MutationT@ster 2025

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Input seems to be ok - now mapping the variant to the different transcripts...
Querying Taster for transcript #1: ENST00000409993
Querying Taster for transcript #2: ENST00000639704
Querying Taster for transcript #3: ENST00000682791
Querying Taster for transcript #4: ENST00000354202
MT speed 0.24 s - this script 2.687907 s

Transcript summary:

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Transcript	Gene symbol	Prediction	Tree vote	Model	Splice site change	Variant type	Protein length	Features at a glance
ENST00000354202(MANE Select)	DPAGT1	Deleterious	55\|45	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Heterozygous in gnomAD Protein features (might be) affected
ENST00000409993	DPAGT1	Deleterious	92\|8	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Heterozygous in gnomAD Protein features (might be) affected
ENST00000682791	DPAGT1	Deleterious	95\|5	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Heterozygous in gnomAD
ENST00000639704	DPAGT1	Deleterious	96\|4	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Heterozygous in gnomAD

MutationT@ster 2025

Variant:

11:119101531C>T_4_ENST00000354202

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Heterozygous in gnomAD
Protein features (might be) affected

Model: simple_aae
Tree vote: 55|45 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr11:119101531C>T (GRCh38)

Gene symbol

DPAGT1

Gene constraints

LOEUF: 0.83, LOF (oe): 0.60, misssense (oe): 0.72, synonymous (oe): 0.90 ? (gnomAD)

Ensembl transcript ID

ENST00000354202.9

Genbank transcript ID

NM_001382 (exact from MANE)

UniProt / AlphaMissense peptide

GPT_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.125G>A
g.6801G>A

AA changes

AAE:	C42Y	?
Score:	194

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs375679649
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	0	809	809

Protein conservation

Species	Match	AA	Alignment
Human		42	A	F	R	G	H	F	I	A	A	R	L	C	G	Q	D	L	N	K	T	S	R	Q	Q	I
mutated	not conserved	42	A	F	R	G	H	F	I	A	A	R	L	Y	G	Q	D	L	N	K	T	S	R	Q	Q
Ptroglodytes	all identical	42	A	F	R	G	H	F	I	A	A	R	L	C	G	Q	D	L	N	K	T	S	R	Q	Q
Mmulatta	all identical	42	A	F	R	G	H	F	I	A	A	R	L	C	G	Q	D	L	N	K	T	S	R	Q	Q
Fcatus	all identical	42	A	F	R	G	H	F	I	A	A	R	L	C	G	Q	D	L	N	K	I	G	Q	Q	Q
Mmusculus	all identical	42	A	F	R	S	H	F	I	A	A	R	L	C	G	Q	D	L	N	K	L	S	Q	Q	Q
Ggallus	not conserved	40	A	F	K	D	H	F	L	A	A	R	L	F	G	E	D	L	N	K	A	F	R	R	P
Trubripes	not conserved	40	A	F	K	D	H	F	I	A	A	R	L	Y	G	I	D	L	N	K	T	S	K	K	E
Drerio	no homologue
Dmelanogaster	not conserved	37	R	F	R	E	M	F	I	K	A	N	L	F	G	N	D	L	C	K	K	D	K	P	Q
Celegans	not conserved	37	T	Y	I	P	I	F	I	A	R	K	M	Y	G	N	D	Q	C	K	V	S	N	A	P
Xtropicalis	not conserved	37	A	F	K	E	H	F	I	A	A	R	L	Y	G	T	D	M	N	K	M	T	K	E	P

Protein features

Start (aa)	End (aa)	Feature	Details
1	408	CHAIN		lost
39	58	TOPO_DOM	Cytoplasmic	lost
42	44	STRAND		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	2.391	1
	0.764	1
(flanking)	7.099	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

11

Strand

-1

Original gDNA sequence snippet

CTTCATTGCTGCGCGCCTCTGTGGTCAGGACCTCAACAAAA

Altered gDNA sequence snippet

CTTCATTGCTGCGCGCCTCTATGGTCAGGACCTCAACAAAA

Original cDNA sequence snippet

CTTCATTGCTGCGCGCCTCTGTGGTCAGGACCTCAACAAAA

Altered cDNA sequence snippet

CTTCATTGCTGCGCGCCTCTATGGTCAGGACCTCAACAAAA

Wildtype AA sequence

MWAFSELPMP LLINLIVSLL GFVATVTLIP AFRGHFIAAR LCGQDLNKTS RQQIPESQGV
ISGAVFLIIL FCFIPFPFLN CFVKEQCKAF PHHEFVALIG ALLAICCMIF LGFADDVLNL
RWRHKLLLPT AASLPLLMVY FTNFGNTTIV VPKPFRPILG LHLDLGILYY VYMGLLAVFC
TNAINILAGI NGLEAGQSLV ISASIIVFNL VELEGDCRDD HVFSLYFMIP FFFTTLGLLY
HNWYPSRVFV GDTFCYFAGM TFAVVGILGH FSKTMLLFFM PQVFNFLYSL PQLLHIIPCP
RHRIPRLNIK TGKLEMSYSK FKTKSLSFLG TFILKVAESL QLVTVHQSET EDGEFTECNN
MTLINLLLKV LGPIHERNLT LLLLLLQILG SAITFSIRYQ LVRLFYDV*

