Capture-MS), SFXN4 (Affinity Capture-MS)

ESM2 similar proteins: A5A761, A6QP55, A8E7G5, B2LU20, B3M6C8, B4H6M2, B4HKS2, B4J252, B4LE89, B4QNU8, B6IJ52, O13793, P00425, P25710, P38857, P53311, P81928, Q09201, Q12029, Q16FT5, Q2LZH7, Q32L86, Q3T0M2, Q54NQ9, Q5E9M8, Q5EA43, Q5FC79, Q5HZA9, Q5RD16, Q63965, Q6BKZ1, Q6CFW6, Q6CXR8, Q6FJJ0, Q6P4A7, Q759E9, Q91V61, Q925N1, Q925N2, Q95QD1

Diamond homologs: A8E7G5, Q3T0M2, Q54NQ9, Q6P4A7, Q8CFD0, Q8TD22, Q925N0, Q925N1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

208 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic6
Likely pathogenic5
Uncertain significance38
Likely benign66
Benign59

Top pathogenic / likely-pathogenic (11)

Variant IDHGVSClassification
1323582NM_213649.2(SFXN4):c.368T>A (p.Leu123Ter)Pathogenic
2175492NM_213649.2(SFXN4):c.668del (p.Lys223fs)Pathogenic
488593NM_213649.2(SFXN4):c.414+1G>APathogenic
638327NM_213649.2(SFXN4):c.940C>T (p.Gln314Ter)Pathogenic
92098NM_213649.2(SFXN4):c.233del (p.Pro78fs)Pathogenic
92099NM_213649.2(SFXN4):c.739dup (p.Arg247fs)Pathogenic
2076813NM_213649.2(SFXN4):c.819-1G>CLikely pathogenic
2182106NM_213649.2(SFXN4):c.818+2T>ALikely pathogenic
2427788NC_000010.10:g.(?120905748)(120905865_?)dupLikely pathogenic
3381959NM_213649.2(SFXN4):c.823C>T (p.Gln275Ter)Likely pathogenic
3767158NM_213649.2(SFXN4):c.361-2A>TLikely pathogenic

SpliceAI

1839 predictions. Top by Δscore:

VariantEffectΔscore
10:119155056:TCTTA:Tdonor_loss1.0000
10:119155057:CTTAC:Cdonor_loss1.0000
10:119155058:TTAC:Tdonor_loss1.0000
10:119155059:TAC:Tdonor_loss1.0000
10:119155060:ACC:Adonor_loss1.0000
10:119155061:C:CGdonor_loss1.0000
10:119156668:T:TAdonor_gain1.0000
10:119156673:CTCA:Cdonor_loss1.0000
10:119156674:TCA:Tdonor_loss1.0000
10:119156675:CACC:Cdonor_loss1.0000
10:119156676:ACC:Adonor_loss1.0000
10:119156752:ATTAC:Aacceptor_gain1.0000
10:119156753:TTAC:Tacceptor_gain1.0000
10:119156754:TAC:Tacceptor_gain1.0000
10:119156755:AC:Aacceptor_gain1.0000
10:119156756:CC:Cacceptor_gain1.0000
10:119156757:C:CCacceptor_gain1.0000
10:119157617:T:TAdonor_gain1.0000
10:119157666:A:ACdonor_gain1.0000
10:119157666:ACT:Adonor_gain1.0000
10:119157667:C:CGdonor_gain1.0000
10:119157667:CT:Cdonor_gain1.0000
10:119157667:CTC:Cdonor_gain1.0000
10:119157869:A:ACdonor_gain1.0000
10:119157870:C:CAdonor_gain1.0000
10:119157870:CGTAA:Cdonor_gain1.0000
10:119157874:A:Cdonor_gain1.0000
10:119160911:TCA:Tdonor_loss1.0000
10:119160912:CAC:Cdonor_loss1.0000
10:119160914:C:CAdonor_loss1.0000

AlphaMissense

2190 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
10:119146257:A:CS305R0.989
10:119146257:A:TS305R0.989
10:119146259:T:GS305R0.989
10:119155072:G:TA241D0.980
10:119155114:A:TV227D0.980
10:119155070:C:AG242W0.979
10:119157898:G:CF148L0.972
10:119157898:G:TF148L0.972
10:119157900:A:GF148L0.972
10:119164172:A:GW46R0.968
10:119164172:A:TW46R0.968
10:119155144:C:GR217P0.966
10:119161058:A:CS92R0.965
10:119161058:A:TS92R0.965
10:119161060:T:GS92R0.965
10:119155081:G:AS238F0.959
10:119155167:A:CS209R0.959
10:119155167:A:TS209R0.959
10:119155169:T:GS209R0.959
10:119141251:T:AR335S0.957
10:119141251:T:GR335S0.957
10:119155082:A:GS238P0.953
10:119160923:C:GR109P0.951
10:119141250:C:AG336W0.946
10:119141259:A:CY333D0.941
10:119147834:T:AR253S0.941
10:119147834:T:GR253S0.941
10:119146251:A:CF307L0.939
10:119146251:A:TF307L0.939
10:119146253:A:GF307L0.939

