View genomic variant #0000025898

Chromosome	2
Allele	Unknown
Affects function (as reported)	Not classified
Affects function (by curator)	Not classified
Type	-
DNA change (genomic) (Relative to hg19 / GRCh37)	g.219525978C>T
Published as	-
GERP	-
Segregation	-
DB-ID	BCS1L_000047
MSCV	-
dbSNP ID	-
Frequency	-
Sources	; clinvar;
Reference	-
Variant remarks	-
Genetic origin	-
Variant_disease	-
Average frequency (large NGS studies)	8.0E-5 View details
Owner	Lishuang Shen

Variant on transcripts

Legend

Please note that a short description of a certain column can be displayed when you move your mouse cursor over the column's header and hold it still. Below, a more detailed description is shown per column.

Affects function: The variant's effect on the protein's function, in the format 'R/C' where R is the value reported by the source and C is the value concluded by the curator; '+' indicating the variant affects function, '+?' probably affects function, '+*' affects function, not associated with individual's disease phenotype, '#' affects function, not associated with any known disease phenotype, '-' does not affect function, '-?' probably does not affect function, '?' effect unknown, '.' effect not classified.

Location: Location of variant at DNA level; note that the variant location can also be derived from the variant description.
All options:

5' gene flanking
5' UTR
Exon
Intron
3' UTR
3' gene flanking

Exon: Number of exon/intron containing variant; 2 = exon 2, 12i = intron 12, 2i_7i = exons 3 to 7, 8i_9 = border intron 8/exon 9.

DNA change (cDNA): Description of variant at DNA level, based on a coding DNA reference sequence (following HGVS recommendations); e.g. c.123C>T, c.123_145del, c.123_126dup.

Position: Position of variant in coding DNA sequence; note that coding DNA position can also be derived from the variant description.

RNA change: Description of variant at RNA level (following HGVS recommendations).

r.123c>u
r.? = unknown
r.(?) = RNA not analysed but probably transcribed copy of DNA variant
r.spl? = RNA not analysed but variant probably affects splicing
r.(spl?) = RNA not analysed but variant may affect splicing
r.0? = change expected to abolish transcription

Protein: Description of variant at protein level (following HGVS recommendations).

p.(Arg345Pro) = change predicted from DNA (RNA not analysed)
p.Arg345Pro = change derived from RNA analysis
p.? = unknown effect
p.0? = probably no protein produced

PolyPhen: Effect of variant, predicted by PolyPhen.
All options:

benign = Benign
possiblyDamaging = Possibly damaging
probablyDamaging = Probably damaging
noPrediction = No prediction

GVS function: The functional annotation of this position from the Genome Variation Server.
All options:

intergenic
near-gene-5
utr-5
coding
coding-near-splice
coding-synonymous
coding-synonymous-near-splice
codingComplex
codingComplex-near-splice
frameshift
frameshift-near-splice
missense
missense-near-splice
splice-5
intron
splice-3
stop-gained
stop-gained-near-splice
stop-lost
stop-lost-near-splice
utr-3
near-gene-3

Splice distance: The distance to the nearest splice site.

SIFT: SIFT Annotation

2 entries on 1 page. Showing entries 1 - 2.

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Gene	Transcript ID	Transcript	Variant ID	Affects function	Location	Exon	DNA change (cDNA)	Position	RNA change	Protein	PolyPhen	GVS function	Splice distance	SIFT
BCS1L	00000013	NM_001079866.1	0000025898	./.	-	-	c.268C>T	-	r.(?)	p.(Arg90Cys)	-	-	-	-
BCS1L	00000012	NM_004328.4	0000025898	./.	-	-	c.268C>T	-	r.(?)	p.(Arg90Cys)	-	-	-	-

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ClinVar @ MSeqDR
RCVaccession	RCV000778592; RCV000850204; RCV001003574; RCV001003575; RCV001855960; RCV003472287;
Chromosome	2:219525978..219525978
Allele frequencies from ESP	0.00008
Allele frequencies from ExAC	0.00002
ClinVar Allele ID	613536
Disease database name and identifier	MONDO:MONDO:0009872, MedGen:C0266006, OMIM:262000, Orphanet:123\|Human Phenotype Ontology:HP:0000252, Human Phenotype Ontology:HP:0001366, Human Phenotype Ontology:HP:0005485, Human Phenotype Ontology:HP:0005489, Human Phenotype Ontology:HP:0005497, MONDO:MONDO:0001149, MedGen:C4551563\|Human Phenotype Ontology:HP:0001294, Human Phenotype Ontology:HP:0100022, MONDO:MONDO:0005395, MedGen:C0026650\|Human Phenotype Ontology:HP:0002237, Human Phenotype Ontology:HP:0002291, Human Phenotype Ontology:HP:0004522, Human Phenotype Ontology:HP:0004538, Human Phenotype Ontology:HP:0008070, MedGen:C5551005\|Human Phenotype Ontology:HP:0007196, Human Phenotype Ontology:HP:0010864, MedGen:C0036857\|Human Phenotype Ontology:HP:0000730, Human Phenotype Ontology:HP:0001249, Human Phenotype Ontology:HP:0001267, Human Phenotype Ontology:HP:0001286, Human Phenotype Ontology:HP:0002122, Human Phenotype Ontology:HP:0002192, Human Phenotype Ontology:HP:0002316, Human Phenotype Ontology:HP:0002382, Human Phenotype Ontology:HP:0002386, Human Phenotype Ontology:HP:0002402, Human Phenotype Ontology:HP:0002458, Human Phenotype Ontology:HP:0002482, Human Phenotype Ontology:HP:0002499, Human Phenotype Ontology:HP:0002543, Human Phenotype Ontology:HP:0003767, Human Phenotype Ontology:HP:0006833, Human Phenotype Ontology:HP:0007154, Human Phenotype Ontology:HP:0007176, Human Phenotype Ontology:HP:0007180, MONDO:MONDO:0001071, MeSH:D008607, MedGen:C3714756\|MedGen:C3661900\|MONDO:MONDO:0007415, MedGen:C3541471, OMIM:124000, Orphanet:254902
ClinVar preferred disease name	Pili torti-deafness syndrome\|Microcephaly\|Abnormality of movement\|Sparse hair\|Intellectual disability, severe\|Intellectual disability\|not provided\|Mitochondrial complex III deficiency nuclear type 1
HGVS variant names	NC 000002.11:g.219525978C>T
ClinVar review status	criteria provided, conflicting interpretations
Clinical Significance	Conflicting interpretations of pathogenicity
Conflicting clinical significance	Likely pathogenic(3)\|Uncertain significance(1)
Variant type	single nucleotide variant
Sequence Ontology for variant type	SO:0001483
Gene symbol:Gene id.	BCS1L:617
Molecular consequence	SO:0001583\|missense variant, SO:0001619\|non-coding transcript variant, SO:0001623\|5 prime UTR variant, SO:0001627\|intron variant
Allele origin	germline
dbSNP ID	369691608
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

MSeqDR View Variant at Gbrowse

Mitomap Mitochondrial Variant Phenotype Information:

None

Ensembl Variant Phenotype Information:

None