View genomic variant #0000000794

Chromosome	2
Allele	Unknown
Affects function (as reported)	Affects function
Affects function (by curator)	Affects function
Type	subst
DNA change (genomic) (Relative to hg19 / GRCh37)	g.26437316A>T
Published as	-
GERP	5.430
Segregation	-
DB-ID	HADHA_000005 See all 2 reported entries
MSCV	MSCV_0000794
dbSNP ID	rs137852774
Frequency	-
Sources	;
Reference	2019931;9739053
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.

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	0000000794	?/?	-	9/20	c.914T>A	p.(Ile305Asn)	probably_damaging(0.98)	missense_variant	-	deleterious(0)
HADHA	00000787	XM_005264275.1	0000000794	?/?	-	9/20	c.776T>A	p.(Ile259Asn)	-	missense_variant	-	-
HADHA	00000788	XM_005264276.1	0000000794	?/?	-	8/19	c.653T>A	p.(Ile218Asn)	-	missense_variant	-	-

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ClinVar @ MSeqDR
RCVaccession	RCV000520333; RCV000674233; RCV001853697; RCV003403243;
Chromosome	2:26437316..26437316
ClinVar Allele ID	443226
Disease database name and identifier	MONDO:MONDO:0012173, MedGen:C3711645, OMIM:609016, Orphanet:5\|MONDO:MONDO:0012172, MedGen:C1969443, OMIM:609015, Orphanet:746\|MedGen:CN169374\|MedGen:C3661900
ClinVar preferred disease name	Long chain 3-hydroxyacyl-CoA dehydrogenase deficiency\|Mitochondrial trifunctional protein deficiency\|not specified\|not provided
HGVS variant names	NC 000002.11:g.26437316A>G
ClinVar review status	criteria provided, conflicting interpretations
Clinical Significance	Conflicting interpretations of pathogenicity
Conflicting clinical significance	Likely pathogenic(2)\|Uncertain significance(2)
Variant type	single nucleotide variant
Sequence Ontology for variant type	SO:0001483
Variant clinical sources reported	ClinGen:CA346091183
Gene symbol:Gene id.	HADHA:3030
Molecular consequence	SO:0001583\|missense variant
Allele origin	germline
dbSNP ID	137852774
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession RCV000009275; RCV000422654; RCV000803503; RCV000984273;
Chromosome 2:26437316..26437316
ClinVar Allele ID 23775
Disease database name and identifier MONDO:MONDO:0012172, MedGen:C1969443, OMIM:609015, Orphanet:746|MONDO:MONDO:0012173, MedGen:C3711645, OMIM:609016, Orphanet:5|MedGen:C3661900
ClinVar preferred disease name Mitochondrial trifunctional protein deficiency|Long chain 3-hydroxyacyl-CoA dehydrogenase deficiency|not provided
HGVS variant names NC 000002.11:g.26437316A>T
ClinVar review status criteria provided, multiple submitters, no conflicts
Clinical Significance Pathogenic/Likely pathogenic
Variant type single nucleotide variant
Sequence Ontology for variant type SO:0001483
Variant clinical sources reported ClinGen:CA340822|OMIM:600890.0009|UniProtKB:P40939#VAR 021126
Gene symbol:Gene id. HADHA:3030
Molecular consequence SO:0001583|missense variant
Allele origin germline
dbSNP ID 137852774
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