View genomic variant #0000022901

Variant on transcripts

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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.

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)	Protein	PolyPhen	GVS function	Splice distance	SIFT
SURF1	00000317	NM_001280787.1	0000022901	./.	-	-	c.-16_-7delinsAT	p.(=)	-	-	-	-
SURF1	00000318	NM_003172.3	0000022901	./.	-	-	c.312_321delinsAT	p.(Leu105*)	-	-	-	-

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ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV001268278;
Chromosome	9:136221516..136221517
ClinVar Allele ID	975261
Disease database name and identifier	MedGen:CN517202
ClinVar preferred disease name	not provided
HGVS variant names	NC 000009.11:g.136221516 136221517del
ClinVar review status	criteria provided, single submitter
Clinical Significance	Pathogenic
Variant type	Deletion
Sequence Ontology for variant type	SO:0000159
Gene symbol:Gene id.	SURF1:6834
Molecular consequence	SO:0001589|frameshift variant, SO:0001623|5 prime UTR variant
Allele origin	germline
dbSNP ID	1836518719
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV000513441; RCV003128413;
Chromosome	9:136221516..136221524
Allele frequencies from ESP	0.00056
Allele frequencies from ExAC	0.00007
ClinVar Allele ID	438426
Disease database name and identifier	MedGen:C3661900|.
ClinVar preferred disease name	not provided|See cases
HGVS variant names	NC 000009.11:g.136221516 136221524del
ClinVar review status	criteria provided, multiple submitters, no conflicts
Clinical Significance	Likely pathogenic
Variant type	Deletion
Sequence Ontology for variant type	SO:0000159
Variant clinical sources reported	ClinGen:CA200833336
Gene symbol:Gene id.	SURF1:6834
Molecular consequence	SO:0001623|5 prime UTR variant, SO:0001822|inframe deletion
Allele origin	germline
dbSNP ID	759270179
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV000874503; RCV001593100;
Chromosome	9:136221516..136221516
Allele frequencies from ESP	0.00008
Allele frequencies from ExAC	0.00006
Allele frequencies from TGP	0.00040
ClinVar Allele ID	692628
Disease database name and identifier	MedGen:CN517202|MONDO:MONDO:0009723, MedGen:C0023264, OMIM:256000, Orphanet:506
ClinVar preferred disease name	not provided|Leigh syndrome
HGVS variant names	NC 000009.11:g.136221516G>A
ClinVar review status	criteria provided, conflicting interpretations
Clinical Significance	Conflicting interpretations of pathogenicity
Conflicting clinical significance	Uncertain significance(1)|Likely benign(2)
Variant type	single nucleotide variant
Sequence Ontology for variant type	SO:0001483
Gene symbol:Gene id.	SURF1:6834
Molecular consequence	SO:0001623|5 prime UTR variant, SO:0001819|synonymous variant
Allele origin	germline
dbSNP ID	141425824
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV002800344;
Chromosome	9:136221516..136221516
ClinVar Allele ID	2036161
Disease database name and identifier	MONDO:MONDO:0009723, MedGen:C0023264, OMIM:256000, Orphanet:506
ClinVar preferred disease name	Leigh syndrome
HGVS variant names	NC 000009.11:g.136221516G>C
ClinVar review status	criteria provided, single submitter
Clinical Significance	Likely benign
Variant type	single nucleotide variant
Sequence Ontology for variant type	SO:0001483
Gene symbol:Gene id.	SURF1:6834
Molecular consequence	SO:0001623|5 prime UTR variant, SO:0001819|synonymous variant
Allele origin	germline
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV000013596; RCV000197023; RCV000235063; RCV002478694; RCV003417716;
Chromosome	9:136221516..136221525
ClinVar Allele ID	211368
Disease database name and identifier	.|MONDO:MONDO:0009068, MedGen:C5435656, OMIM:220110, Orphanet:254905|MONDO:MONDO:0014733, MedGen:C4225246, OMIM:616684, Orphanet:391351|MedGen:C3661900|MONDO:MONDO:0009723, MedGen:C0023264, OMIM:256000, Orphanet:506
ClinVar preferred disease name	SURF1-related condition|Cytochrome-c oxidase deficiency disease|Charcot-Marie-Tooth disease type 4K|not provided|Leigh syndrome
HGVS variant names	NC 000009.11:g.136221516 136221525delinsAT
ClinVar review status	criteria provided, multiple submitters, no conflicts
Clinical Significance	Pathogenic
Variant type	Indel
Sequence Ontology for variant type	SO:1000032
Variant clinical sources reported	ClinGen:CA321457|OMIM:185620.0003
Gene symbol:Gene id.	SURF1:6834
Molecular consequence	SO:0001589|frameshift variant, SO:0001623|5 prime UTR variant
Allele origin	germline
dbSNP ID	863224228
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV000512891; RCV002289700; RCV003128406; RCV003147496;
Chromosome	9:136221525..136221526
Allele frequencies from ESP	0.00056
Allele frequencies from ExAC	0.00019
ClinVar Allele ID	438427
Disease database name and identifier	MONDO:MONDO:0014733, MedGen:C4225246, OMIM:616684, Orphanet:391351|MedGen:C3661900|MONDO:MONDO:0009068, MedGen:C5435656, OMIM:220110, Orphanet:254905|.
ClinVar preferred disease name	Charcot-Marie-Tooth disease type 4K|not provided|Cytochrome-c oxidase deficiency disease|See cases
HGVS variant names	NC 000009.11:g.136221525 136221526insT
ClinVar review status	criteria provided, multiple submitters, no conflicts
Clinical Significance	Pathogenic/Likely pathogenic
Variant type	Insertion
Sequence Ontology for variant type	SO:0000667
Variant clinical sources reported	ClinGen:CA200833343
Gene symbol:Gene id.	SURF1:6834
Molecular consequence	SO:0001589|frameshift variant, SO:0001623|5 prime UTR variant
Allele origin	germline
dbSNP ID	764928653
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