VCV001054726.12 - ClinVar

NM_005138.3(SCO2):c.303G>C (p.Gln101His)

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.

(4)

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.303G>C (p.Gln101His)

Variation ID: 1054726 Accession: VCV001054726.12

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 22q13.33 22: 50524109 (GRCh38) [ NCBI UCSC ] 22: 50962538 (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	Apr 13, 2021	Nov 24, 2024	Aug 15, 2022

HGVS

Nucleotide	Protein	Molecular consequence
NM_005138.3:c.303G>C MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_005129.2:p.Gln101His	missense
NM_152299.4:c.*734C>G MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.		3 prime UTR
NM_001169109.2:c.303G>C	NP_001162580.1:p.Gln101His	missense
NM_001169110.1:c.303G>C	NP_001162581.1:p.Gln101His	missense
NM_001169111.2:c.303G>C	NP_001162582.1:p.Gln101His	missense
NM_001185011.2:c.*734C>G		3 prime UTR
NC_000022.11:g.50524109C>G
NC_000022.10:g.50962538C>G
NG_011860.1:g.10977G>C
NG_016235.1:g.7331G>C
NG_021419.1:g.20894C>G
LRG_727:g.10977G>C

... more HGVS ... less HGVS

Protein change

Q101H

Other names

Canonical SPDI

NC_000022.11:50524108:C:G

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.

Exome Aggregation Consortium (ExAC) 0.00004

The Genome Aggregation Database (gnomAD), exomes 0.00006

NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00008

Trans-Omics for Precision Medicine (TOPMed) 0.00011

The Genome Aggregation Database (gnomAD) 0.00014

Links

dbSNP: rs141551295 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 (3)	criteria provided, multiple submitters, no conflicts	Aug 15, 2022	RCV001363284.13
Cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 1	Uncertain significance (1)	criteria provided, single submitter	Aug 28, 2019	RCV004789546.1

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 (Aug 15, 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: SCV001559390.3 First in ClinVar: Apr 13, 2021 Last updated: Feb 07, 2023	Comment: This sequence change replaces glutamine, which is neutral and polar, with histidine, which is basic and polar, at codon 101 of the SCO2 protein (p.Gln101His). … (more) This sequence change replaces glutamine, which is neutral and polar, with histidine, which is basic and polar, at codon 101 of the SCO2 protein (p.Gln101His). This variant is present in population databases (rs141551295, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with SCO2-related conditions. ClinVar contains an entry for this variant (Variation ID: 1054726). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). 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 (May 13, 2022)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Not provided Affected status: unknown Allele origin: germline	Mayo Clinic Laboratories, Mayo Clinic Accession: SCV001715393.2 First in ClinVar: Jun 15, 2021 Last updated: Jan 26, 2024	Number of individuals with the variant: 2
Uncertain significance (Feb 12, 2021)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	not provided Affected status: unknown Allele origin: germline	Revvity Omics, Revvity Accession: SCV003819232.2 First in ClinVar: Mar 04, 2023 Last updated: Feb 04, 2024
Uncertain significance (Aug 28, 2019)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 1 Affected status: yes Allele origin: germline	Victorian Clinical Genetics Services, Murdoch Childrens Research Institute Additional submitter: Shariant Australia, Australian Genomics Accession: SCV005398077.1 First in ClinVar: Nov 24, 2024 Last updated: Nov 24, 2024	Comment: A heterozygous missense variant was identified, NM_005138.2(SCO2):c.303G>C in exon 2 of 2 of the SCO2 gene. This substitution is predicted to create a minor amino … (more) A heterozygous missense variant was identified, NM_005138.2(SCO2):c.303G>C in exon 2 of 2 of the SCO2 gene. This substitution is predicted to create a minor amino acid change from glutamine to histidine at position 101 of the protein, NP_005129.2(SCO2):p.(Gln101His). The glutamine at this position has moderate conservation (100 vertebrates, UCSC), and is located within the thioredoxin functional domain. In silico software predicts this variant to be disease causing. The variant is present in the gnomAD population database at a frequency of 0.0071% (20 heterozygotes, 0 homozygotes). The variant has not been previously reported in a clinical case. Analysis of parental samples indicates that this variant is paternally inherited. Based on information available at the time of curation, this variant has been classified as a VARIANT of UNCERTAIN SIGNIFICANCE (VUS). (less)

Comment:

This sequence change replaces glutamine, which is neutral and polar, with histidine, which is basic and polar, at codon 101 of the SCO2 protein (p.Gln101His). This variant is present in population databases (rs141551295, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with SCO2-related conditions. ClinVar contains an entry for this variant (Variation ID: 1054726). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). 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:

A heterozygous missense variant was identified, NM_005138.2(SCO2):c.303G>C in exon 2 of 2 of the SCO2 gene. This substitution is predicted to create a minor amino acid change from glutamine to histidine at position 101 of the protein, NP_005129.2(SCO2):p.(Gln101His). The glutamine at this position has moderate conservation (100 vertebrates, UCSC), and is located within the thioredoxin functional domain. In silico software predicts this variant to be disease causing. The variant is present in the gnomAD population database at a frequency of 0.0071% (20 heterozygotes, 0 homozygotes). The variant has not been previously reported in a clinical case. Analysis of parental samples indicates that this variant is paternally inherited. Based on information available at the time of curation, this variant has been classified as a VARIANT of UNCERTAIN SIGNIFICANCE (VUS).

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

There are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs141551295 ...

These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Nov 25, 2024

ClinVar Genomic variation as it relates to human health

NM_005138.3(SCO2):c.303G>C (p.Gln101His)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for rs141551295 ...