SFXN5

sideroflexin 5, the group of Solute carrier family 56, sideroflexins

Basic information

Region (hg38): 2:72942036-73075619

Links

ENSG00000144040 ∙ NCBI:94097 ∙ OMIM:615572 ∙ HGNC:16073 ∙ Uniprot:Q8TD22 ∙ 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 SFXN5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SFXN5 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			30	1		31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	30	1	0

Variants in SFXN5

This is a list of pathogenic ClinVar variants found in the SFXN5 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-72945032-T-C		not specified	Uncertain significance (Jun 16, 2024)
2-72945051-G-A		not specified	Uncertain significance (Jan 23, 2024)
2-72945094-T-A		not specified	Uncertain significance (Nov 07, 2022)
2-72961139-T-A		not specified	Uncertain significance (May 15, 2024)
2-72961159-G-A		not specified	Uncertain significance (Jul 12, 2023)
2-72961222-C-T		not specified	Uncertain significance (Oct 05, 2023)
2-72961229-G-A		not specified	Uncertain significance (Dec 03, 2021)
2-72961241-G-A		not specified	Uncertain significance (Dec 23, 2022)
2-72968467-C-T		not specified	Uncertain significance (Aug 10, 2021)
2-72968490-G-C		not specified	Uncertain significance (May 01, 2024)
2-72968511-G-A		not specified	Uncertain significance (Apr 25, 2022)
2-72968520-G-A		not specified	Uncertain significance (Dec 13, 2022)
2-72971571-T-C		not specified	Uncertain significance (Dec 30, 2023)
2-72971574-C-T		not specified	Uncertain significance (Jul 20, 2021)
2-72971581-C-T		not specified	Uncertain significance (Jun 06, 2023)
2-72971586-T-C		not specified	Likely benign (Dec 01, 2022)
2-72971602-G-A		not specified	Uncertain significance (Jan 10, 2022)
2-72971603-G-T		not specified	Uncertain significance (Jul 09, 2021)
2-72971652-C-T		not specified	Uncertain significance (Sep 09, 2024)
2-72998968-A-G		not specified	Uncertain significance (Nov 08, 2024)
2-72999005-C-A		not specified	Uncertain significance (Jun 02, 2023)
2-73000445-G-A		not specified	Uncertain significance (Feb 23, 2023)
2-73000451-C-T		not specified	Uncertain significance (Feb 15, 2023)
2-73000453-T-C		not specified	Uncertain significance (Sep 06, 2022)
2-73001554-G-T		not specified	Uncertain significance (Aug 16, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SFXN5	protein_coding	protein_coding	ENST00000272433	14	133583

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000147	0.993	125699	1	48	125748	0.000195

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.892	168	204	0.824	0.0000121	2159
Missense in Polyphen		57	82.501	0.6909		821
Synonymous	-1.23	102	87.4	1.17	0.00000540	701
Loss of Function	2.38	10	22.1	0.453	0.00000120	234

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000389	0.000388
Ashkenazi Jewish	0.0000996	0.0000992
East Asian	0.000109	0.000109
Finnish	0.0000470	0.0000462
European (Non-Finnish)	0.000248	0.000237
Middle Eastern	0.000109	0.000109
South Asian	0.000262	0.000229
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transports citrate. Potential iron transporter (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.114

Intolerance Scores

• loftool: 0.699
• rvis_EVS: -0.78
• rvis_percentile_EVS: 12.88

Haploinsufficiency Scores

• pHI: 0.182
• hipred: N
• hipred_score: 0.488
• ghis: 0.662

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.302

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sfxn5

Gene ontology

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