NM_001032386.2(SUOX):c.1312_1313del (p.Val438fs) AND Sulfite oxidase deficiency

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Oct 28, 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:: RCV001943502.6

Allele description [Variation Report for NM_001032386.2(SUOX):c.1312_1313del (p.Val438fs)]

NM_001032386.2(SUOX):c.1312_1313del (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.1312_1313del (p.Val438fs)

HGVS:

NC_000012.12:g.56004701_56004702del
NG_008136.1:g.12443_12444del
NM_000456.3:c.1312_1313del
NM_001032386.2:c.1312_1313delMANE SELECT
NM_001032387.2:c.1312_1313del
NP_000447.2:p.Val438fs
NP_001027558.1:p.Val438fs
NP_001027559.1:p.Val438fs
NC_000012.11:g.56398484_56398485del
NC_000012.11:g.56398485_56398486del

Protein change:

V438fs

Links:

dbSNP: rs2136513040

NCBI 1000 Genomes Browser:

rs2136513040

Molecular consequence:

NM_000456.3:c.1312_1313del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001032386.2:c.1312_1313del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001032387.2:c.1312_1313del - 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
SCV002193022	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Oct 28, 2022)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 17940249, 28980090, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002193022

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Oct 28, 2022)

germline

clinical testing

PubMed (3)
[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

Magnetic resonance imaging and magnetic resonance spectroscopy in isolated sulfite oxidase deficiency.

Hoffmann C, Ben-Zeev B, Anikster Y, Nissenkorn A, Brand N, Kuint J, Kushnir T.

J Child Neurol. 2007 Oct;22(10):1214-21.

PubMed [citation]

PMID:: 17940249

Isolated sulfite oxidase deficiency.

Claerhout H, Witters P, Régal L, Jansen K, Van Hoestenberghe MR, Breckpot J, Vermeersch P.

J Inherit Metab Dis. 2018 Jan;41(1):101-108. doi: 10.1007/s10545-017-0089-4. Epub 2017 Oct 4. Review.

PubMed [citation]

PMID:: 28980090

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV002193022.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. This variant disrupts a region of the SUOX protein in which other variant(s) (p.Arg529*) have been determined to be pathogenic (PMID: 17940249, 28980090). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. ClinVar contains an entry for this variant (Variation ID: 1420277). This variant has not been reported in the literature in individuals affected with SUOX-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Val438Argfs*36) 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: Feb 14, 2024

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