SFXN4

sideroflexin 4, the group of Solute carrier family 56, sideroflexins

Basic information

Region (hg38): 10:119140767-119165714

Links

ENSG00000183605

∙ NCBI:119559 ∙ OMIM:615564 ∙ HGNC:16088 ∙ Uniprot:Q6P4A7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

growth and developmental delay-hypotonia-vision impairment-lactic acidosis syndrome (Supportive), mode of inheritance: AR
growth and developmental delay-hypotonia-vision impairment-lactic acidosis syndrome (Moderate), mode of inheritance: AR
growth and developmental delay-hypotonia-vision impairment-lactic acidosis syndrome (Strong), mode of inheritance: AR
mitochondrial disease (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Combined oxidative phosphorylation deficiency 18	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Biochemical; Hematologic; Neurologic	24119684

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SFXN4 gene.

not_provided (74 variants)
Inborn_genetic_diseases (43 variants)
not_specified (15 variants)
Growth_and_developmental_delay-hypotonia-vision_impairment-lactic_acidosis_syndrome (13 variants)
SFXN4-related_disorder (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SFXN4 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000213649.2. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				17 clinvar	4 clinvar	21
missense			35 clinvar	13 clinvar		48
nonsense	3 clinvar	2 clinvar				5
start loss						0
frameshift	3 clinvar	1 clinvar	1 clinvar			5
splice donor/acceptor (+/-2bp)	1 clinvar	4 clinvar				5
Total	7	7	36	30	4

Highest pathogenic variant AF is 0.0000501884

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SFXN4	protein_coding	protein_coding	ENST00000355697	14	24901

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.24e-7	0.946	125688	0	60	125748	0.000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.765	156	185	0.842	0.00000955	2172
Missense in Polyphen		31	44.446	0.69748		532
Synonymous	0.326	64	67.4	0.949	0.00000371	626
Loss of Function	1.90	15	25.3	0.592	0.00000149	265

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000448	0.000426
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.000587	0.000554
European (Non-Finnish)	0.000223	0.000211
Middle Eastern	0.0000544	0.0000544
South Asian	0.000327	0.000327
Other	0.000374	0.000326

dbNSFP

Source: dbNSFP

Function: FUNCTION: Potential iron transporter. {ECO:0000250}.;
Disease: DISEASE: 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. {ECO:0000269|PubMed:24119684}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec: 0.0633

Intolerance Scores

loftool
rvis_EVS: -0.71
rvis_percentile_EVS: 14.4

Haploinsufficiency Scores

pHI: 0.0456
hipred: N
hipred_score: 0.281
ghis: 0.583

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.796

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Sfxn4
Phenotype: hematopoietic system phenotype; immune system phenotype;

Zebrafish Information Network

Gene name: sfxn4
Affected structure: nucleate erythrocyte
Phenotype tag: abnormal
Phenotype quality: decreased amount

Gene ontology

Biological process: ion transmembrane transport;iron ion homeostasis
Cellular component: mitochondrial inner membrane;integral component of membrane;intracellular membrane-bounded organelle
Molecular function: ion transmembrane transporter activity