View genomic variant #0000001439

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

1 entry on 1 page. Showing entry 1.

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Gene	Transcript ID	Transcript	Variant ID	Affects function	Location	Exon	DNA change (cDNA)	Protein	PolyPhen	GVS function	Splice distance	SIFT
MT-ATP6	00001337	MT-ATP6-201	0000001439	+/+	-	.	c.467T>G	p.L156R	-	-	-	-

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ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV000010273; RCV000010274; RCV000191106; RCV000224643; RCV000414771; RCV000495419; RCV000754646; RCV001376274; RCV001542706; RCV002285006;
Chromosome	M:8993..8993
ClinVar Allele ID	24680
Disease database name and identifier	Human Phenotype Ontology:HP:0001251, Human Phenotype Ontology:HP:0001253, Human Phenotype Ontology:HP:0002513, Human Phenotype Ontology:HP:0007050, Human Phenotype Ontology:HP:0007157, MONDO:MONDO:0000437, MedGen:C0007758, Orphanet:102002|MONDO:MONDO:0027069, MedGen:C3275684, OMIM:500015|MedGen:CN169374|MedGen:C3661900|MONDO:MONDO:0044970, MeSH:D028361, MedGen:C0751651, Orphanet:68380|MONDO:MONDO:0010794, MedGen:C1328349, OMIM:551500, Orphanet:644|Human Phenotype Ontology:HP:0001086, Human Phenotype Ontology:HP:0001112, MONDO:MONDO:0010788, MedGen:C0917796, OMIM:535000, Orphanet:104|MONDO:MONDO:0009723, MedGen:C0023264, OMIM:256000, Orphanet:506|Human Phenotype Ontology:HP:0005651, Human Phenotype Ontology:HP:0005662, Human Phenotype Ontology:HP:0005713, Human Phenotype Ontology:HP:0005801, Human Phenotype Ontology:HP:0005821, Human Phenotype Ontology:HP:0006195, Human Phenotype Ontology:HP:0006218, Human Phenotype Ontology:HP:0006240, Human Phenotype Ontology:HP:0009698, Human Phenotype Ontology:HP:0100490, MedGen:C0409348|Human Phenotype Ontology:HP:0002744, MedGen:C1398522|Human Phenotype Ontology:HP:0000316, Human Phenotype Ontology:HP:0000578, Human Phenotype Ontology:HP:0002001, Human Phenotype Ontology:HP:0004657, Human Phenotype Ontology:HP:0007871, MedGen:C0020534, OMIM:145400|Human Phenotype Ontology:HP:0001162, Human Phenotype Ontology:HP:0004698, Human Phenotype Ontology:HP:0005763, Human Phenotype Ontology:HP:0009984, MONDO:MONDO:0017426, MedGen:C0431904|MedGen:C0431659|Human Phenotype Ontology:HP:0001622, MedGen:C0151526|Human Phenotype Ontology:HP:0000779, Human Phenotype Ontology:HP:0001554, Human Phenotype Ontology:HP:0006610, MedGen:C1827524|Human Phenotype Ontology:HP:0000369, MedGen:C0239234|Human Phenotype Ontology:HP:0000510, Human Phenotype Ontology:HP:0001127, Human Phenotype Ontology:HP:0007635, Human Phenotype Ontology:HP:0007645, Human Phenotype Ontology:HP:0007742, Human Phenotype Ontology:HP:0007816, Human Phenotype Ontology:HP:0007826, Human Phenotype Ontology:HP:0007927, Human Phenotype Ontology:HP:0008036, MedGen:C4551714
ClinVar preferred disease name	Cerebellar ataxia|Mitochondrial complex 5 (ATP synthase) deficiency, mitochondrial type 1|not specified|not provided|Mitochondrial disease|NARP syndrome|Leber optic atrophy|Leigh syndrome|Camptodactyly of finger|Bilateral cleft lip and palate|Hypertelorism|Postaxial hand polydactyly|Hypoplasia of scrotum|Premature birth|Wide intermamillary distance|Low-set ears|Rod-cone dystrophy
HGVS variant names	NC 012920.1:m.8993T>G
ClinVar review status	reviewed by expert panel
Clinical Significance	Pathogenic
Variant type	single nucleotide variant
Sequence Ontology for variant type	SO:0001483
Variant clinical sources reported	ClinGen:CA250380|Genetic Testing Registry (GTR):GTR000500595|Genetic Testing Registry (GTR):GTR000556568|Genetic Testing Registry (GTR):GTR000556575|Genetic Testing Registry (GTR):GTR000591967|Genetic Testing Registry (GTR):GTR000591969|Genetic Testing Registry (GTR):GTR000591975|Genetic Testing Registry (GTR):GTR000591976|OMIM:516060.0001
Gene symbol:Gene id.	MT-ATP6:4508|MT-ATP8:4509|MT-TC:4511|MT-CO1:4512|MT-CO2:4513|MT-CO3:4514|MT-ND1:4535|MT-ND2:4536|MT-ND3:4537|MT-ND4:4538
Allele origin
dbSNP ID	199476133
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV000854391;
Chromosome	M:8993..8994
ClinVar Allele ID	681583
Disease database name and identifier	MONDO:MONDO:0010794, MedGen:C1328349, OMIM:551500, Orphanet:644
ClinVar preferred disease name	NARP syndrome
HGVS variant names	NC 012920.1:m.8993 8994inv
ClinVar review status	criteria provided, single submitter
Clinical Significance	Pathogenic
Variant type	Inversion
Sequence Ontology for variant type	SO:1000036
Gene symbol:Gene id.	MT-ATP6:4508
Allele origin	germline
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

MSeqDR View Variant at Gbrowse

Mitomap Mitochondrial Variant Phenotype Information:

Ensembl Variant Phenotype Information:

None