SFXN2

sideroflexin 2, the group of Solute carrier family 56, sideroflexins

Basic information

Region (hg38): 10:102714537-102743492

Links

ENSG00000156398 ∙ NCBI:118980 ∙ OMIM:615570 ∙ HGNC:16086 ∙ Uniprot:Q96NB2 ∙ 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 SFXN2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SFXN2 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			23	2		25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	2	0

Variants in SFXN2

This is a list of pathogenic ClinVar variants found in the SFXN2 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-102726670-G-A		not specified	Uncertain significance (Feb 28, 2024)
10-102726688-C-T		not specified	Likely benign (Jul 27, 2022)
10-102726728-C-T		not specified	Uncertain significance (Feb 27, 2023)
10-102726736-C-T		not specified	Uncertain significance (Jun 06, 2022)
10-102726737-G-A		not specified	Uncertain significance (Aug 08, 2022)
10-102726758-G-A		not specified	Likely benign (Jul 08, 2022)
10-102727055-C-A		not specified	Uncertain significance (Mar 04, 2024)
10-102727059-C-A		not specified	Uncertain significance (Feb 22, 2023)
10-102727066-G-A		not specified	Uncertain significance (Nov 02, 2021)
10-102727069-A-G		not specified	Uncertain significance (Jul 19, 2023)
10-102727082-T-C		not specified	Uncertain significance (Apr 24, 2024)
10-102727120-G-A		not specified	Uncertain significance (Feb 12, 2024)
10-102727133-C-T		not specified	Uncertain significance (Apr 08, 2023)
10-102727139-T-C		not specified	Uncertain significance (May 03, 2023)
10-102727142-T-G		not specified	Uncertain significance (Nov 17, 2022)
10-102728499-A-G		not specified	Uncertain significance (Sep 25, 2023)
10-102729342-C-T		not specified	Uncertain significance (Jun 17, 2024)
10-102729371-G-T		not specified	Uncertain significance (Aug 12, 2021)
10-102729727-C-T		not specified	Uncertain significance (Jul 12, 2023)
10-102729730-C-T		not specified	Uncertain significance (Apr 13, 2023)
10-102729733-C-T		not specified	Uncertain significance (May 23, 2024)
10-102729745-G-A		not specified	Uncertain significance (Oct 04, 2022)
10-102729762-G-A		not specified	Uncertain significance (Aug 17, 2022)
10-102729775-C-T		not specified	Uncertain significance (Jun 29, 2022)
10-102729802-G-A		not specified	Uncertain significance (Feb 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SFXN2	protein_coding	protein_coding	ENST00000369893	11	28955

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00106	0.989	125102	6	639	125747	0.00257

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.452	185	203	0.911	0.0000119	2128
Missense in Polyphen		76	97.044	0.78315		978
Synonymous	-0.192	80	77.8	1.03	0.00000492	624
Loss of Function	2.27	8	18.5	0.431	8.71e-7	206

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00281	0.00281
Ashkenazi Jewish	0.00585	0.00587
East Asian	0.00	0.00
Finnish	0.00222	0.00222
European (Non-Finnish)	0.00367	0.00362
Middle Eastern	0.00	0.00
South Asian	0.000621	0.000621
Other	0.00358	0.00359

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Potential iron transporter.

Recessive Scores

• pRec: 0.102

Intolerance Scores

• loftool: 0.786
• rvis_EVS: -0.42
• rvis_percentile_EVS: 25.56

Haploinsufficiency Scores

• pHI: 0.0663
• hipred: N
• hipred_score: 0.289
• ghis: 0.527

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.627

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sfxn2

Gene ontology

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