View genomic variant #0000025648

Chromosome	2
Allele	Unknown
Affects function (as reported)	Not classified
Affects function (by curator)	Not classified
Type	-
DNA change (genomic) (Relative to hg19 / GRCh37)	g.26415259_26415260insTGA
Published as	-
GERP	-
Segregation	-
DB-ID	HADHA_000092
MSCV	-
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	Lishuang Shen

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.

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

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

Legend

Gene	Transcript ID	Transcript	Variant ID	Affects function	Location	Exon	DNA change (cDNA)	Protein	PolyPhen	GVS function	Splice distance	SIFT
HADHA	00000786	NM_000182.4	0000025648	./.	-	-	c.1919_1920insTCA	p.(Tyr639_Gln640insHis)	-	-	-	-
HADHA	00000787	XM_005264275.1	0000025648	./.	-	-	c.1781_1782insTCA	p.(Tyr593_Gln594insHis)	-	-	-	-
HADHA	00000788	XM_005264276.1	0000025648	./.	-	-	c.1658_1659insTCA	p.(Tyr552_Gln553insHis)	-	-	-	-

Legend

ClinVar @ MSeqDR
RCVaccession	RCV000671365;
Chromosome	2:26415259..26415260
ClinVar Allele ID	541965
Disease database name and identifier	MONDO:MONDO:0012173, MedGen:C3711645, OMIM:609016, Orphanet:5
ClinVar preferred disease name	Long chain 3-hydroxyacyl-CoA dehydrogenase deficiency
HGVS variant names	NC 000002.11:g.26415261 26415263dup
ClinVar review status	criteria provided, single submitter
Clinical Significance	Uncertain significance
Variant type	Duplication
Sequence Ontology for variant type	SO:1000035
Gene symbol:Gene id.	HADHA:3030\|GAREM2:150946
Molecular consequence	SO:0001821\|inframe insertion
Allele origin	unknown
dbSNP ID	796051971
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession RCV000185935; RCV002252030; RCV002513955;
Chromosome 2:26415259..26415260
ClinVar Allele ID 199995
Disease database name and identifier MONDO:MONDO:0012172, MedGen:C1969443, OMIM:609015, Orphanet:746|MONDO:MONDO:0012173, MedGen:C3711645, OMIM:609016, Orphanet:5|MedGen:CN517202|.
ClinVar preferred disease name Mitochondrial trifunctional protein deficiency|Long chain 3-hydroxyacyl-CoA dehydrogenase deficiency|not provided|See cases
HGVS variant names NC 000002.11:g.26415260 26415263dup
ClinVar review status criteria provided, multiple submitters, no conflicts
Clinical Significance Pathogenic
Variant type Duplication
Sequence Ontology for variant type SO:1000035
Variant clinical sources reported ClinGen:CA312583
Gene symbol:Gene id. HADHA:3030|GAREM2:150946
Molecular consequence SO:0001589|frameshift variant
Allele origin germline
dbSNP ID 796051971
Variant Flags
:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession RCV000409331; RCV001234387;
Chromosome 2:26415261..26415264
ClinVar Allele ID 357251
Disease database name and identifier MONDO:MONDO:0012172, MedGen:C1969443, OMIM:609015, Orphanet:746|MONDO:MONDO:0012173, MedGen:C3711645, OMIM:609016, Orphanet:5
ClinVar preferred disease name Mitochondrial trifunctional protein deficiency|Long chain 3-hydroxyacyl-CoA dehydrogenase deficiency
HGVS variant names NC 000002.11:g.26415264 26415267del
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:CA16040871
Gene symbol:Gene id. HADHA:3030|GAREM2:150946
Molecular consequence SO:0001589|frameshift variant
Allele origin germline
dbSNP ID 1057517397
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