NM_005138.3(SCO2):c.179G>A (p.Arg60Gln) AND not provided

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Aug 31, 2022
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:: RCV003015445.2

Allele description

NM_005138.3(SCO2):c.179G>A (p.Arg60Gln)

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.179G>A (p.Arg60Gln)

Other names:

p.Arg60Gln

HGVS:

NC_000022.11:g.50524233C>T
NG_011860.1:g.10853G>A
NG_016235.1:g.7207G>A
NG_021419.1:g.21018C>T
NM_001169109.2:c.179G>A
NM_001169110.1:c.179G>A
NM_001169111.2:c.179G>A
NM_001185011.2:c.*858C>T
NM_005138.3:c.179G>AMANE SELECT
NM_152299.4:c.*858C>TMANE SELECT
NP_001162580.1:p.Arg60Gln
NP_001162581.1:p.Arg60Gln
NP_001162582.1:p.Arg60Gln
NP_005129.2:p.Arg60Gln
LRG_727:g.10853G>A
NC_000022.10:g.50962662C>T
NM_005138.2:c.179G>A

Protein change:

R60Q

Molecular consequence:

NM_001185011.2:c.*858C>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_152299.4:c.*858C>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001169109.2:c.179G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001169110.1:c.179G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001169111.2:c.179G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_005138.3:c.179G>A - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003302559	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 10, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004225642	Mayo Clinic Laboratories, Mayo Clinic	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Aug 31, 2022)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 34746378, 25741868

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003302559

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 10, 2022)

germline

clinical testing

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

SCV004225642

Mayo Clinic Laboratories, Mayo Clinic

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Aug 31, 2022)

germline

clinical testing

PubMed (2)
[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	1	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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Adult Cerebellar Ataxia, Axonal Neuropathy, and Sensory Impairments Caused by Biallelic SCO2 Variants.

Rucheton B, Ewenczyk C, Gaignard P, de Sainte Agathe JM, Fauret AL, Saillour V, Leonard-Louis S, Touitou V, Mochel F.

Neurol Genet. 2021 Dec;7(6):e630. doi: 10.1212/NXG.0000000000000630. No abstract available.

PubMed [citation]

PMID:: 34746378
PMCID:: PMC8569615

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV003302559.1

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

Description

This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 60 of the SCO2 protein (p.Arg60Gln). This variant is present in population databases (rs777622192, gnomAD 0.01%). 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 tolerated. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. 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.

#	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 Mayo Clinic Laboratories, Mayo Clinic, SCV004225642.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	PubMed (2)

Description

PM2, PM3

#	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		1	not provided	not provided	not provided

Last Updated: Sep 1, 2024

ClinVar

Relating variation to medicine