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

Germline classification:: Conflicting classifications of pathogenicity (2 submissions)
Last evaluated:: Jun 7, 2018
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

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:: RCV000049824.3

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

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

Gene:

BCS1L:BCS1 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

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:: FELLMAN SYNDROME; FINNISH LETHAL NEONATAL METABOLIC SYNDROME
Identifiers:: MONDO: MONDO:0011308; MedGen: C1864002; Orphanet: 53693; OMIM: 603358

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000082233	Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM)	no assertion criteria provided	Likely pathogenic	unknown	not provided
SCV000800718	Counsyl	no assertion criteria provided	Uncertain significance (Jun 7, 2018)	unknown	clinical testing	PubMed (2) [See all records that cite these PMIDs] 22277166, 12215968

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000082233

Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM)

no assertion criteria provided

Likely pathogenic

unknown

not provided

SCV000800718

Counsyl

no assertion criteria provided

Uncertain significance
(Jun 7, 2018)

unknown

clinical testing

PubMed (2)
[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	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	not provided	not provided	not provided	not provided	not provided	1	not provided	literature only

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), SCV000082233.2

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

Description

Converted during submission from probable-pathogenic to Likely pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	not provided	1	not provided	not provided		not provided	not provided	not provided	not provided

From Counsyl, SCV000800718.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This submission and the accompanying classification are no longer maintained by the submitter. For more information on current observations and classification, please contact variantquestions@myriad.com.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Nov 2, 2025

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