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: ENST00000405546
Querying Taster for transcript #2: ENST00000402096
Querying Taster for transcript #3: ENST00000404914
Querying Taster for transcript #4: ENST00000625810
MT speed 0.84 s - this script 3.239941 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
ENST00000402096	ATG4B	Deleterious	52\|45	5utr	No	Single base exchange	N/A
ENST00000405546	ATG4B	Deleterious	79\|21	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000404914(MANE Select)	ATG4B	Deleterious	79\|21	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000625810	ATG4B	Deleterious	86\|14	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed

MutationT@ster 2025

Variant:

2:241651275A>G_2_ENST00000402096

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Prediction:

DeleteriousPermalink

Summary:

Model: 5utr
Tree vote: 52|45 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr2:241651275A>G (GRCh38)

Gene symbol

ATG4B

Gene constraints

LOEUF: 0.82, LOF (oe): 0.57, misssense (oe): 0.93, synonymous (oe): 1.21 ? (gnomAD)

Ensembl transcript ID

ENST00000402096.5

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

5'UTR

DNA changes

cDNA.227A>G
g.14063A>G

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

	Not in dbSNP
	Allele 'G' was not found in gnomAD

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.875	1
	1.744	1
(flanking)	5.386	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

12

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

2

Strand

1

Original gDNA sequence snippet

AACCTCTAGAAAAGGACGAGATCTTGTCTGATGTGGCATCT

Altered gDNA sequence snippet

AACCTCTAGAAAAGGACGAGGTCTTGTCTGATGTGGCATCT

Original cDNA sequence snippet

TTTTCACAGAAAAGGACGAGATCTTGTCTGATGTGGCATCT

Altered cDNA sequence snippet

TTTTCACAGAAAAGGACGAGGTCTTGTCTGATGTGGCATCT

Wildtype AA sequence

MLRCGQMIFA QALVCRHLGR DWRWTQRKRQ PDSYFSVLNA FIDRKDSYYS IHQIAQMGVG
EGKSIGQWYG PNTVAQVLKK LAVFDTWSSL AVHIAMDNTV VMEEIRRLCR TSVPCAGATA
FPADSDRHCN GFPAGAEVTN RPSPWRPLVL LIPLRLGLTD INEAYVETLK HCFMMPQSLG
VIGGKPNSAH YFIGYVGEEL IYLDPHTTQP AVEPTDGCFI PDESFHCQHP PCRMSIAELD
PSIAVGFFCK TEDDFNDWCQ QVKKLSLLGG ALPMFELVEL QPSHLACPDV LNLSLGESCQ
VQVGSLGDSS DVERLERFFD SEDEDFEILS L*

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

326 / 326

Last intron/exon boundary

1247

Theoretical NMD boundary in CDS

871

Length of CDS

996

Coding sequence (CDS) position

N/A

cDNA position

227

gDNA position

14063

Chromosomal position

241651275

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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MutationT@ster 2025

Variant:

2:241651275A>G_1_ENST00000405546

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 79|21 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr2:241651275A>G (GRCh38)

Gene symbol

ATG4B

Gene constraints

LOEUF: 0.88, LOF (oe): 0.65, misssense (oe): 0.97, synonymous (oe): 1.18 ? (gnomAD)

Ensembl transcript ID

ENST00000405546.7

Genbank transcript ID

NM_178326 (by similarity)

UniProt / AlphaMissense peptide

ATG4B_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.124A>G
g.14063A>G

AA changes

AAE:	I42V	?
Score:	29

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

	Not in dbSNP
	Allele 'G' was not found in gnomAD

Protein conservation

Species	Match	AA	Alignment
Human		42	R	K	Y	S	I	F	T	E	K	D	E	I	L	S	D	V	A	S	R	L	W	F	T	Y
mutated	all conserved	42	R	K	Y	S	I	F	T	E	K	D	E	V	L	S	D	V	A	S	R	L	W	F	T
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	393	CHAIN		lost
39	48	HELIX		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.875	1
	1.744	1
(flanking)	5.386	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

12

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

2

Strand

1

Original gDNA sequence snippet

AACCTCTAGAAAAGGACGAGATCTTGTCTGATGTGGCATCT

Altered gDNA sequence snippet

AACCTCTAGAAAAGGACGAGGTCTTGTCTGATGTGGCATCT

Original cDNA sequence snippet

TTTTCACAGAAAAGGACGAGATCTTGTCTGATGTGGCATCT

Altered cDNA sequence snippet

TTTTCACAGAAAAGGACGAGGTCTTGTCTGATGTGGCATCT

Wildtype AA sequence

MDAATLTYDT LRFAEFEDFP ETSEPVWILG RKYSIFTEKD EILSDVASRL WFTYRKNFPA
IGGTGPTSDT GWGCMLRCGQ MIFAQALVCR HLGRDWRWTQ RKRQPDSYFS VLNAFIDRKD
SYYSIHQIAQ MGVGEGKSIG QWYGPNTVAQ VLKKLAVFDT WSSLAVHIAM DNTVVMEEIR
RLCRTSVPCA GATAFPADSD RHCNGFPAGA EVTNRPSPWR PLVLLIPLRL GLTDINEAYV
ETLKHCFMMP QSLGVIGGKP NSAHYFIGYV GEELIYLDPH TTQPAVEPTD GCFIPDESFH
CQHPPCRMSI AELDPSIAVG FFCKTEDDFN DWCQQVKKLS LLGGALPMFE LVELQPSHLA
CPDVLNLSLG ESCQVQILLM *

