View genomic variant #0000017224

Variant on transcripts

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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

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.

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.

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

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

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

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

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

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

Splice distance: The distance to the nearest splice site.

SIFT: SIFT Annotation

3 entries on 1 page. Showing entries 1 - 3.

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Gene	Transcript ID	Transcript	Variant ID	Affects function	Location	DNA change (cDNA)	Exon	Protein	GVS function	Position	PolyPhen	RNA change	Splice distance	SIFT
SLC25A15	00001152	NM_014252.3	0000017224	./.	-	c.553_555del	-	p.(Phe188del)	-	-	-	r.(?)	-	-
TPTE2P5	00003113	NR_038258.1	0000017224	./.	-	n.623-6672_623-6670del	-	-	-	-	-	-	-	-
SLC25A15	00001153	XM_005266210.1	0000017224	./.	-	c.514_516del	-	p.(Phe175del)	-	-	-	r.(?)	-	-

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ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV000006358; RCV002460886; RCV003421907;
Chromosome	13:41381530..41381532
ClinVar Allele ID	21031
Disease database name and identifier	.|MedGen:C3661900|MONDO:MONDO:0009393, MedGen:C0268540, OMIM:238970, Orphanet:415
ClinVar preferred disease name	SLC25A15-related condition|not provided|Hyperornithinemia-hyperammonemia-homocitrullinuria syndrome
HGVS variant names	NC 000013.10:g.41381530TTC[3]
ClinVar review status	criteria provided, multiple submitters, no conflicts
Clinical Significance	Pathogenic
Variant type	Microsatellite
Sequence Ontology for variant type	SO:0000289
Variant clinical sources reported	ClinGen:CA340486|OMIM:603861.0001
Gene symbol:Gene id.	SLC25A15:10166
Molecular consequence	SO:0001822|inframe deletion
Allele origin	germline
dbSNP ID	202247803
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV002806583;
Chromosome	13:41381531..41381531
ClinVar Allele ID	2059729
Disease database name and identifier	MONDO:MONDO:0009393, MedGen:C0268540, OMIM:238970, Orphanet:415
ClinVar preferred disease name	Hyperornithinemia-hyperammonemia-homocitrullinuria syndrome
HGVS variant names	NC 000013.10:g.41381531T>C
ClinVar review status	criteria provided, single submitter
Clinical Significance	Uncertain significance
Variant type	single nucleotide variant
Sequence Ontology for variant type	SO:0001483
Gene symbol:Gene id.	SLC25A15:10166
Molecular consequence	SO:0001583|missense variant
Allele origin	germline
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV001403001;
Chromosome	13:41381532..41381532
ClinVar Allele ID	1080082
Disease database name and identifier	MONDO:MONDO:0009393, MedGen:C0268540, OMIM:238970, Orphanet:415
ClinVar preferred disease name	Hyperornithinemia-hyperammonemia-homocitrullinuria syndrome
HGVS variant names	NC 000013.10:g.41381532C>T
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.	SLC25A15:10166
Molecular consequence	SO:0001819|synonymous variant
Allele origin	germline
dbSNP ID	1489139087
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