dbSNP variants (sampled 300 via entrez): RS1000105689 (10:119141702 C>T), RS1000170489 (10:119158446 C>T), RS1000300559 (10:119146981 A>C), RS1000412845 (10:119165183 C>A,G,T), RS1000461166 (10:119157382 G>A), RS1000492032 (10:119156993 G>A), RS1000539777 (10:119141545 C>A,G), RS1000777530 (10:119152438 C>G), RS1000798706 (10:119165974 G>C), RS1000955792 (10:119153357 C>T), RS1001026942 (10:119163275 G>A,T), RS1001029439 (10:119153077 C>T), RS1001214233 (10:119150802 A>T), RS1001239714 (10:119152569 C>T), RS1001301939 (10:119141800 G>A)

Disease associations

OMIM: gene MIM:615564 | disease phenotypes: MIM:615578

GenCC curated gene-disease

DiseaseClassificationInheritance
growth and developmental delay-hypotonia-vision impairment-lactic acidosis syndromeStrongAutosomal recessive

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

DiseaseClassificationInheritance
mitochondrial diseaseDefinitiveAR

Mondo (1): growth and developmental delay-hypotonia-vision impairment-lactic acidosis syndrome (MONDO:0014261)

Orphanet (1): Growth and developmental delay-hypotonia-vision impairment-lactic acidosis syndrome (Orphanet:391348)

HPO phenotypes

20 total (20 of 20 shown, HPO-id order):

HPOTerm
HP:0000007Autosomal recessive inheritance
HP:0000505Visual impairment
HP:0000750Delayed speech and language development
HP:0001252Hypotonia
HP:0001256Mild intellectual disability
HP:0001310Dysmetria
HP:0001337Tremor
HP:0001511Intrauterine growth retardation
HP:0001562Oligohydramnios
HP:0001972Macrocytic anemia
HP:0002151Increased circulating lactate concentration
HP:0003128Lactic acidosis
HP:0003202Skeletal muscle atrophy
HP:0003577Congenital onset
HP:0004821Hypersegmentation of neutrophil nuclei
HP:0009046Difficulty running
HP:0010862Delayed fine motor development
HP:0011923Decreased activity of mitochondrial complex I
HP:0012120Methylmalonic aciduria
HP:0040014Increased mitochondrial number

GWAS associations

3 associations (top):

StudyTraitp-value
GCST004860_17Alcoholic chronic pancreatitis6.000000e-06
GCST011176_5Stroke1.000000e-07
GCST90020029_302Waist circumference adjusted for body mass index2.000000e-08

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0007789BMI-adjusted waist circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

PharmGKB variants

2 variants.

VariantGenesLevelScore#Clin annotsDrugs
rs2275112EIF3A, SFXN40.000
rs11198804EIF3A, SFXN40.000

CTD chemical–gene interactions

46 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
(+)-JQ1 compounddecreases expression5
Acetaminophendecreases expression4
Valproic Aciddecreases expression, increases expression, increases methylation, affects expression4
sodium arsenitedecreases expression, affects cotreatment, increases abundance, increases expression2
Hydrogen Peroxideaffects expression, decreases expression2
Plant Extractsaffects cotreatment, increases expression, decreases expression2
Cadmium Chloridedecreases expression, increases abundance, increases expression2
Particulate Matterincreases expression, affects cotreatment, decreases expression, increases abundance2
aristolochic acid Idecreases expression1
methylmercuric chloridedecreases expression1
cobaltous chloridedecreases expression1
manganese chlorideincreases abundance, increases expression, affects cotreatment1
caffeic aciddecreases expression, increases reaction1
isobutyl alcoholincreases abundance, affects cotreatment, decreases expression1
4-methoxycinnamate methyl esterdecreases expression, increases reaction1
perfluoro-n-nonanoic acidincreases expression1
ICG 001increases expression1
14-deoxy-11,12-didehydroandrographolidedecreases expression1
bisphenol Saffects expression1
NSC 689534affects binding, decreases expression1
3-(2-hydroxy-4-(2-methylnonan-2-yl)phenyl)cyclohexan-1-olincreases expression1
Resveratrolaffects cotreatment, increases expression1
Air Pollutantsincreases abundance, increases expression1
Arsenicincreases expression, affects cotreatment, increases abundance1
Atrazinedecreases expression1
Benzo(a)pyreneaffects methylation1
Cadmiumincreases expression, increases abundance1
Caffeineincreases phosphorylation1
Carbamazepineaffects expression1
Copperaffects binding, decreases expression1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_D4HEHCT116-SFXN4-KO-c34Cancer cell lineMale

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.