NM_001032386.2(SUOX):c.1313_1316del (p.Val438fs) AND Sulfite oxidase deficiency

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Jun 9, 2023
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:: RCV002254601.14

Allele description [Variation Report for NM_001032386.2(SUOX):c.1313_1316del (p.Val438fs)]

NM_001032386.2(SUOX):c.1313_1316del (p.Val438fs)

Gene:

SUOX:sulfite oxidase [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

12q13.2

Genomic location:

Preferred name:

NM_001032386.2(SUOX):c.1313_1316del (p.Val438fs)

HGVS:

NC_000012.12:g.56004702_56004705del
NG_008136.1:g.12444_12447del
NM_000456.3:c.1313_1316del
NM_001032386.2:c.1313_1316delMANE SELECT
NM_001032387.2:c.1313_1316del
NP_000447.2:p.Val438fs
NP_001027558.1:p.Val438fs
NP_001027559.1:p.Val438fs
NC_000012.11:g.56398486_56398489del
NM_000456.2:c.1313_1316del

Protein change:

V438fs

Links:

dbSNP: rs778431071

NCBI 1000 Genomes Browser:

rs778431071

Molecular consequence:

NM_000456.3:c.1313_1316del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001032386.2:c.1313_1316del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001032387.2:c.1313_1316del - frameshift variant - [Sequence Ontology: SO:0001589]

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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001379468	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely pathogenic (Jun 9, 2023)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 16140720, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001379468

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely pathogenic
(Jun 9, 2023)

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

Isolated sulfite oxidase deficiency: a case report with a novel mutation and review of the literature.

Tan WH, Eichler FS, Hoda S, Lee MS, Baris H, Hanley CA, Grant PE, Krishnamoorthy KS, Shih VE.

Pediatrics. 2005 Sep;116(3):757-66. Review. Erratum in: Pediatrics. 2005 Dec;116(6):1615.

PubMed [citation]

PMID:: 16140720

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, SCV001379468.5

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

Description

In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. ClinVar contains an entry for this variant (Variation ID: 938805). This premature translational stop signal has been observed in individual(s) with sulfite oxidase deficiency (PMID: 16140720; Invitae). This variant is present in population databases (rs778431071, gnomAD 0.02%). This sequence change creates a premature translational stop signal (p.Val438Aspfs*5) in the SUOX gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 108 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: Oct 13, 2024

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