View genomic variant #0000000154

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.

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

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.

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.

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

SIFT: SIFT Annotation

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

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Gene	Transcript ID	Transcript	Variant ID	Affects function	DNA change (cDNA)	Protein	GVS function	Position	Exon	PolyPhen	RNA change	SIFT
USH2A	00003116	NM_007123.5	0000000154	?/?	c.4133_4134insTC	p.(Asn1379Profs*54)	frameshift_variant	-	19/21	-	r.(?)	-
USH2A	00003348	NM_206933.2	0000000154	?/?	c.4133_4134insTC	p.(Asn1379Profs*54)	frameshift_variant	-	19/21	-	r.(?)	-

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ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV002863199;
Chromosome	1:216370012..216370012
ClinVar Allele ID	2077055
Disease database name and identifier	MedGen:CN517202
ClinVar preferred disease name	not provided
HGVS variant names	NC 000001.10:g.216370012G>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.	USH2A:7399|USH2A-AS1:105372918
Molecular consequence	SO:0001819|synonymous variant
Allele origin	germline
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV001074304; RCV001243846; RCV002471033; RCV003323795;
Chromosome	1:216370013..216370013
ClinVar Allele ID	855990
Disease database name and identifier	MONDO:MONDO:0019501, MeSH:D052245, MedGen:C0271097, OMIM:PS276900, Orphanet:886|Human Phenotype Ontology:HP:0000556, Human Phenotype Ontology:HP:0007736, Human Phenotype Ontology:HP:0007910, Human Phenotype Ontology:HP:0007974, Human Phenotype Ontology:HP:0007982, MONDO:MONDO:0019118, MeSH:D058499, MedGen:C0854723, Orphanet:71862|MedGen:CN517202|MONDO:MONDO:0010169, MedGen:C1848634, OMIM:276901, Orphanet:231178, Orphanet:886
ClinVar preferred disease name	Usher syndrome|Retinal dystrophy|not provided|Usher syndrome type 2A
HGVS variant names	NC 000001.10:g.216370013A>G
ClinVar review status	criteria provided, conflicting interpretations
Clinical Significance	Conflicting interpretations of pathogenicity
Conflicting clinical significance	Pathogenic(2)|Likely pathogenic(1)|Uncertain significance(1)
Variant type	single nucleotide variant
Sequence Ontology for variant type	SO:0001483
Gene symbol:Gene id.	USH2A:7399|USH2A-AS1:105372918
Molecular consequence	SO:0001583|missense variant
Allele origin	germline
dbSNP ID	2034852728
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