SUOX

sulfite oxidase

Basic information

Region (hg38): 12:55997180-56006641

Links

ENSG00000139531 ∙ NCBI:6821 ∙ OMIM:606887 ∙ HGNC:11460 ∙ Uniprot:P51687 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• isolated sulfite oxidase deficiency (Strong), mode of inheritance: AR
• isolated sulfite oxidase deficiency (Strong), mode of inheritance: AR
• isolated sulfite oxidase deficiency (Definitive), mode of inheritance: AR
• isolated sulfite oxidase deficiency (Definitive), mode of inheritance: AR
• isolated sulfite oxidase deficiency (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Sulfite oxidase deficiency	AR	Biochemical	Dietary measures (eg, low protein diet and synthetic amino acid mixture without cystine or methionine) have been described as beneficial in early reports	Biochemical; Neurologic; Ophthalmologic	302914; 509724; 9428520; 10682307; 15952210; 12368985; 19793632

ClinVar

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

• Sulfite_oxidase_deficiency (461 variants)
• Inborn_genetic_diseases (54 variants)
• not_provided (25 variants)
• SUOX-related_disorder (14 variants)
• Sulfocysteinuria (12 variants)
• not_specified (10 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SUOX gene is commonly pathogenic or not. These statistics are base on transcript: NM_001032386.2. 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				164	1	165
missense	1	19	183	14	1	218
nonsense	20	6				26
start loss						0
frameshift	33	7				40
splice donor/acceptor (+/-2bp)	1	3	1			5
Total	55	35	184	178	2

Highest pathogenic variant AF is 0.000086739085

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SUOX	protein_coding	protein_coding	ENST00000394109	3	9462

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		125689	0	59	125748	0.000235

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.448	289	311	0.928	0.0000185	3490
Missense in Polyphen		75	103.51	0.7246		1150
Synonymous	0.851	108	120	0.901	0.00000609	1185
Loss of Function	1.31	12	18.0	0.666	8.71e-7	207

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000474	0.000474
Ashkenazi Jewish	0.00	0.00
East Asian	0.000924	0.000925
Finnish	0.00	0.00
European (Non-Finnish)	0.000176	0.000176
Middle Eastern	0.000924	0.000925
South Asian	0.000261	0.000261
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Disease: DISEASE: Sulfite oxidase deficiency, isolated (ISOD) [MIM:272300]: A life-threatening, autosomal recessive neurometabolic disorder characterized by severe neurological impairment. Classic ISOD manifests in the first few hours to days of life and is characterized by intractable seizures, feeding difficulties, rapidly progressive encephalopathy, microcephaly, and profound intellectual disability. Children usually die during the first few months of life. Mild ISOD manifests in infancy or early childhood and is characterized by ectopia lentis that is variably present, developmental delay and regression, movement disorder characterized by dystonia and choreoathetosis, ataxia, and rarely acute hemiplegia due to metabolic stroke. {ECO:0000269|PubMed:10519592, ECO:0000269|PubMed:12112661, ECO:0000269|PubMed:12368985, ECO:0000269|PubMed:9428520, ECO:0000269|PubMed:9600976}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Sulfur metabolism - Homo sapiens (human);Sulfate/Sulfite Metabolism;Sulfite oxidase deficiency;Sulfide oxidation to sulfate;Degradation of cysteine and homocysteine;Metabolism of amino acids and derivatives;sulfite oxidation;Metabolism;Methionine and cysteine metabolism;Sulfur amino acid metabolism;superpathway of methionine degradation (Consensus)

Recessive Scores

• pRec: 0.233

Intolerance Scores

• loftool: 0.0692
• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.61

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.989

Gene Damage Prediction

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

Gene ontology

• Biological process: sulfur compound metabolic process;nitrate assimilation;sulfide oxidation, using sulfide:quinone oxidoreductase
• Cellular component: mitochondrion;mitochondrial intermembrane space;mitochondrial matrix
• Molecular function: protein binding;sulfite oxidase activity;heme binding;molybdenum ion binding;molybdopterin cofactor binding