Mutated AA sequence

MDAATLTYDT LRFAEFEDFP ETSEPVWILG RKYSIFTEKD EVLSDVASRL WFTYRKNFPA
IGGTGPTSDT GWGCMLRCGQ MIFAQALVCR HLGRDWRWTQ RKRQPDSYFS VLNAFIDRKD
SYYSIHQIAQ MGVGEGKSIG QWYGPNTVAQ VLKKLAVFDT WSSLAVHIAM DNTVVMEEIR
RLCRTSVPCA GATAFPADSD RHCNGFPAGA EVTNRPSPWR PLVLLIPLRL GLTDINEAYV
ETLKHCFMMP QSLGVIGGKP NSAHYFIGYV GEELIYLDPH TTQPAVEPTD GCFIPDESFH
CQHPPCRMSI AELDPSIAVG FFCKTEDDFN DWCQQVKKLS LLGGALPMFE LVELQPSHLA
CPDVLNLSLG ESCQVQILLM *

Position of stopcodon in wt / mu CDS

1143 / 1143

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

381 / 381

Position of stopcodon in wt / mu cDNA

1645 / 1645

Position of start ATG in wt / mu cDNA

503 / 503

Last intron/exon boundary

1630

Theoretical NMD boundary in CDS

1077

Length of CDS

1143

Coding sequence (CDS) position

124

cDNA position

626

gDNA position

14063

Chromosomal position

241651275

Speed

0.31 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:

2:241651275A>G_3_ENST00000404914

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 79|21 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr2:241651275A>G (GRCh38)

Gene symbol

ATG4B

Gene constraints

LOEUF: 0.85, LOF (oe): 0.62, misssense (oe): 0.97, synonymous (oe): 1.20 ? (gnomAD)

Ensembl transcript ID

ENST00000404914.8

Genbank transcript ID

NM_013325 (exact from MANE)

UniProt / AlphaMissense peptide

ATG4B_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.124A>G
g.14063A>G

AA changes

AAE:	I42V	?
Score:	29

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

	Not in dbSNP
	Allele 'G' was not found in gnomAD

Protein conservation

Species	Match	AA	Alignment
Human		42	R	K	Y	S	I	F	T	E	K	D	E	I	L	S	D	V	A	S	R	L	W	F	T	Y
mutated	all conserved	42	R	K	Y	S	I	F	T	E	K	D	E	V	L	S	D	V	A	S	R	L	W	F	T
Ptroglodytes	all identical	42	R	K	Y	S	I	F	T	E	K	D	E	I	L	S	D	V	A	S	R	L	W	F	T
Mmulatta	all identical	157	R	K	Y	S	I	F	T	E	K	D	E	I	L	S	D	V	A	S	R	L	W	F	T
Fcatus	all identical	213	R	K	Y	S	I	S	T	E	K	D	E	I	L	S	D	V	A	S	R	L	W	F	T
Mmusculus	all identical	42	R	K	Y	S	I	F	T	E	K	D	E	I	L	S	D	V	A	S	R	L	W	F	T
Ggallus	all identical	88	R	K	Y	S	V	F	T	E	K	E	E	I	L	L	D	V	T	S	R	L	W	F	T
Trubripes	all identical	42	N	E	Y	S	A	L	T	E	K	E	E	I	L	S	D	V	T	S	R	L	W	F	T
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	all conserved	80	K	E	I	S	K	E	D	G	I	E	A	M	K	K	Y	V	T	S	R	F	W	F	T
Xtropicalis	all conserved	43	R	K	Y	S	A	L	T	E	K	E	Q	L	L	N	D	I	T	S	R	L	W	F	T

Protein features

Start (aa)	End (aa)	Feature	Details
1	393	CHAIN		lost
39	48	HELIX		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.875	1
	1.744	1
(flanking)	5.386	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