Mutated AA sequence

MWAFSELPMP LLINLIVSLL GFVATVTLIP AFRGHFIAAR LYGQDLNKTS RQQIPESQGV
ISGAVFLIIL FCFIPFPFLN CFVKEQCKAF PHHEFVALIG ALLAICCMIF LGFADDVLNL
RWRHKLLLPT AASLPLLMVY FTNFGNTTIV VPKPFRPILG LHLDLGILYY VYMGLLAVFC
TNAINILAGI NGLEAGQSLV ISASIIVFNL VELEGDCRDD HVFSLYFMIP FFFTTLGLLY
HNWYPSRVFV GDTFCYFAGM TFAVVGILGH FSKTMLLFFM PQVFNFLYSL PQLLHIIPCP
RHRIPRLNIK TGKLEMSYSK FKTKSLSFLG TFILKVAESL QLVTVHQSET EDGEFTECNN
MTLINLLLKV LGPIHERNLT LLLLLLQILG SAITFSIRYQ LVRLFYDV*

Position of stopcodon in wt / mu CDS

1227 / 1227

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

409 / 409

Position of stopcodon in wt / mu cDNA

1425 / 1425

Position of start ATG in wt / mu cDNA

199 / 199

Last intron/exon boundary

1359

Theoretical NMD boundary in CDS

1110

Length of CDS

1227

Coding sequence (CDS) position

125

cDNA position

323

gDNA position

6801

Chromosomal position

119101531

Speed

0.06 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

MutationT@ster 2025

Variant:

11:119101531C>T_1_ENST00000409993

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Heterozygous in gnomAD
Protein features (might be) affected

Model: simple_aae
Tree vote: 92|8 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr11:119101531C>T (GRCh38)

Gene symbol

DPAGT1

Gene constraints

LOEUF: 0.83, LOF (oe): 0.60, misssense (oe): 0.72, synonymous (oe): 0.90 ? (gnomAD)

Ensembl transcript ID

ENST00000409993.6

Genbank transcript ID

UniProt / AlphaMissense peptide

GPT_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.125G>A
g.6801G>A

AA changes

AAE:	C42Y	?
Score:	194

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs375679649
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	0	809	809

Protein conservation

Species	Match	AA	Alignment
Human		42	A	F	R	G	H	F	I	A	A	R	L	C	G	Q	D	L	N	K	T	S	R	Q	Q	I
mutated	not conserved	42	A	F	R	G	H	F	I	A	A	R	L	Y	G	Q	D	L	N	K	T	S	R	Q	Q
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

Start (aa)	End (aa)	Feature	Details
1	408	CHAIN		lost
39	58	TOPO_DOM	Cytoplasmic	lost
42	44	STRAND		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	2.391	1
	0.764	1
(flanking)	7.099	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

11

Strand

-1

Original gDNA sequence snippet

CTTCATTGCTGCGCGCCTCTGTGGTCAGGACCTCAACAAAA

Altered gDNA sequence snippet

CTTCATTGCTGCGCGCCTCTATGGTCAGGACCTCAACAAAA

Original cDNA sequence snippet

CTTCATTGCTGCGCGCCTCTGTGGTCAGGACCTCAACAAAA

Altered cDNA sequence snippet

CTTCATTGCTGCGCGCCTCTATGGTCAGGACCTCAACAAAA

Wildtype AA sequence

MWAFSELPMP LLINLIVSLL GFVATVTLIP AFRGHFIAAR LCGQDLNKTS RQQIPESQGV
ISGAVFLIIL FCFIPFPFLN CFVKEQCKAF PHHEFVALIG ALLAICCMIF LGFADDVLNL
RWRHKLLLPT AASLPLLMVY FTNFGNTTIV VPKPFRPILG LHLDLGILYY VYMGLLAVFC
TNAINILAGI NGLEAGQSLV ISASIIVFNL VELEGDCRDD HVFSLYFMIP FFFTTLGLLY
HNWYPSRVFV GDTFCYFAGM TFAVVGILGH FSKTMLLFFM PQVFNFLYSL PQLLHIIPCP
RHRIPRLNIK TGKLEMSYSK FKTKSLSFLG TFILKVAESL QLVTVHQSET EDGEFTECNN
MTLINLLLKV LGPIHERNLT LLLLLLQILG SAITFSIRYQ LVRLFYDV*

