NM_001079866.2(BCS1L):c.-50+405A>G AND GRACILE syndrome

Germline classification:: Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:: May 28, 2019
Review status:: criteria provided, conflicting classifications

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:: RCV000668517.4

Allele description [Variation Report for NM_001079866.2(BCS1L):c.-50+405A>G]

NM_001079866.2(BCS1L):c.-50+405A>G

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.-50+405A>G

HGVS:

NC_000002.12:g.218660148A>G
NG_008018.1:g.5493A>G
NG_033099.1:g.4393T>C
NM_001079866.2:c.-50+405A>GMANE SELECT
NM_001257342.2:c.-68A>G
NM_001257343.2:c.-120A>G
NM_001257344.2:c.-50+348A>G
NM_001318836.2:c.-41+405A>G
NM_001320717.2:c.-164-159A>G
NM_001371443.1:c.-164-159A>G
NM_001371444.1:c.-323A>G
NM_001371446.1:c.-650A>G
NM_001371447.1:c.-32+405A>G
NM_001371448.1:c.-164-159A>G
NM_001371449.1:c.-235A>G
NM_001371450.1:c.-323A>G
NM_001371451.1:c.-641A>G
NM_001371452.1:c.-42+405A>G
NM_001371453.1:c.-1316A>G
NM_001371454.1:c.-799A>G
NM_001371455.1:c.-526+405A>G
NM_001371456.1:c.-544A>G
NM_001374085.1:c.-840A>G
NM_001374086.1:c.-1316A>G
NM_004328.5:c.-147A>G
LRG_539t1:c.-147A>G
LRG_539:g.5493A>G
NC_000002.11:g.219524871A>G
NM_004328.4:c.-147A>G
NR_163955.1:n.173A>G

Links:

dbSNP: rs898301590

NCBI 1000 Genomes Browser:

rs898301590

Molecular consequence:

NM_001257342.2:c.-68A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001257343.2:c.-120A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001371444.1:c.-323A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001371446.1:c.-650A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001371449.1:c.-235A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001371450.1:c.-323A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001371451.1:c.-641A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001371453.1:c.-1316A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001371454.1:c.-799A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001371456.1:c.-544A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001374085.1:c.-840A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001374086.1:c.-1316A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_004328.5:c.-147A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001079866.2:c.-50+405A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001257344.2:c.-50+348A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001318836.2:c.-41+405A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001320717.2:c.-164-159A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001371443.1:c.-164-159A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001371447.1:c.-32+405A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001371448.1:c.-164-159A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001371452.1:c.-42+405A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001371455.1:c.-526+405A>G - intron variant - [Sequence Ontology: SO:0001627]
NR_163955.1:n.173A>G - 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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000793135	Counsyl	criteria provided, single submitter (Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))	Uncertain significance (Jul 28, 2017)	unknown	clinical testing	PubMed (2) [See all records that cite these PMIDs] 19389488, 28496993 Citation Link,
SCV001136212	Mendelics	criteria provided, single submitter (Mendelics Assertion Criteria 2017)	Likely pathogenic (May 28, 2019)	unknown	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000793135

Counsyl

criteria provided, single submitter

(Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))

Uncertain significance
(Jul 28, 2017)

unknown

clinical testing

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

Citation Link,

SCV001136212

Mendelics

criteria provided, single submitter

(Mendelics Assertion Criteria 2017)

Likely pathogenic
(May 28, 2019)

unknown

clinical testing

Citation Link

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

Citations

PubMed

Pathogenic mutations in the 5' untranslated region of BCS1L mRNA in mitochondrial complex III deficiency.

Gil-Borlado MC, González-Hoyuela M, Blázquez A, García-Silva MT, Gabaldón T, Manzanares J, Vara J, Martín MA, Seneca S, Arenas J, Ugalde C.

Mitochondrion. 2009 Sep;9(5):299-305. doi: 10.1016/j.mito.2009.04.001. Epub 2009 Apr 21.

PubMed [citation]

PMID:: 19389488

Successful Application of Whole Genome Sequencing in a Medical Genetics Clinic.

Bick D, Fraser PC, Gutzeit MF, Harris JM, Hambuch TM, Helbling DC, Jacob HJ, Kersten JN, Leuthner SR, May T, North PE, Prisco SZ, Schuler BA, Shimoyama M, Strong KA, Van Why SK, Veith R, Verbsky J, Weborg AM Jr, Wilk BM, Willoughby RE Jr, Worthey EA, et al.

J Pediatr Genet. 2017 Jun;6(2):61-76. doi: 10.1055/s-0036-1593968. Epub 2016 Nov 28.

PubMed [citation]

PMID:: 28496993
PMCID:: PMC5423809

Details of each submission

From Counsyl, SCV000793135.1

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

#	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

From Mendelics, SCV001136212.1

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

#	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: Feb 4, 2024

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