SFXN1

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

Basic information

Region (hg38): 5:175477062-175529742

Links

ENSG00000164466 ∙ NCBI:94081 ∙ OMIM:615569 ∙ HGNC:16085 ∙ Uniprot:Q9H9B4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SFXN1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SFXN1 gene is commonly pathogenic or not.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			18		1	19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	0	2

Variants in SFXN1

This is a list of pathogenic ClinVar variants found in the SFXN1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
5-175492132-A-G		not specified	Uncertain significance (Sep 24, 2024)
5-175492141-A-G		not specified	Uncertain significance (Aug 04, 2023)
5-175492180-A-G			Benign (Mar 29, 2018)
5-175492244-G-A			Benign (Jul 26, 2018)
5-175509048-C-G		not specified	Uncertain significance (Aug 07, 2024)
5-175509078-G-C		not specified	Uncertain significance (Apr 16, 2024)
5-175509091-A-G		not specified	Uncertain significance (Dec 18, 2023)
5-175509096-T-G		not specified	Uncertain significance (Feb 16, 2023)
5-175509107-T-A		not specified	Uncertain significance (Sep 26, 2023)
5-175509109-C-T		not specified	Uncertain significance (Sep 26, 2023)
5-175510137-T-C		not specified	Uncertain significance (Dec 16, 2022)
5-175510188-G-C		not specified	Uncertain significance (Jun 23, 2023)
5-175511488-G-A		not specified	Uncertain significance (Jul 26, 2022)
5-175511491-G-A		not specified	Uncertain significance (Aug 10, 2021)
5-175512165-A-C		not specified	Uncertain significance (Sep 28, 2021)
5-175512178-T-C		not specified	Uncertain significance (Jun 06, 2023)
5-175512187-T-C		not specified	Uncertain significance (Sep 06, 2022)
5-175513519-C-T		not specified	Uncertain significance (Feb 23, 2023)
5-175513522-C-T		not specified	Uncertain significance (Jul 25, 2023)
5-175513558-T-C		not specified	Uncertain significance (Jan 04, 2024)
5-175513579-C-G		not specified	Uncertain significance (Nov 24, 2024)
5-175516653-C-T		not specified	Uncertain significance (Apr 04, 2023)
5-175522379-G-A		not specified	Uncertain significance (Oct 06, 2021)
5-175526663-G-A		not specified	Uncertain significance (Jun 25, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SFXN1	protein_coding	protein_coding	ENST00000321442	10	52681

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000972	0.988	125729	0	18	125747	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.507	170	190	0.896	0.0000108	2109
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000150	0.000148
Ashkenazi Jewish	0.00	0.00
East Asian	0.000220	0.000217
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.0000620	0.0000615
Middle Eastern	0.000220	0.000217
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Might be involved in the transport of a component required for iron utilization into or out of the mitochondria.
• Pathway: miR-targeted genes in leukocytes - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase (Consensus)

Recessive Scores

• pRec: 0.156

Intolerance Scores

• loftool: 0.496
• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.96

Haploinsufficiency Scores

• pHI: 0.239
• hipred: Y
• hipred_score: 0.530
• ghis: 0.533

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.712

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sfxn1

Gene ontology

• Biological process: iron ion transport;erythrocyte differentiation;ion transmembrane transport;iron ion homeostasis
• Cellular component: mitochondrion;integral component of membrane;mitochondrial membrane
• Molecular function: ion transmembrane transporter activity