Mutated AA sequence

MWAFSELPMP LLINLIVSLL GFVATVTLIP AFRGHFIAAR LYGQDLNKTS RQQIPESQGV
ISGAVFLIIL FCFIPFPFLN CFVKEQCKAF PHHEFVALIG ALLAICCMIF LGFADDVLNL
RWRHKLLLPT AASLPLLMVY FTNFGNTTIV VPKPFRPILG LHLDLGILYY VYMGLLAVFC
TNAINILAGI NGLEAGQSLV ISASIIVFNL VELEGDCRDD HVFSLYFMIP FFFTTLGLLY
HNWYPSRVFV GDTFCYFAGM TFAVVGILGH FSKTMLLFFM PQVFNFLYSL PQLLHIIPCP
RHRIPRLNIK TGKLEMSYSK FKTKSLSFLG TFILKVAESL QLVTVHQSET EDGEFTECNN
MTLINLLLKV LGPIHERNLT LLLLLLQILG SAITFSIRYQ LVRLFYDV*

Position of stopcodon in wt / mu CDS

1227 / 1227

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

409 / 409

Position of stopcodon in wt / mu cDNA

2779 / 2779

Position of start ATG in wt / mu cDNA

1553 / 1553

Last intron/exon boundary

2713

Theoretical NMD boundary in CDS

1110

Length of CDS

1227

Coding sequence (CDS) position

125

cDNA position

1677

gDNA position

6801

Chromosomal position

119101531

Speed

0.06 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

MutationT@ster 2025

Variant:

11:119101531C>T_3_ENST00000682791

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Heterozygous in gnomAD

Model: simple_aae
Tree vote: 95|5 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr11:119101531C>T (GRCh38)

Gene symbol

DPAGT1

Gene constraints

LOEUF: 0.95, LOF (oe): 0.69, misssense (oe): 0.71, synonymous (oe): 0.93 ? (gnomAD)

Ensembl transcript ID

ENST00000682791.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.125G>A
g.6801G>A

AA changes

AAE:	C42Y	?
Score:	194

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs375679649
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	0	809	809

Protein conservation

Species	Match	AA	Alignment
Human		42	A	F	R	G	H	F	I	A	A	R	L	C	G	Q	D	L	N	K	T	S	R	Q	Q	M
mutated	not conserved	42	A	F	R	G	H	F	I	A	A	R	L	Y	G	Q	D	L	N	K	T	S	R	Q	Q
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	2.391	1
	0.764	1
(flanking)	7.099	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

11

Strand

-1

Original gDNA sequence snippet

CTTCATTGCTGCGCGCCTCTGTGGTCAGGACCTCAACAAAA

Altered gDNA sequence snippet

CTTCATTGCTGCGCGCCTCTATGGTCAGGACCTCAACAAAA

Original cDNA sequence snippet

CTTCATTGCTGCGCGCCTCTGTGGTCAGGACCTCAACAAAA

Altered cDNA sequence snippet

CTTCATTGCTGCGCGCCTCTATGGTCAGGACCTCAACAAAA

Wildtype AA sequence

MWAFSELPMP LLINLIVSLL GFVATVTLIP AFRGHFIAAR LCGQDLNKTS RQQMLESWTC
PSLPQFVALI GALLAICCMI FLGFADDVLN LRWRHKLLLP TAASLPLLMV YFTNFGNTTI
VVPKPFRPIL GLHLDLGILY YVYMGLLAVF CTNAINILAG INGLEAGQSL VISASIIVFN
LVELEGDCRD DHVFSLYFMI PFFFTTLGLL YHNWYPSRVF VGDTFCYFAG MTFAVVGILG
HFSKTMLLFF MPQVFNFLYS LPQLLHIIPC PRHRIPRLNI KTGKLEMSYS KFKTKSLSFL
GTFILKVAES LQLVTVHQSE TEDGEFTECN NMTLINLLLK VLGPIHERNL TLLLLLLQIL
GSAITFSIRY QLVRLFYDV*

Mutated AA sequence

MWAFSELPMP LLINLIVSLL GFVATVTLIP AFRGHFIAAR LYGQDLNKTS RQQMLESWTC
PSLPQFVALI GALLAICCMI FLGFADDVLN LRWRHKLLLP TAASLPLLMV YFTNFGNTTI
VVPKPFRPIL GLHLDLGILY YVYMGLLAVF CTNAINILAG INGLEAGQSL VISASIIVFN
LVELEGDCRD DHVFSLYFMI PFFFTTLGLL YHNWYPSRVF VGDTFCYFAG MTFAVVGILG
HFSKTMLLFF MPQVFNFLYS LPQLLHIIPC PRHRIPRLNI KTGKLEMSYS KFKTKSLSFL
GTFILKVAES LQLVTVHQSE TEDGEFTECN NMTLINLLLK VLGPIHERNL TLLLLLLQIL
GSAITFSIRY QLVRLFYDV*

