NM_005138.3(SCO2):c.222_223delinsGG (p.Trp75Gly) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 20, 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:: RCV002726183.3

Allele description [Variation Report for NM_005138.3(SCO2):c.222_223delinsGG (p.Trp75Gly)]

NM_005138.3(SCO2):c.222_223delinsGG (p.Trp75Gly)

Genes:

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

Variant type:

Indel

Cytogenetic location:

22q13.33

Genomic location:

Preferred name:

NM_005138.3(SCO2):c.222_223delinsGG (p.Trp75Gly)

HGVS:

NC_000022.11:g.50524189_50524190delinsCC
NG_011860.1:g.10896_10897delinsGG
NG_016235.1:g.7250_7251delinsGG
NG_021419.1:g.20974_20975delinsCC
NM_001169109.2:c.222_223delinsGG
NM_001169110.1:c.222_223delinsGG
NM_001169111.2:c.222_223delinsGG
NM_001185011.2:c.*814_*815delinsCC
NM_005138.3:c.222_223delinsGGMANE SELECT
NM_152299.4:c.*814_*815delinsCCMANE SELECT
NP_001162580.1:p.Trp75Gly
NP_001162581.1:p.Trp75Gly
NP_001162582.1:p.Trp75Gly
NP_005129.2:p.Trp75Gly
LRG_727:g.10896_10897delinsGG
NC_000022.10:g.50962618_50962619delinsCC

Protein change:

W75G

Molecular consequence:

NM_001185011.2:c.*814_*815delinsCC - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_152299.4:c.*814_*815delinsCC - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001169109.2:c.222_223delinsGG - missense variant - [Sequence Ontology: SO:0001583]
NM_001169110.1:c.222_223delinsGG - missense variant - [Sequence Ontology: SO:0001583]
NM_001169111.2:c.222_223delinsGG - missense variant - [Sequence Ontology: SO:0001583]
NM_005138.3:c.222_223delinsGG - 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
SCV003002901	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jun 20, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003002901

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jun 20, 2022)

germline

clinical testing

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

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

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, SCV003002901.2

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

Description

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. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. This variant has not been reported in the literature in individuals affected with SCO2-related conditions. Information on the frequency of this variant in the gnomAD database is not available, as this variant may be reported differently in the database. This sequence change replaces tryptophan, which is neutral and slightly polar, with glycine, which is neutral and non-polar, at codon 75 of the SCO2 protein (p.Trp75Gly).

#	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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