NM_005138.3(SCO2):c.290C>T (p.Ala97Val) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 27, 2022
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV002037370.5

Allele description [Variation Report for NM_005138.3(SCO2):c.290C>T (p.Ala97Val)]

NM_005138.3(SCO2):c.290C>T (p.Ala97Val)

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.290C>T (p.Ala97Val)

HGVS:

NC_000022.11:g.50524122G>A
NG_011860.1:g.10964C>T
NG_016235.1:g.7318C>T
NG_021419.1:g.20907G>A
NM_001169109.2:c.290C>T
NM_001169110.1:c.290C>T
NM_001169111.2:c.290C>T
NM_001185011.2:c.*747G>A
NM_005138.3:c.290C>TMANE SELECT
NM_152299.4:c.*747G>AMANE SELECT
NP_001162580.1:p.Ala97Val
NP_001162581.1:p.Ala97Val
NP_001162582.1:p.Ala97Val
NP_005129.2:p.Ala97Val
LRG_727:g.10964C>T
NC_000022.10:g.50962551G>A

Protein change:

A97V

Links:

dbSNP: rs748093648

NCBI 1000 Genomes Browser:

rs748093648

Molecular consequence:

NM_001185011.2:c.*747G>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_152299.4:c.*747G>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001169109.2:c.290C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001169110.1:c.290C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001169111.2:c.290C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_005138.3:c.290C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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cytosolic 5'-nucleotidase 1B isoform 2 [Homo sapiens]
cytosolic 5'-nucleotidase 1B isoform 2 [Homo sapiens]
gi|50593108|ref|NP_150278.2|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002115818	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Sep 27, 2022)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 27052445, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002115818

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Sep 27, 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	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Association between SCO2 mutation and extreme myopia in Japanese patients.

Wakazono T, Miyake M, Yamashiro K, Yoshikawa M, Yoshimura N.

Jpn J Ophthalmol. 2016 Jul;60(4):319-25. doi: 10.1007/s10384-016-0442-4. Epub 2016 Apr 6.

PubMed [citation]

PMID:: 27052445

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

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002115818.2

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

Description

This sequence change replaces alanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 97 of the SCO2 protein (p.Ala97Val). This variant is present in population databases (rs748093648, gnomAD 0.04%). This missense change has been observed in individual(s) with myopia (PMID: 27052445). ClinVar contains an entry for this variant (Variation ID: 1345540). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt SCO2 protein function. 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

Last Updated: Sep 29, 2024

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