mutation t@sting

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Input seems to be ok - now mapping the variant to the different transcripts...
Querying Taster for transcript #1: ENST00000264734
Querying Taster for transcript #2: ENST00000456423
MT speed 0.15 s - this script 2.460649 s

Transcript summary:

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Transcript	Gene symbol	Prediction	Tree vote	Model	Prediction problem	Splice site change	Known ClinVar disease mutation	Potential ClinVar disease mutation	Amino acid changes	Variant type	dbSNP ID	Protein length	Features at a glance
ENST00000456423	CLDN16	Deleterious (ClinVar)	35\|65	without_aae		No	Yes			Single base exchange		N/A	Known disease mutation at this position (HGMD CM993497) Known disease mutation: ClinVar ID 5927 (pathogenic)
ENST00000264734	CLDN16	Deleterious (ClinVar)	87\|13	simple_aae		No	Yes		G191R	Single base exchange		Normal	Amino acid sequence changed Known disease mutation at this position (HGMD CM993497) Known disease mutation: ClinVar ID 5927 (pathogenic) Protein features (might be) affected

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

No

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

3

Strand

1

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

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mutation t@sting

Variant:

3:190122694G>A_1_ENST00000264734

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation at this position (HGMD CM993497)
Known disease mutation: ClinVar ID 5927 (pathogenic)
Protein features (might be) affected

Model: simple_aae
Tree vote: 87|13 (del | benign) ?
Automatic classification due to ClinVar

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

ENST00000264734.2

Genbank transcript ID

NM_006580 (exact from MANE)

UniProt peptide

Q9Y5I7

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.571G>A
g.82365G>A

AA changes

G191R Score: 125 ?

Frameshift

No

Length of protein

Normal

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

22

Kozak consensus sequence altered?

No

poly(A) signal

N/A

Protein conservation

Species	Match	Gene	AA	Alignment
Human			191	P	Y	I	K	V	R	I	C	F	V	A	G	A	T	L	L	I	A	G	T	P	G	I	I
mutated	not conserved		191		Y	I	K	V	R	I	C	F	V	A	R	A	T	L	L	I	A	G	T	P	G	I
Ptroglodytes	all identical	ENSPTRG00000015739	191		Y	I	K	V	R	I	C	F	V	A	G	T	T	L	L	I	A	G	T	P	G	I
Mmulatta	all identical	ENSMMUG00000018671	121												G	T	T	L	L	I	A	G	T	P	G	I
Fcatus	all identical	ENSFCAG00000003329	121												G	T	I	L	L	I	A	G	A	P	G	I
Mmusculus	all identical	ENSMUSG00000038148	121												G	T	T	L	L	I	A	G	T	P	G	I
Ggallus	all identical	ENSGALG00000025821	121												G	V	T	L	L	I	A	G	L	P	G	I
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	all identical	ENSXETG00000015045	121												G	I	T	L	L	I	G	G	V	P	G	I

Protein features

Start (aa)	End (aa)	Feature	Details
186	206	TRANSMEM	Helical	lost

AA sequence altered

Yes

Chromosome

3

Strand

1

Original gDNA sequence snippet

TCCGCATCTGCTTTGTTGCTGGAGCCACGTTACTAATAGCA

Altered gDNA sequence snippet

TCCGCATCTGCTTTGTTGCTAGAGCCACGTTACTAATAGCA

Original cDNA sequence snippet

TCCGCATCTGCTTTGTTGCTGGAGCCACGTTACTAATAGCA

Altered cDNA sequence snippet

TCCGCATCTGCTTTGTTGCTAGAGCCACGTTACTAATAGCA

Wildtype AA sequence

MTSRTPLLVT ACLYYSYCNS RHLQQGVRKS KRPVFSHCQV PETQKTDTRH LSGARAGVCP
CCHPDGLLAT MRDLLQYIAC FFAFFSAGFL IVATWTDCWM VNADDSLEVS TKCRGLWWEC
VTNAFDGIRT CDEYDSILAE HPLKLVVTRA LMITADILAG FGFLTLLLGL DCVKFLPDEP
YIKVRICFVA GATLLIAGTP GIIGSVWYAV DVYVERSTLV LHNIFLGIQY KFGWSCWLGM
AGSLGCFLAG AVLTCCLYLF KDVGPERNYP YSLRKAYSAA GVSMAKSYSA PRTETAKMYA
VDTRV*

Mutated AA sequence

MTSRTPLLVT ACLYYSYCNS RHLQQGVRKS KRPVFSHCQV PETQKTDTRH LSGARAGVCP
CCHPDGLLAT MRDLLQYIAC FFAFFSAGFL IVATWTDCWM VNADDSLEVS TKCRGLWWEC
VTNAFDGIRT CDEYDSILAE HPLKLVVTRA LMITADILAG FGFLTLLLGL DCVKFLPDEP
YIKVRICFVA RATLLIAGTP GIIGSVWYAV DVYVERSTLV LHNIFLGIQY KFGWSCWLGM
AGSLGCFLAG AVLTCCLYLF KDVGPERNYP YSLRKAYSAA GVSMAKSYSA PRTETAKMYA
VDTRV*

Position of stopcodon in wt / mu CDS

918 / 918

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

306 / 306

Position of stopcodon in wt / mu cDNA

1166 / 1166

Position of start ATG in wt / mu cDNA

249 / 249

Last intron/exon boundary

1032

Theoretical NMD boundary in CDS

733

Length of CDS

918

Coding sequence (CDS) position

571

cDNA position

819

gDNA position

82365

Chromosomal position

190122694

Speed

0.14 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

Back to summary table