VCV002062321.8 - ClinVar

NM_005138.3(SCO2):c.202G>A (p.Gly68Arg)

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(3)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Uncertain significance

criteria provided, multiple submitters, no conflicts

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_005138.3(SCO2):c.202G>A (p.Gly68Arg)

Variation ID: 2062321 Accession: VCV002062321.8

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 22q13.33 22: 50524210 (GRCh38) [ NCBI UCSC ] 22: 50962639 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Feb 8, 2023	Aug 11, 2024	May 31, 2024

HGVS

Nucleotide	Protein	Molecular consequence
NM_005138.3:c.202G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_005129.2:p.Gly68Arg	missense
NM_152299.4:c.*835C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.		3 prime UTR
NM_001169109.2:c.202G>A	NP_001162580.1:p.Gly68Arg	missense
NM_001169110.1:c.202G>A	NP_001162581.1:p.Gly68Arg	missense
NM_001169111.2:c.202G>A	NP_001162582.1:p.Gly68Arg	missense
NM_001185011.2:c.*835C>T		3 prime UTR
NC_000022.11:g.50524210C>T
NC_000022.10:g.50962639C>T
NG_011860.1:g.10876G>A
NG_016235.1:g.7230G>A
NG_021419.1:g.20995C>T
LRG_727:g.10876G>A

... more HGVS ... less HGVS

Protein change

G68R

Other names

Canonical SPDI

NC_000022.11:50524209:C:T

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
NCAPH2		-	-	GRCh38 GRCh37	53	573
SCO2		-	-	GRCh38 GRCh37	4	884

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
not provided	Uncertain significance (1)	criteria provided, single submitter	Jul 5, 2022	RCV002953353.2
Cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 1	Uncertain significance (1)	criteria provided, single submitter	Jan 31, 2023	RCV003108135.3
not specified	Uncertain significance (1)	criteria provided, single submitter	May 31, 2024	RCV004690336.1

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Uncertain significance (Jul 05, 2022)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	not provided Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV003273787.1 First in ClinVar: Feb 07, 2023 Last updated: Feb 07, 2023	Comment: This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 68 of the SCO2 protein (p.Gly68Arg). … (more) This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 68 of the SCO2 protein (p.Gly68Arg). This variant is present in population databases (no rsID available, gnomAD 0.003%). This variant has not been reported in the literature in individuals affected with SCO2-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. (less)
Uncertain significance (Jan 31, 2023)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 1 (Autosomal recessive inheritance) Affected status: yes Allele origin: maternal	Laboratory of Inherited Metabolic Diseases, Research centre for medical genetics Accession: SCV003762134.2 First in ClinVar: Feb 13, 2023 Last updated: Nov 11, 2023	Number of individuals with the variant: 1
Uncertain significance (May 31, 2024)	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015) Method: clinical testing	not specified Affected status: unknown Allele origin: germline	Women's Health and Genetics/Laboratory Corporation of America, LabCorp Accession: SCV005184962.1 First in ClinVar: Aug 11, 2024 Last updated: Aug 11, 2024	Publications: PubMed (1) PubMed: 36675121 Comment: Variant summary: SCO2 c.202G>A (p.Gly68Arg) results in a non-conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a damaging … (more) Variant summary: SCO2 c.202G>A (p.Gly68Arg) results in a non-conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 1.2e-05 in 242564 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.202G>A has been reported in the literature in at least one individual with unknown zygosity affected with Leigh syndrome (Kistol_2023). These report(s) do not provide unequivocal conclusions about association of the variant with Mitochondrial complex IV deficiency, nuclear type 2. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publication has been ascertained in the context of this evaluation (PMID: 36675121). ClinVar contains an entry for this variant (Variation ID: 2062321). Based on the evidence outlined above, the variant was classified as uncertain significance. (less)

Comment:

This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 68 of the SCO2 protein (p.Gly68Arg). This variant is present in population databases (no rsID available, gnomAD 0.003%). This variant has not been reported in the literature in individuals affected with SCO2-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

Comment:

Variant summary: SCO2 c.202G>A (p.Gly68Arg) results in a non-conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 1.2e-05 in 242564 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.202G>A has been reported in the literature in at least one individual with unknown zygosity affected with Leigh syndrome (Kistol_2023). These report(s) do not provide unequivocal conclusions about association of the variant with Mitochondrial complex IV deficiency, nuclear type 2. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publication has been ascertained in the context of this evaluation (PMID: 36675121). ClinVar contains an entry for this variant (Variation ID: 2062321). Based on the evidence outlined above, the variant was classified as uncertain significance.

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Comment:

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
Leigh Syndrome: Spectrum of Molecular Defects and Clinical Features in Russia.	Kistol D	International journal of molecular sciences	2023	PMID: 36675121

Text-mined citations for this variant ...

Record last updated Sep 29, 2024

ClinVar Genomic variation as it relates to human health

NM_005138.3(SCO2):c.202G>A (p.Gly68Arg)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...