mutation t@sting

Variant:

3:190122694G>A_2_ENST00000456423

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Prediction:

DeleteriousPermalink

Summary:

Known disease mutation at this position (HGMD CM993497)
Known disease mutation: ClinVar ID 5927 (pathogenic)

Model: without_aae
Tree vote: 35|65 (del | benign) ?
Automatic classification due to ClinVar,
tree vote conflicts with the automatic classification ?

Analysed issue

Analysis result

Phys. location

chr3:190122694G>A show variant in all transcripts IGV

Gene symbol

CLDN16

ExAC LOF metrics

LOF: 0.03, misssense: -0.38, synonymous: -1.12

Ensembl transcript ID

ENST00000456423.1

Genbank transcript ID

UniProt peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.325-4998G>A
g.82365G>A

AA changes

N/A

Frameshift

Length of protein

N/A

Known variant

Allele 'A' was not found in ExAC, 1000G, or gnomAD.
Known disease mutation: ClinVar variation ID 5927 (pathogenic for Primary hypomagnesemia) OMIM
Known disease mutation at this position, please check HGMD for details (HGMD ID CM993497)
Known disease mutation at this position, please check HGMD for details (HGMD ID CM993497)

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.222	0.992
	4.236	1
(flanking)	4.236	0.996

Splice sites

No abrogation of potential splice sites

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

Protein conservation

N/A

Protein features

N/A

AA sequence altered

N/A

Chromosome

Strand

Original gDNA sequence snippet

TCCGCATCTGCTTTGTTGCTGGAGCCACGTTACTAATAGCA

Altered gDNA sequence snippet

TCCGCATCTGCTTTGTTGCTAGAGCCACGTTACTAATAGCA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MTSRTPLLVT ACLYYSYCNS RHLQQGVRKS KRPVFSHCQV PETQKTDTRH LSGARAGVCP
CCHPDGLLAT MRDLLQYIAC FFAFFSAGFL IVATWTDCWM VNADDSLEML DLRETILIP*

Mutated AA sequence

Position of stopcodon in wt / mu CDS

N/A

Position (AA) of stopcodon in wt / mu AA sequence

N/A

Position of stopcodon in wt / mu cDNA

N/A

Position of start ATG in wt / mu cDNA

1 / 1

Last intron/exon boundary

324

Theoretical NMD boundary in CDS

273

Length of CDS

360

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

82365

Chromosomal position

190122694

Speed

0.01 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project