View genomic variant #0000018701

Chromosome	19
Allele	Unknown
Affects function (as reported)	Affects function
Affects function (by curator)	Affects function
Type	-
DNA change (genomic) (Relative to hg19 / GRCh37)	g.30193879_30193881del
Published as	-
GERP	-
Segregation	-
DB-ID	C19orf12_000001 See all 2 reported entries
MSCV	MSCV_0000768
dbSNP ID	-
Frequency	-
Sources	; clinvar;
Reference	-
Variant remarks	-
Genetic origin	-
Variant_disease	-
Average frequency (large NGS studies)	Variant not found in online data sets
Owner	LOVD

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

1 entry on 1 page. Showing entry 1.

Legend

Gene	Transcript ID	Transcript	Variant ID	Affects function	Location	Exon	DNA change (cDNA)	Position	RNA change	Protein	PolyPhen	GVS function	Splice distance	SIFT
C19orf12	00003109	NM_031448.4	0000018701	./.	-	-	c.164_166del	-	r.(?)	p.(Gly55del)	-	-	-	-

Legend

ClinVar @ MSeqDR
RCVaccession	RCV002237737; RCV002293552;
Chromosome	19:30193878..30193879
ClinVar Allele ID	1674731
Disease database name and identifier	MedGen:C3661900\|MONDO:MONDO:0014024, MedGen:C2680446, OMIM:615043, Orphanet:320370
ClinVar preferred disease name	not provided\|Hereditary spastic paraplegia 43
HGVS variant names	NC 000019.9:g.30193885dup
ClinVar review status	criteria provided, conflicting interpretations
Clinical Significance	Conflicting interpretations of pathogenicity
Conflicting clinical significance	Likely pathogenic(1)\|Uncertain significance(1)
Variant type	Duplication
Sequence Ontology for variant type	SO:1000035
Gene symbol:Gene id.	C19orf12:83636
Allele origin	germline
dbSNP ID	398122409
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession RCV001848364; RCV002236027; RCV002473307;
Chromosome 19:30193879..30193879
ClinVar Allele ID 1335964
Disease database name and identifier MONDO:MONDO:0019064, MedGen:C0037773, OMIM:PS303350, Orphanet:685|MONDO:MONDO:0014024, MedGen:C2680446, OMIM:615043, Orphanet:320370|MedGen:C3661900
ClinVar preferred disease name Hereditary spastic paraplegia|Hereditary spastic paraplegia 43|not provided
HGVS variant names NC 000019.9:g.30193885del
ClinVar review status criteria provided, multiple submitters, no conflicts
Clinical Significance Pathogenic/Likely pathogenic
Variant type Deletion
Sequence Ontology for variant type SO:0000159
Gene symbol:Gene id. C19orf12:83636
Allele origin germline
dbSNP ID 398122409
Variant Flags
:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession RCV000074455; RCV001311507; RCV002265593;
Chromosome 19:30193879..30193881
ClinVar Allele ID 94435
Disease database name and identifier MONDO:MONDO:0018307, MedGen:C2931845, OMIM:PS234200, Orphanet:385|MedGen:C3661900|MONDO:MONDO:0013674, MedGen:C3280371, OMIM:614298, Orphanet:289560
ClinVar preferred disease name Neurodegeneration with brain iron accumulation|not provided|Neurodegeneration with brain iron accumulation 4
HGVS variant names NC 000019.9:g.30193883 30193885del
ClinVar review status criteria provided, multiple submitters, no conflicts
Clinical Significance Pathogenic/Likely pathogenic
Variant type Deletion
Sequence Ontology for variant type SO:0000159
Variant clinical sources reported ClinGen:CA266201|OMIM:614297.0007
Gene symbol:Gene id. C19orf12:83636
Molecular consequence SO:0001574|splice acceptor variant
Allele origin
dbSNP ID 398122409
Variant Flags
:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession RCV002235479;
Chromosome 19:30193880..30193880
Allele frequencies from TGP 0.00020
ClinVar Allele ID 688978
Disease database name and identifier MONDO:MONDO:0014024, MedGen:C2680446, OMIM:615043, Orphanet:320370
ClinVar preferred disease name Hereditary spastic paraplegia 43
HGVS variant names NC 000019.9:g.30193880C>A
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. C19orf12:83636
Molecular consequence SO:0001623|5 prime UTR variant, SO:0001819|synonymous variant
Allele origin germline
dbSNP ID 201194487
Variant Flags
:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession RCV000869606; RCV002265905;
Chromosome 19:30193880..30193880
Allele frequencies from ESP 0.00031
ClinVar Allele ID 688979
Disease database name and identifier MedGen:CN169374|MONDO:MONDO:0014024, MedGen:C2680446, OMIM:615043, Orphanet:320370
ClinVar preferred disease name not specified|Hereditary spastic paraplegia 43
HGVS variant names NC 000019.9:g.30193880C>T
ClinVar review status criteria provided, multiple submitters, no conflicts
Clinical Significance Likely benign
Variant type single nucleotide variant
Sequence Ontology for variant type SO:0001483
Gene symbol:Gene id. C19orf12:83636
Molecular consequence SO:0001623|5 prime UTR variant, SO:0001819|synonymous variant
Allele origin germline
dbSNP ID 201194487
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