12

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

2

Strand

1

Original gDNA sequence snippet

AACCTCTAGAAAAGGACGAGATCTTGTCTGATGTGGCATCT

Altered gDNA sequence snippet

AACCTCTAGAAAAGGACGAGGTCTTGTCTGATGTGGCATCT

Original cDNA sequence snippet

TTTTCACAGAAAAGGACGAGATCTTGTCTGATGTGGCATCT

Altered cDNA sequence snippet

TTTTCACAGAAAAGGACGAGGTCTTGTCTGATGTGGCATCT

Wildtype AA sequence

MDAATLTYDT LRFAEFEDFP ETSEPVWILG RKYSIFTEKD EILSDVASRL WFTYRKNFPA
IGGTGPTSDT GWGCMLRCGQ MIFAQALVCR HLGRDWRWTQ RKRQPDSYFS VLNAFIDRKD
SYYSIHQIAQ MGVGEGKSIG QWYGPNTVAQ VLKKLAVFDT WSSLAVHIAM DNTVVMEEIR
RLCRTSVPCA GATAFPADSD RHCNGFPAGA EVTNRPSPWR PLVLLIPLRL GLTDINEAYV
ETLKHCFMMP QSLGVIGGKP NSAHYFIGYV GEELIYLDPH TTQPAVEPTD GCFIPDESFH
CQHPPCRMSI AELDPSIAVG FFCKTEDDFN DWCQQVKKLS LLGGALPMFE LVELQPSHLA
CPDVLNLSLD SSDVERLERF FDSEDEDFEI LSL*

Mutated AA sequence

MDAATLTYDT LRFAEFEDFP ETSEPVWILG RKYSIFTEKD EVLSDVASRL WFTYRKNFPA
IGGTGPTSDT GWGCMLRCGQ MIFAQALVCR HLGRDWRWTQ RKRQPDSYFS VLNAFIDRKD
SYYSIHQIAQ MGVGEGKSIG QWYGPNTVAQ VLKKLAVFDT WSSLAVHIAM DNTVVMEEIR
RLCRTSVPCA GATAFPADSD RHCNGFPAGA EVTNRPSPWR PLVLLIPLRL GLTDINEAYV
ETLKHCFMMP QSLGVIGGKP NSAHYFIGYV GEELIYLDPH TTQPAVEPTD GCFIPDESFH
CQHPPCRMSI AELDPSIAVG FFCKTEDDFN DWCQQVKKLS LLGGALPMFE LVELQPSHLA
CPDVLNLSLD SSDVERLERF FDSEDEDFEI LSL*

Position of stopcodon in wt / mu CDS

1182 / 1182

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

394 / 394

Position of stopcodon in wt / mu cDNA

1204 / 1204

Position of start ATG in wt / mu cDNA

23 / 23

Last intron/exon boundary

1130

Theoretical NMD boundary in CDS

1057

Length of CDS

1182

Coding sequence (CDS) position

124

cDNA position

146

gDNA position

14063

Chromosomal position

241651275

Speed

0.30 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:

2:241651275A>G_4_ENST00000625810

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed

Model: simple_aae
Tree vote: 86|14 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr2:241651275A>G (GRCh38)

Gene symbol

ATG4B

Gene constraints

LOEUF: 0.98, LOF (oe): 0.43, misssense (oe): 0.92, synonymous (oe): 0.92 ? (gnomAD)

Ensembl transcript ID

ENST00000625810.2

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.124A>G
g.14063A>G

AA changes

AAE:	I42V	?
Score:	29

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

	Not in dbSNP
	Allele 'G' was not found in gnomAD

Protein conservation

Species	Match	AA	Alignment
Human		42	R	K	Y	S	I	F	T	E	K	D	E	I	L	S	D	V	A	S	R	L	W	F	T	Y
mutated	all conserved	42	R	K	Y	S	I	F	T	E	K	D	E	V	L	S	D	V	A	S	R	L	W	F	T
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)	1.875	1
	1.744	1
(flanking)	5.386	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

12

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

2

Strand

1

Original gDNA sequence snippet

AACCTCTAGAAAAGGACGAGATCTTGTCTGATGTGGCATCT

Altered gDNA sequence snippet

AACCTCTAGAAAAGGACGAGGTCTTGTCTGATGTGGCATCT

Original cDNA sequence snippet

TTTTCACAGAAAAGGACGAGATCTTGTCTGATGTGGCATCT

Altered cDNA sequence snippet

TTTTCACAGAAAAGGACGAGGTCTTGTCTGATGTGGCATCT

Wildtype AA sequence

MDAATLTYDT LRFAEFEDFP ETSEPVWILG RKYSIFTEKD EILSDVASRL WFTYRKNFPA
IAIHHCCIPW SWKEMGTGSQ PCLSPAEN*

Mutated AA sequence

MDAATLTYDT LRFAEFEDFP ETSEPVWILG RKYSIFTEKD EVLSDVASRL WFTYRKNFPA
IAIHHCCIPW SWKEMGTGSQ PCLSPAEN*

Position of stopcodon in wt / mu CDS

267 / 267

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

89 / 89

Position of stopcodon in wt / mu cDNA

370 / 370

Position of start ATG in wt / mu cDNA

104 / 104

Last intron/exon boundary

287

Theoretical NMD boundary in CDS

133

Length of CDS

267

Coding sequence (CDS) position

124

cDNA position

227

gDNA position

14063

Chromosomal position

241651275

Speed

0.22 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