SFXN3

sideroflexin 3, the group of Solute carrier family 56, sideroflexins

Basic information

Region (hg38): 10:101031233-101041241

Links

ENSG00000107819 ∙ NCBI:81855 ∙ OMIM:615571 ∙ HGNC:16087 ∙ Uniprot:Q9BWM7 ∙ 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 SFXN3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SFXN3 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						0
missense			15			15
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	0	0

Variants in SFXN3

This is a list of pathogenic ClinVar variants found in the SFXN3 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-101034824-G-A		not specified	Uncertain significance (Feb 16, 2023)
10-101034842-G-A		not specified	Uncertain significance (Apr 09, 2024)
10-101034851-T-C		not specified	Uncertain significance (Mar 29, 2024)
10-101035607-G-A		not specified	Uncertain significance (Jun 22, 2021)
10-101036073-C-T		not specified	Uncertain significance (Jan 08, 2024)
10-101036074-G-A		not specified	Uncertain significance (Jan 23, 2024)
10-101036499-G-A		not specified	Uncertain significance (Sep 13, 2023)
10-101036533-C-T		not specified	Uncertain significance (May 17, 2023)
10-101036535-G-A		not specified	Uncertain significance (Jan 25, 2023)
10-101036727-T-C		not specified	Uncertain significance (Sep 27, 2021)
10-101037107-G-A		not specified	Uncertain significance (Dec 18, 2023)
10-101037108-AG-A		Neurodevelopmental disorder	Uncertain significance (Jan 01, 2019)
10-101037141-C-T		not specified	Uncertain significance (Mar 30, 2024)
10-101037146-A-G		not specified	Uncertain significance (May 16, 2022)
10-101037195-C-T		not specified	Uncertain significance (Jun 05, 2023)
10-101037400-T-G		not specified	Uncertain significance (Oct 25, 2023)
10-101038646-C-T		not specified	Uncertain significance (Nov 10, 2022)
10-101038661-G-C		not specified	Uncertain significance (May 24, 2023)
10-101038671-A-G		not specified	Uncertain significance (Feb 15, 2023)
10-101039191-C-T		not specified	Uncertain significance (May 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SFXN3	protein_coding	protein_coding	ENST00000224807	11	10008

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.44e-8	0.478	125007	3	738	125748	0.00295

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.436	173	190	0.911	0.0000104	2098
Missense in Polyphen		47	49.712	0.94544		550
Synonymous	-0.0911	78	77.0	1.01	0.00000449	672
Loss of Function	0.947	14	18.4	0.762	8.57e-7	201

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00466	0.00465
Ashkenazi Jewish	0.00338	0.00338
East Asian	0.000707	0.000707
Finnish	0.000139	0.000139
European (Non-Finnish)	0.00441	0.00440
Middle Eastern	0.000707	0.000707
South Asian	0.000593	0.000555
Other	0.00490	0.00490

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Potential iron transporter.
• Pathway: Urea cycle and metabolism of arginine, proline, glutamate, aspartate and asparagine;Validated targets of C-MYC transcriptional repression (Consensus)

Recessive Scores

• pRec: 0.0883

Intolerance Scores

• loftool: 0.871
• rvis_EVS: 0.33
• rvis_percentile_EVS: 73.41

Haploinsufficiency Scores

• pHI: 0.0789
• hipred: N
• hipred_score: 0.352
• ghis: 0.485

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.273

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sfxn3

Gene ontology

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