NM_005138.3(SCO2):c.686A>G (p.Tyr229Cys) AND not provided

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Dec 28, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV003136531.4

Allele description [Variation Report for NM_005138.3(SCO2):c.686A>G (p.Tyr229Cys)]

NM_005138.3(SCO2):c.686A>G (p.Tyr229Cys)

Genes:

NCAPH2:non-SMC condensin II complex subunit H2 [Gene - OMIM - HGNC]
SCO2:synthesis of cytochrome C oxidase 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

22q13.33

Genomic location:

Preferred name:

NM_005138.3(SCO2):c.686A>G (p.Tyr229Cys)

HGVS:

NC_000022.11:g.50523726T>C
NG_016235.1:g.7714A>G
NG_021419.1:g.20511T>C
NM_001169109.2:c.686A>G
NM_001169110.1:c.686A>G
NM_001169111.2:c.686A>G
NM_001185011.2:c.*351T>C
NM_005138.3:c.686A>GMANE SELECT
NM_152299.4:c.*351T>CMANE SELECT
NP_001162580.1:p.Tyr229Cys
NP_001162581.1:p.Tyr229Cys
NP_001162582.1:p.Tyr229Cys
NP_005129.2:p.Tyr229Cys
NC_000022.10:g.50962155T>C
NM_005138.2:c.686A>G

Protein change:

Y229C

Molecular consequence:

NM_001185011.2:c.*351T>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_152299.4:c.*351T>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001169109.2:c.686A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001169110.1:c.686A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001169111.2:c.686A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_005138.3:c.686A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003819231	Revvity Omics, Revvity	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Nov 7, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV005384019	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (Dec 28, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003819231

Revvity Omics, Revvity

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Nov 7, 2022)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

SCV005384019

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(Dec 28, 2023)

germline

clinical testing

Citation Link

Help

Summary from all submissions

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

Citations

PubMed

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 Revvity Omics, Revvity, SCV003819231.2

#	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 GeneDx, SCV005384019.1

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

Description

Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge

#	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

Last Updated: Nov 3, 2024

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