NM_001079866.2(BCS1L):c.372dup (p.Asp125fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Nov 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:: RCV003768005.1

Allele description [Variation Report for NM_001079866.2(BCS1L):c.372dup (p.Asp125fs)]

NM_001079866.2(BCS1L):c.372dup (p.Asp125fs)

Gene:

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

Variant type:

Duplication

Cytogenetic location:

2q35

Genomic location:

Preferred name:

NM_001079866.2(BCS1L):c.372dup (p.Asp125fs)

HGVS:

NC_000002.12:g.218661457dup
NG_008018.1:g.6802dup
NG_033099.1:g.3084dup
NM_001079866.2:c.372dupMANE SELECT
NM_001257342.2:c.372dup
NM_001257343.2:c.372dup
NM_001257344.2:c.372dup
NM_001318836.2:c.12dup
NM_001320717.2:c.372dup
NM_001371443.1:c.372dup
NM_001371444.1:c.372dup
NM_001371446.1:c.372dup
NM_001371447.1:c.372dup
NM_001371448.1:c.372dup
NM_001371449.1:c.372dup
NM_001371450.1:c.372dup
NM_001371451.1:c.12dup
NM_001371452.1:c.-41-302dup
NM_001371453.1:c.-105dup
NM_001371454.1:c.-105dup
NM_001371455.1:c.-105dup
NM_001371456.1:c.-105dup
NM_001374085.1:c.372dup
NM_001374086.1:c.-105dup
NM_004328.5:c.372dup
NP_001073335.1:p.Asp125fs
NP_001244271.1:p.Asp125fs
NP_001244272.1:p.Asp125fs
NP_001244273.1:p.Asp125fs
NP_001305765.1:p.Asp5fs
NP_001307646.1:p.Asp125fs
NP_001358372.1:p.Asp125fs
NP_001358373.1:p.Asp125fs
NP_001358375.1:p.Asp125fs
NP_001358376.1:p.Asp125fs
NP_001358377.1:p.Asp125fs
NP_001358378.1:p.Asp125fs
NP_001358379.1:p.Asp125fs
NP_001358380.1:p.Asp5fs
NP_001361014.1:p.Asp125fs
NP_004319.1:p.Asp125fs
LRG_539:g.6802dup
NC_000002.11:g.219526179_219526180insA
NC_000002.11:g.219526180dup
NM_004328.4:c.372dupA
NR_163955.1:n.1384dup

Protein change:

D125fs

Links:

dbSNP: rs1553596638

NCBI 1000 Genomes Browser:

rs1553596638

Molecular consequence:

NM_001371453.1:c.-105dup - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001371454.1:c.-105dup - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001371455.1:c.-105dup - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001371456.1:c.-105dup - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001374086.1:c.-105dup - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001079866.2:c.372dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001257342.2:c.372dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001257343.2:c.372dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001257344.2:c.372dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001318836.2:c.12dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001320717.2:c.372dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001371443.1:c.372dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001371444.1:c.372dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001371446.1:c.372dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001371447.1:c.372dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001371448.1:c.372dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001371449.1:c.372dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001371450.1:c.372dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001371451.1:c.12dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374085.1:c.372dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_004328.5:c.372dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001371452.1:c.-41-302dup - intron variant - [Sequence Ontology: SO:0001627]
NR_163955.1:n.1384dup - 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
SCV004678099	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Nov 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

SCV004678099

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Nov 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 Invitae, SCV004678099.1

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

Description

This variant is not present in population databases (gnomAD no frequency). For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 557160). This variant has not been reported in the literature in individuals affected with BCS1L-related conditions. This sequence change creates a premature translational stop signal (p.Asp125Argfs*19) 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).

#	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: Jun 17, 2024

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