FDX2

ferredoxin 2, the group of Mitochondrial respiratory chain complex assembly factors|Ferredoxin family

Basic information

Region (hg38): 19:10309916-10316015

Previous symbols: [ "FDX1L" ]

Links

ENSG00000267673 ∙ NCBI:112812 ∙ OMIM:614585 ∙ HGNC:30546 ∙ Uniprot:Q6P4F2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• mitochondrial myopathy, episodic, with optic atrophy and reversible leukoencephalopathy (Moderate), mode of inheritance: AR
• mitochondrial myopathy, episodic, with optic atrophy and reversible leukoencephalopathy (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Mitochondrial myopathy, episodic, with or without optic atrophy and reversible leukoencephalopathy	AR	Musculoskeletal; Renal	Among other features, the condition can include rhabdomyolysis, and awareness may allow medical management	Biochemical; Musculoskeletal; Neurologic; Renal	24281368;30010796

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the FDX2 gene.

• not_provided (112 variants)
• FDX2-related_disorder (5 variants)
• not_specified (4 variants)
• Mitochondrial_myopathy,_episodic,_with_optic_atrophy_and_reversible_leukoencephalopathy (2 variants)
• Inborn_mitochondrial_myopathy (2 variants)
• Inborn_genetic_diseases (1 variants)
• Mitochondrial_myopathy,_episodic,_without_optic_atrophy_and_reversible_leukoencephalopathy (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FDX2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001397406.1. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				38	2	40
missense		1	33	1	2	37
nonsense			1			1
start loss		2				2
frameshift	1		1			2
splice donor/acceptor (+/-2bp)			1			1
Total	1	3	36	39	4

Highest pathogenic variant AF is 0.00006775846

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FDX2	protein_coding	protein_coding	ENST00000393708	5	10589

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00165	0.716	125632	0	22	125654	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.529	91	106	0.856	0.00000535	1151
Missense in Polyphen		20	33.665	0.59409		342
Synonymous	-1.64	61	46.8	1.30	0.00000256	387
Loss of Function	0.807	5	7.36	0.679	3.12e-7	88

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000160	0.000157
Ashkenazi Jewish	0.00	0.00
East Asian	0.000333	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.0000952	0.0000880
Middle Eastern	0.000333	0.000326
South Asian	0.000105	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Essential for heme A and Fe/S protein biosynthesis. {ECO:0000269|PubMed:20547883}.
• Pathway: Phase I - Functionalization of compounds;Electron transport from NADPH to Ferredoxin;Metabolism of lipids;Endogenous sterols;Cytochrome P450 - arranged by substrate type;Biological oxidations;Mitochondrial iron-sulfur cluster biogenesis;Metabolism;Pregnenolone biosynthesis;Metabolism of steroid hormones;Metabolism of steroids;Steroid hormones (Consensus)

Recessive Scores

• pRec: 0.105

Intolerance Scores

• rvis_EVS: 0.35
• rvis_percentile_EVS: 74.18

Haploinsufficiency Scores

• pHI: 0.116
• hipred: N
• hipred_score: 0.162

Essentials

• essential_gene_gene_trap: E

Mouse Genome Informatics

• Gene name: Fdx1l

Gene ontology

• Biological process: C21-steroid hormone biosynthetic process;sterol metabolic process;electron transport chain;small molecule metabolic process
• Cellular component: mitochondrial matrix
• Molecular function: protein binding;electron transfer activity;metal ion binding;2 iron, 2 sulfur cluster binding