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NM_001079866.2(BCS1L):c.355C>T (p.Arg119Ter) AND not provided

Germline classification:
Pathogenic/Likely pathogenic (2 submissions)
Last evaluated:
Dec 11, 2023
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV001070513.8

Allele description [Variation Report for NM_001079866.2(BCS1L):c.355C>T (p.Arg119Ter)]

NM_001079866.2(BCS1L):c.355C>T (p.Arg119Ter)

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.355C>T (p.Arg119Ter)
HGVS:
  • NC_000002.12:g.218661440C>T
  • NG_008018.1:g.6785C>T
  • NG_033099.1:g.3101G>A
  • NM_001079866.2:c.355C>TMANE SELECT
  • NM_001257342.2:c.355C>T
  • NM_001257343.2:c.355C>T
  • NM_001257344.2:c.355C>T
  • NM_001318836.2:c.-6C>T
  • NM_001320717.2:c.355C>T
  • NM_001371443.1:c.355C>T
  • NM_001371444.1:c.355C>T
  • NM_001371446.1:c.355C>T
  • NM_001371447.1:c.355C>T
  • NM_001371448.1:c.355C>T
  • NM_001371449.1:c.355C>T
  • NM_001371450.1:c.355C>T
  • NM_001371451.1:c.-6C>T
  • NM_001371452.1:c.-41-319C>T
  • NM_001371453.1:c.-122C>T
  • NM_001371454.1:c.-122C>T
  • NM_001371455.1:c.-122C>T
  • NM_001371456.1:c.-122C>T
  • NM_001374085.1:c.355C>T
  • NM_001374086.1:c.-122C>T
  • NM_004328.5:c.355C>T
  • NP_001073335.1:p.Arg119Ter
  • NP_001244271.1:p.Arg119Ter
  • NP_001244272.1:p.Arg119Ter
  • NP_001244273.1:p.Arg119Ter
  • NP_001307646.1:p.Arg119Ter
  • NP_001358372.1:p.Arg119Ter
  • NP_001358373.1:p.Arg119Ter
  • NP_001358375.1:p.Arg119Ter
  • NP_001358376.1:p.Arg119Ter
  • NP_001358377.1:p.Arg119Ter
  • NP_001358378.1:p.Arg119Ter
  • NP_001358379.1:p.Arg119Ter
  • NP_001361014.1:p.Arg119Ter
  • NP_004319.1:p.Arg119Ter
  • LRG_539t1:c.355C>T
  • LRG_539:g.6785C>T
  • NC_000002.11:g.219526163C>T
  • NM_001257342.2:c.355C>T
  • NM_004328.4:c.355C>T
  • NR_163955.1:n.1367C>T
Protein change:
R119*
Links:
dbSNP: rs770749420
NCBI 1000 Genomes Browser:
rs770749420
Molecular consequence:
  • NM_001318836.2:c.-6C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001371451.1:c.-6C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001371453.1:c.-122C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001371454.1:c.-122C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001371455.1:c.-122C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001371456.1:c.-122C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001374086.1:c.-122C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001371452.1:c.-41-319C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NR_163955.1:n.1367C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_001079866.2:c.355C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001257342.2:c.355C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001257343.2:c.355C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001257344.2:c.355C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001320717.2:c.355C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001371443.1:c.355C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001371444.1:c.355C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001371446.1:c.355C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001371447.1:c.355C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001371448.1:c.355C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001371449.1:c.355C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001371450.1:c.355C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001374085.1:c.355C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_004328.5:c.355C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001235762Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Pathogenic
(Dec 11, 2023)
germlineclinical testing

PubMed (7)
[See all records that cite these PMIDs]

SCV003822160Revvity Omics, Revvity
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(Jun 3, 2022)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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 (8)

Details of each submission

From Invitae, SCV001235762.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (7)

Description

This sequence change creates a premature translational stop signal (p.Arg119*) 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 present in population databases (rs770749420, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with BCS1L-related conditions. ClinVar contains an entry for this variant (Variation ID: 863524). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Revvity Omics, Revvity, SCV003822160.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jun 17, 2024