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NM_001079866.2(BCS1L):c.-49-539T>A AND GRACILE syndrome

Germline classification:
Uncertain significance (2 submissions)
Last evaluated:
Jun 7, 2018
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:
RCV000049824.1

Allele description [Variation Report for NM_001079866.2(BCS1L):c.-49-539T>A]

NM_001079866.2(BCS1L):c.-49-539T>A

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.-49-539T>A
HGVS:
  • NC_000002.12:g.218660400T>A
  • NG_008018.1:g.5745T>A
  • NG_033099.1:g.4141A>T
  • NM_001079866.2:c.-49-539T>AMANE SELECT
  • NM_001257342.2:c.-50+234T>A
  • NM_001257343.2:c.-50+182T>A
  • NM_001257344.2:c.-49-539T>A
  • NM_001318836.2:c.-41+657T>A
  • NM_001320717.2:c.-71T>A
  • NM_001371443.1:c.-71T>A
  • NM_001371444.1:c.-71T>A
  • NM_001371446.1:c.-398T>A
  • NM_001371447.1:c.-31-557T>A
  • NM_001371448.1:c.-71T>A
  • NM_001371449.1:c.-71T>A
  • NM_001371450.1:c.-71T>A
  • NM_001371451.1:c.-389T>A
  • NM_001371452.1:c.-42+657T>A
  • NM_001371453.1:c.-1064T>A
  • NM_001371454.1:c.-547T>A
  • NM_001371455.1:c.-525-539T>A
  • NM_001371456.1:c.-526+234T>A
  • NM_001374085.1:c.-588T>A
  • NM_001374086.1:c.-1064T>A
  • NM_004328.5:c.-50+155T>A
  • LRG_539t1:c.-50+155T>A
  • LRG_539:g.5745T>A
  • NC_000002.11:g.219525123T>A
  • NM_004328.4:c.-50+155T>A
  • NR_163955.1:n.425T>A
Links:
dbSNP: rs386833855
NCBI 1000 Genomes Browser:
rs386833855
Molecular consequence:
  • NM_001320717.2:c.-71T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001371443.1:c.-71T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001371444.1:c.-71T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001371446.1:c.-398T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001371448.1:c.-71T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001371449.1:c.-71T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001371450.1:c.-71T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001371451.1:c.-389T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001371453.1:c.-1064T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001371454.1:c.-547T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001374085.1:c.-588T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001374086.1:c.-1064T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001079866.2:c.-49-539T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001257342.2:c.-50+234T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001257343.2:c.-50+182T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001257344.2:c.-49-539T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001318836.2:c.-41+657T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001371447.1:c.-31-557T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001371452.1:c.-42+657T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001371455.1:c.-525-539T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001371456.1:c.-526+234T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_004328.5:c.-50+155T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NR_163955.1:n.425T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
GRACILE syndrome (FLNMS)
Synonyms:
Finnish lactic acidosis with hepatic hemosiderosis; Fellman syndrome; Growth Retardation, Aminoaciduria, Cholestasis, Iron overload, Lactic acidosis and Early death; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0011308; MedGen: C1864002; Orphanet: 53693; OMIM: 603358

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000082233Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM)
no assertion criteria provided
probable-pathogenicnot providednot provided

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

SCV000800718Counsyl
criteria provided, single submitter

(Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))
Uncertain significance
(Jun 7, 2018)
unknownclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Citation Link

Description

FinDis database variant: This variant was not found or characterized by our laboratory, data were collected from public sources: see reference

SCV000082233

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providednot providednot providednot providednot providednot provided1not providedliterature only
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

BCS1L gene mutation presenting with GRACILE-like syndrome and complex III deficiency.

Lynn AM, King RI, Mackay RJ, Florkowski CM, Wilson CJ.

Ann Clin Biochem. 2012 Mar;49(Pt 2):201-3. doi: 10.1258/acb.2011.011180. Epub 2012 Jan 25.

PubMed [citation]
PMID:
22277166

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

Details of each submission

From Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM), SCV000082233.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providednot provided PubMed (1)

Description

Converted during submission to Likely pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1not providednot provided1not providednot providednot providednot providednot providednot provided

From Counsyl, SCV000800718.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Feb 20, 2024