NM_001032386.2(SUOX):c.849G>A (p.Trp283Ter) AND Sulfite oxidase deficiency

Germline classification:: Pathogenic (1 submission)
Last evaluated:: May 3, 2022
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV003040667.3

Allele description [Variation Report for NM_001032386.2(SUOX):c.849G>A (p.Trp283Ter)]

NM_001032386.2(SUOX):c.849G>A (p.Trp283Ter)

Gene:

SUOX:sulfite oxidase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

12q13.2

Genomic location:

Preferred name:

NM_001032386.2(SUOX):c.849G>A (p.Trp283Ter)

HGVS:

NC_000012.12:g.56004238G>A
NG_008136.1:g.11980G>A
NM_000456.3:c.849G>A
NM_001032386.2:c.849G>AMANE SELECT
NM_001032387.2:c.849G>A
NP_000447.2:p.Trp283Ter
NP_001027558.1:p.Trp283Ter
NP_001027559.1:p.Trp283Ter
NC_000012.11:g.56398022G>A

Protein change:

W283*

Molecular consequence:

NM_000456.3:c.849G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001032386.2:c.849G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001032387.2:c.849G>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Sulfite oxidase deficiency
Synonyms:: Isolated sulfite oxidase deficiency
Identifiers:: MONDO: MONDO:0010089; MedGen: C0268624; Orphanet: 833; OMIM: 272300; Human Phenotype Ontology: HP:0003643

Recent activity

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Oryza sativa Japonica Group cDNA clone:J033112B07, full insert sequence
Oryza sativa Japonica Group cDNA clone:J033112B07, full insert sequence
gi|32988081|dbj|AK102872.1|

Nucleotide
essv16438135 (0)
BioProject
essv16437947 (0)
ClinVar
ammonium transporter Rh type B [Oryctolagus cuniculus]
ammonium transporter Rh type B [Oryctolagus cuniculus]
gi|126723199|ref|NP_001075605.1|

Protein
SPOC domain-containing protein 1 isoform 3 [Homo sapiens]
SPOC domain-containing protein 1 isoform 3 [Homo sapiens]
gi|530354695|ref|NP_001268917.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003348498	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (May 3, 2022)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 31870341, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003348498

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(May 3, 2022)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Stable clinical course in three siblings with late-onset isolated sulfite oxidase deficiency: a case series and literature review.

Tian M, Qu Y, Huang L, Su X, Li S, Ying J, Zhao F, Mu D.

BMC Pediatr. 2019 Dec 23;19(1):510. doi: 10.1186/s12887-019-1889-5. Review.

PubMed [citation]

PMID:: 31870341
PMCID:: PMC6927172

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003348498.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This variant is present in population databases (no rsID available, gnomAD 0.007%). This variant has not been reported in the literature in individuals affected with SUOX-related conditions. This variant disrupts a region of the SUOX protein in which other variant(s) (p.Arg459Gln) have been determined to be pathogenic (PMID: 31870341). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic. This sequence change creates a premature translational stop signal (p.Trp283*) in the SUOX gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 263 amino acid(s) of the SUOX protein.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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