NM_001032386.2(SUOX):c.1281G>C (p.Ser427=) AND Sulfite oxidase deficiency

Clinical significance:Benign (Last evaluated: Dec 19, 2021)
Review status:2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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Based on:: 5 submissions [Details]
Record status:: current
Accession:: RCV000363638.13

Allele description [Variation Report for NM_001032386.2(SUOX):c.1281G>C (p.Ser427=)]

NM_001032386.2(SUOX):c.1281G>C (p.Ser427=)

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.1281G>C (p.Ser427=)

HGVS:

NC_000012.12:g.56004670G>C
NG_008136.1:g.12412G>C
NM_000456.3:c.1281G>C
NM_001032386.2:c.1281G>CMANE SELECT
NM_001032387.2:c.1281G>C
NP_000447.2:p.Ser427=
NP_001027558.1:p.Ser427=
NP_001027559.1:p.Ser427=
NC_000012.11:g.56398454G>C
NM_000456.2:c.1281G>C

Links:

dbSNP: rs773115

NCBI 1000 Genomes Browser:

rs773115

Molecular consequence:

NM_000456.3:c.1281G>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001032386.2:c.1281G>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001032387.2:c.1281G>C - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:: Sulfite oxidase deficiency (ISOD)
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
SCV000380316	Illumina Laboratory Services,Illumina	criteria provided, single submitter ICSL Variant Classification Criteria 13 December 2019	Benign (Jan 13, 2018)	germline	clinical testing	Citation Link,
SCV000733183	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus	no assertion criteria provided	Benign	germline	clinical testing
SCV000745691	Genome Diagnostics Laboratory, Amsterdam University Medical Center - VKGL Data-share Consensus	no assertion criteria provided ACGS Guidelines, 2013	Benign (Jan 23, 2017)	germline	clinical testing	Citation Link,
SCV001724465	Invitae	criteria provided, single submitter Invitae Variant Classification Sherloc (09022015)	Benign (Dec 19, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002062299	Genome-Nilou Lab	criteria provided, single submitter ACMG Guidelines, 2015	Benign (Jul 15, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Summary from all submissions

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Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	no	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

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):240-242.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Illumina Laboratory Services,Illumina, SCV000380316.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.

#	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

From Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus, SCV000733183.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

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

From Genome Diagnostics Laboratory, Amsterdam University Medical Center - VKGL Data-share Consensus, SCV000745691.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

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

From Invitae, SCV001724465.2

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

#	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

From Genome-Nilou Lab, SCV002062299.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Jan 21, 2023

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