Position of stopcodon in wt / mu CDS

1140 / 1140

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

380 / 380

Position of stopcodon in wt / mu cDNA

1316 / 1316

Position of start ATG in wt / mu cDNA

177 / 177

Last intron/exon boundary

1250

Theoretical NMD boundary in CDS

1023

Length of CDS

1140

Coding sequence (CDS) position

125

cDNA position

301

gDNA position

6801

Chromosomal position

119101531

Speed

0.06 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

MutationT@ster 2025

Variant:

11:119101531C>T_2_ENST00000639704

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Heterozygous in gnomAD

Model: simple_aae
Tree vote: 96|4 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr11:119101531C>T (GRCh38)

Gene symbol

DPAGT1

Gene constraints

LOEUF: 0.83, LOF (oe): 0.59, misssense (oe): 0.71, synonymous (oe): 0.87 ? (gnomAD)

Ensembl transcript ID

ENST00000639704.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.125G>A
g.6801G>A

AA changes

AAE:	C42Y	?
Score:	194

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs375679649
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	0	809	809

Protein conservation

Species	Match	AA	Alignment
Human		42	A	F	R	G	H	F	I	A	A	R	L	C	G	Q	D	L	N	K	T	S	R	Q	Q	I
mutated	not conserved	42	A	F	R	G	H	F	I	A	A	R	L	Y	G	Q	D	L	N	K	T	S	R	Q	Q
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	2.391	1
	0.764	1
(flanking)	7.099	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

11

Strand

-1

Original gDNA sequence snippet

CTTCATTGCTGCGCGCCTCTGTGGTCAGGACCTCAACAAAA

Altered gDNA sequence snippet

CTTCATTGCTGCGCGCCTCTATGGTCAGGACCTCAACAAAA

Original cDNA sequence snippet

CTTCATTGCTGCGCGCCTCTGTGGTCAGGACCTCAACAAAA

Altered cDNA sequence snippet

CTTCATTGCTGCGCGCCTCTATGGTCAGGACCTCAACAAAA

Wildtype AA sequence

MWAFSELPMP LLINLIVSLL GFVATVTLIP AFRGHFIAAR LCGQDLNKTS RQQIPESQGV
ISGAVFLIIL FCFIPFPFLN CFVKEQCKAF PHHELLLPTA ASLPLLMVYF TNFGNTTIVV
PKPFRPILGL HLDLGILYYV YMGLLAVFCT NAINILAGIN GLEAGQSLVI SASIIVFNLV
ELEGDCRDDH VFSLYFMIPF FFTTLGLLYH NWYPSRVFVG DTFCYFAGMT FAVVGILGHF
SKTMLLFFMP QVFNFLYSLP QLLHIIPCPR HRIPRLNIKT GKLEMSYSKF KTKSLSFLGT
FILKVAESLQ LVTVHQSETE DGEFTECNNM TLINLLLKVL GPIHERNLTL LLLLLQILGS
AITFSIRYQL VRLFYDV*

Mutated AA sequence

MWAFSELPMP LLINLIVSLL GFVATVTLIP AFRGHFIAAR LYGQDLNKTS RQQIPESQGV
ISGAVFLIIL FCFIPFPFLN CFVKEQCKAF PHHELLLPTA ASLPLLMVYF TNFGNTTIVV
PKPFRPILGL HLDLGILYYV YMGLLAVFCT NAINILAGIN GLEAGQSLVI SASIIVFNLV
ELEGDCRDDH VFSLYFMIPF FFTTLGLLYH NWYPSRVFVG DTFCYFAGMT FAVVGILGHF
SKTMLLFFMP QVFNFLYSLP QLLHIIPCPR HRIPRLNIKT GKLEMSYSKF KTKSLSFLGT
FILKVAESLQ LVTVHQSETE DGEFTECNNM TLINLLLKVL GPIHERNLTL LLLLLQILGS
AITFSIRYQL VRLFYDV*

Position of stopcodon in wt / mu CDS

1134 / 1134

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

378 / 378

Position of stopcodon in wt / mu cDNA

1316 / 1316

Position of start ATG in wt / mu cDNA

183 / 183

Last intron/exon boundary

1250

Theoretical NMD boundary in CDS

1017

Length of CDS

1134

Coding sequence (CDS) position

125

cDNA position

307

gDNA position

6801

Chromosomal position

119101531

Speed

0.06 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