NM_001079866.2(BCS1L):c.217C>T (p.Arg73Cys) AND not provided

Germline classification:: Conflicting interpretations of pathogenicity (3 submissions)
Last evaluated:: Jan 29, 2024
Review status:: criteria provided, conflicting classifications

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:: RCV001171821.32

Allele description [Variation Report for NM_001079866.2(BCS1L):c.217C>T (p.Arg73Cys)]

NM_001079866.2(BCS1L):c.217C>T (p.Arg73Cys)

Gene:

BCS1L:BCS1 homolog, ubiquinol-cytochrome c reductase complex chaperone [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2q35

Genomic location:

Preferred name:

NM_001079866.2(BCS1L):c.217C>T (p.Arg73Cys)

HGVS:

NC_000002.12:g.218661204C>T
NG_008018.1:g.6549C>T
NG_033099.1:g.3337G>A
NM_001079866.2:c.217C>TMANE SELECT
NM_001257342.2:c.217C>T
NM_001257343.2:c.217C>T
NM_001257344.2:c.217C>T
NM_001318836.2:c.-40-202C>T
NM_001320717.2:c.217C>T
NM_001371443.1:c.217C>T
NM_001371444.1:c.217C>T
NM_001371446.1:c.217C>T
NM_001371447.1:c.217C>T
NM_001371448.1:c.217C>T
NM_001371449.1:c.217C>T
NM_001371450.1:c.217C>T
NM_001371451.1:c.-40-202C>T
NM_001371452.1:c.-41-555C>T
NM_001371453.1:c.-260C>T
NM_001371454.1:c.-260C>T
NM_001371455.1:c.-260C>T
NM_001371456.1:c.-260C>T
NM_001374085.1:c.217C>T
NM_001374086.1:c.-260C>T
NM_004328.5:c.217C>T
NP_001073335.1:p.Arg73Cys
NP_001244271.1:p.Arg73Cys
NP_001244272.1:p.Arg73Cys
NP_001244273.1:p.Arg73Cys
NP_001307646.1:p.Arg73Cys
NP_001358372.1:p.Arg73Cys
NP_001358373.1:p.Arg73Cys
NP_001358375.1:p.Arg73Cys
NP_001358376.1:p.Arg73Cys
NP_001358377.1:p.Arg73Cys
NP_001358378.1:p.Arg73Cys
NP_001358379.1:p.Arg73Cys
NP_001361014.1:p.Arg73Cys
NP_004319.1:p.Arg73Cys
NP_004319.1:p.Arg73Cys
LRG_539t1:c.217C>T
LRG_539:g.6549C>T
LRG_539p1:p.Arg73Cys
NC_000002.11:g.219525927C>T
NM_004328.4:c.217C>T
NR_163955.1:n.1229C>T

Protein change:

R73C

Links:

dbSNP: rs140812286

NCBI 1000 Genomes Browser:

rs140812286

Molecular consequence:

NM_001371453.1:c.-260C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001371454.1:c.-260C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001371455.1:c.-260C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001371456.1:c.-260C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001374086.1:c.-260C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001318836.2:c.-40-202C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001371451.1:c.-40-202C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001371452.1:c.-41-555C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001079866.2:c.217C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001257342.2:c.217C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001257343.2:c.217C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001257344.2:c.217C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001320717.2:c.217C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001371443.1:c.217C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001371444.1:c.217C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001371446.1:c.217C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001371447.1:c.217C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001371448.1:c.217C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001371449.1:c.217C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001371450.1:c.217C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001374085.1:c.217C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_004328.5:c.217C>T - missense variant - [Sequence Ontology: SO:0001583]
NR_163955.1:n.1229C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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cdc42 effector protein 3 [Homo sapiens]
cdc42 effector protein 3 [Homo sapiens]
gi|19923356|ref|NP_006440.2|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001334690	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Pathogenic (Mar 1, 2020)	germline	clinical testing	Citation Link,
SCV001689654	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Jan 29, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004170563	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (Oct 30, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001334690

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)

Pathogenic
(Mar 1, 2020)

germline

clinical testing

Citation Link,

SCV001689654

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Jan 29, 2024)

germline

clinical testing

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

SCV004170563

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(Oct 30, 2023)

germline

clinical testing

Citation Link

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
not provided	germline	yes	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

Details of each submission

From CeGaT Center for Human Genetics Tuebingen, SCV001334690.25

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

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001689654.4

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

#	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 GeneDx, SCV004170563.1

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

Description

Identified with a second variant in a patient with BCS1L-related mitochondrial complex III deficiency in the published literature (PMID: 17403714); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 22310368, 23168492, 30582773, 17403714)

#	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: Oct 20, 2024

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