NM_005138.3(SCO2):c.59G>C (p.Arg20Pro) AND not specified

Germline classification:: Benign (3 submissions)
Last evaluated:: Jul 1, 2011
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:: RCV000128012.11

Allele description [Variation Report for NM_005138.3(SCO2):c.59G>C (p.Arg20Pro)]

NM_005138.3(SCO2):c.59G>C (p.Arg20Pro)

Genes:

TYMP:thymidine phosphorylase [Gene - OMIM - HGNC]
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.59G>C (p.Arg20Pro)

Other names:

p.R20P:CGG>CCG

HGVS:

NC_000022.11:g.50524353C>G
NG_011860.1:g.10733G>C
NG_016235.1:g.7087G>C
NG_021419.1:g.21138C>G
NM_001169109.2:c.59G>C
NM_001169110.1:c.59G>C
NM_001169111.2:c.59G>C
NM_001185011.2:c.*978C>G
NM_005138.3:c.59G>CMANE SELECT
NM_152299.4:c.*978C>GMANE SELECT
NP_001162580.1:p.Arg20Pro
NP_001162581.1:p.Arg20Pro
NP_001162582.1:p.Arg20Pro
NP_005129.2:p.Arg20Pro
LRG_727:g.10733G>C
NC_000022.10:g.50962782C>G
NM_001953.4:c.*1417G>C
NM_005138.2:c.59G>C
O43819:p.Arg20Pro
p.R20P

Protein change:

R20P

Links:

UniProtKB: O43819#VAR_011738; dbSNP: rs140523

NCBI 1000 Genomes Browser:

rs140523

Molecular consequence:

NM_001185011.2:c.*978C>G - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_152299.4:c.*978C>G - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001169109.2:c.59G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001169110.1:c.59G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001169111.2:c.59G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_005138.3:c.59G>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000171602	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Benign (Jul 1, 2011)	germline	clinical testing	Citation Link,
SCV001978570	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus	no assertion criteria provided	Benign	germline	clinical testing
SCV001979251	Clinical Genetics, Academic Medical Center - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Benign	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000171602

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Benign
(Jul 1, 2011)

germline

clinical testing

Citation Link,

SCV001978570

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus

no assertion criteria provided

Benign

germline

clinical testing

SCV001979251

Clinical Genetics, Academic Medical Center - VKGL Data-share Consensus

See additional submitters

no assertion criteria provided

Benign

germline

clinical testing

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000171602.12

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

Description

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus, SCV001978570.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Clinical Genetics, Academic Medical Center - VKGL Data-share Consensus, SCV001979251.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Apr 20, 2024

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