NM_001079866.2(BCS1L):c.217del (p.Arg73fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jun 10, 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:: RCV002815977.3

Allele description [Variation Report for NM_001079866.2(BCS1L):c.217del (p.Arg73fs)]

NM_001079866.2(BCS1L):c.217del (p.Arg73fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

2q35

Genomic location:

Preferred name:

NM_001079866.2(BCS1L):c.217del (p.Arg73fs)

HGVS:

NC_000002.12:g.218661204del
NG_008018.1:g.6549del
NG_033099.1:g.3339del
NG_033099.2:g.3421del
NM_001079866.2:c.217delMANE SELECT
NM_001257342.2:c.217del
NM_001257343.2:c.217del
NM_001257344.2:c.217del
NM_001318836.2:c.-40-202del
NM_001320717.2:c.217del
NM_001371443.1:c.217del
NM_001371444.1:c.217del
NM_001371446.1:c.217del
NM_001371447.1:c.217del
NM_001371448.1:c.217del
NM_001371449.1:c.217del
NM_001371450.1:c.217del
NM_001371451.1:c.-40-202del
NM_001371452.1:c.-41-555del
NM_001371453.1:c.-260del
NM_001371454.1:c.-260del
NM_001371455.1:c.-260del
NM_001371456.1:c.-260del
NM_001374085.1:c.217del
NM_001374086.1:c.-260del
NM_004328.5:c.217del
NP_001073335.1:p.Arg73fs
NP_001244271.1:p.Arg73fs
NP_001244272.1:p.Arg73fs
NP_001244273.1:p.Arg73Valfs
NP_001244273.1:p.Arg73fs
NP_001307646.1:p.Arg73fs
NP_001358372.1:p.Arg73fs
NP_001358373.1:p.Arg73fs
NP_001358375.1:p.Arg73fs
NP_001358376.1:p.Arg73fs
NP_001358377.1:p.Arg73fs
NP_001358378.1:p.Arg73fs
NP_001358379.1:p.Arg73fs
NP_001361014.1:p.Arg73fs
NP_004319.1:p.Arg73Valfs
NP_004319.1:p.Arg73fs
LRG_539t1:c.217del
LRG_539t2:c.217del
LRG_539:g.6549del
LRG_539p1:p.Arg73Valfs
LRG_539p2:p.Arg73Valfs
NC_000002.11:g.219525925del
NC_000002.11:g.219525927del
NM_001257344.1:c.217delC
NM_004328.4:c.217delC
NR_163955.1:n.1229del

Protein change:

R73fs

Molecular consequence:

NM_001371453.1:c.-260del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001371454.1:c.-260del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001371455.1:c.-260del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001371456.1:c.-260del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001374086.1:c.-260del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001079866.2:c.217del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001257342.2:c.217del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001257343.2:c.217del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001257344.2:c.217del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001320717.2:c.217del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001371443.1:c.217del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001371444.1:c.217del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001371446.1:c.217del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001371447.1:c.217del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001371448.1:c.217del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001371449.1:c.217del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001371450.1:c.217del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374085.1:c.217del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_004328.5:c.217del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001318836.2:c.-40-202del - intron variant - [Sequence Ontology: SO:0001627]
NM_001371451.1:c.-40-202del - intron variant - [Sequence Ontology: SO:0001627]
NM_001371452.1:c.-41-555del - intron variant - [Sequence Ontology: SO:0001627]
NR_163955.1:n.1229del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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
SCV003210715	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jun 10, 2022)	germline	clinical testing	PubMed (7) [See all records that cite these PMIDs] 12215968, 17314340, 19162478, 19508421, 22277166, 25895478, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003210715

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jun 10, 2022)

germline

clinical testing

PubMed (7)
[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

GRACILE syndrome, a lethal metabolic disorder with iron overload, is caused by a point mutation in BCS1L.

Visapää I, Fellman V, Vesa J, Dasvarma A, Hutton JL, Kumar V, Payne GS, Makarow M, Van Coster R, Taylor RW, Turnbull DM, Suomalainen A, Peltonen L.

Am J Hum Genet. 2002 Oct;71(4):863-76. Epub 2002 Sep 5.

PubMed [citation]

PMID:: 12215968
PMCID:: PMC378542

Missense mutations in the BCS1L gene as a cause of the Björnstad syndrome.

Hinson JT, Fantin VR, Schönberger J, Breivik N, Siem G, McDonough B, Sharma P, Keogh I, Godinho R, Santos F, Esparza A, Nicolau Y, Selvaag E, Cohen BH, Hoppel CL, Tranebjaerg L, Eavey RD, Seidman JG, Seidman CE.

N Engl J Med. 2007 Feb 22;356(8):809-19.

PubMed [citation]

PMID:: 17314340

See all PubMed Citations (7)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003210715.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (7)

Description

This sequence change creates a premature translational stop signal (p.Arg73Valfs*43) in the BCS1L gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in BCS1L are known to be pathogenic (PMID: 12215968, 17314340, 19162478, 19508421, 22277166, 25895478). This variant is not present in population databases (gnomAD no frequency). For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with BCS1L-related conditions.

#	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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