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: ENST00000305883
Querying Taster for transcript #2: ENST00000540845
Querying Taster for transcript #3: ENST00000535335
MT speed 0.18 s - this script 2.581413 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
ENST00000305883(MANE Select)	KLF11	Deleterious	86\|14	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000540845	KLF11	Deleterious	88\|12	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000535335	KLF11	Deleterious	88\|12	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected

MutationT@ster 2025

Variant:

2:10048542G>A_1_ENST00000305883

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

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

Analysed issue

Analysis result

Variant

Chr2:10048542G>A (GRCh38)

Gene symbol

KLF11

Gene constraints

LOEUF: 1.07, LOF (oe): 0.76, misssense (oe): 1.10, synonymous (oe): 1.17 ? (gnomAD)

Ensembl transcript ID

ENST00000305883.6

Genbank transcript ID

NM_003597 (exact from MANE)

UniProt / AlphaMissense peptide

KLF11_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1205G>A
g.5694G>A

AA changes

AAE:	R402Q	?
Score:	43

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs34762805
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	308	308

Protein conservation

Species	Match	AA	Alignment
Human		402	R	R	N	Y	V	C	S	F	P	G	C	R	K	T	Y	F	K	S	S	H	L	K	A	H
mutated	all conserved	402	R	R	N	Y	V	C	S	F	P	G	C	Q	K	T	Y	F	K	S	S	H	L	K	A
Ptroglodytes	all identical	402	R	R	N	Y	V	C	S	F	P	G	C	R	K	T	Y	F	K	S	S	H	L	K	A
Mmulatta	all identical	402	R	R	N	Y	V	C	S	F	P	G	C	R	K	T	Y	F	K	S	S	H	L	K	A
Fcatus	all identical	408	R	R	N	Y	V	C	N	V	P	G	C	R	K	T	Y	F	K	S	S	H	L	K	A
Mmusculus	all identical	392	R	R	N	Y	V	C	N	F	P	G	C	R	K	T	Y	F	K	S	S	H	L	K	A
Ggallus	all conserved	422	R	R	N	Y	V	C	N	F	P	G	C	K	K	T	Y	F	K	S	S	H	L	K	A
Trubripes	all conserved	317	R	R	N	Y	V	C	N	F	P	G	C	K	K	T	Y	F	K	S	S	H	L	K	A
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	all identical	391	R	R	N	Y	V	C	N	F	S	G	C	R	K	T	Y	F	K	S	S	H	L	K	A

Protein features

Start (aa)	End (aa)	Feature	Details
1	512	CHAIN		lost
394	418	ZN_FING	C2H2-type	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	2.41	1
	2.952	1
(flanking)	3.828	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

2

Strand

1

Original gDNA sequence snippet

ATGCAGCTTCCCAGGTTGCCGGAAGACCTACTTCAAAAGTT

Altered gDNA sequence snippet

ATGCAGCTTCCCAGGTTGCCAGAAGACCTACTTCAAAAGTT

Original cDNA sequence snippet

ATGCAGCTTCCCAGGTTGCCGGAAGACCTACTTCAAAAGTT

Altered cDNA sequence snippet

ATGCAGCTTCCCAGGTTGCCAGAAGACCTACTTCAAAAGTT

Wildtype AA sequence

MHTPDFAGPD DARAVDIMDI CESILERKRH DSERSTCSIL EQTDMEAVEA LVCMSSWGQR
SQKGDLLRIR PLTPVSDSGD VTTTVHMDAA TPELPKDFHS LSTLCITPPQ SPDLVEPSTR
TPVSPQVTDS KACTATDVLQ SSAVVARALS GGAERGLLGL EPVPSSPCRA KGTSVIRHTG
ESPAACFPTI QTPDCRLSDS REGEEQLLGH FETLQDTHLT DSLLSTNLVS CQPCLHKSGG
LLLTDKGQQA GWPGAVQTCS PKNYENDLPR KTTPLISVSV PAPPVLCQMI PVTGQSSMLP
AFLKPPPQLS VGTVRPILAQ AAPAPQPVFV GPAVPQGAVM LVLPQGALPP PAPCAANVMA
AGNTKLLPLA PAPVFITSSQ NCVPQVDFSR RRNYVCSFPG CRKTYFKSSH LKAHLRTHTG
EKPFNCSWDG CDKKFARSDE LSRHRRTHTG EKKFVCPVCD RRFMRSDHLT KHARRHMTTK
KIPGWQAEVG KLNRIASAES PGSPLVSMPA SA*

Mutated AA sequence

MHTPDFAGPD DARAVDIMDI CESILERKRH DSERSTCSIL EQTDMEAVEA LVCMSSWGQR
SQKGDLLRIR PLTPVSDSGD VTTTVHMDAA TPELPKDFHS LSTLCITPPQ SPDLVEPSTR
TPVSPQVTDS KACTATDVLQ SSAVVARALS GGAERGLLGL EPVPSSPCRA KGTSVIRHTG
ESPAACFPTI QTPDCRLSDS REGEEQLLGH FETLQDTHLT DSLLSTNLVS CQPCLHKSGG
LLLTDKGQQA GWPGAVQTCS PKNYENDLPR KTTPLISVSV PAPPVLCQMI PVTGQSSMLP
AFLKPPPQLS VGTVRPILAQ AAPAPQPVFV GPAVPQGAVM LVLPQGALPP PAPCAANVMA
AGNTKLLPLA PAPVFITSSQ NCVPQVDFSR RRNYVCSFPG CQKTYFKSSH LKAHLRTHTG
EKPFNCSWDG CDKKFARSDE LSRHRRTHTG EKKFVCPVCD RRFMRSDHLT KHARRHMTTK
KIPGWQAEVG KLNRIASAES PGSPLVSMPA SA*

Position of stopcodon in wt / mu CDS

1539 / 1539

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

513 / 513

Position of stopcodon in wt / mu cDNA

1706 / 1706

Position of start ATG in wt / mu cDNA

168 / 168

Last intron/exon boundary

1425

Theoretical NMD boundary in CDS

1207

Length of CDS

1539

Coding sequence (CDS) position

1205

cDNA position

1372

gDNA position

5694

Chromosomal position

10048542

Speed

0.05 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:

2:10048542G>A_2_ENST00000540845

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 88|12 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr2:10048542G>A (GRCh38)

Gene symbol

KLF11

Gene constraints

LOEUF: 1.07, LOF (oe): 0.76, misssense (oe): 1.09, synonymous (oe): 1.17 ? (gnomAD)

Ensembl transcript ID

ENST00000540845.5

Genbank transcript ID

NM_001177716 (by similarity)

UniProt / AlphaMissense peptide

KLF11_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1154G>A
g.5694G>A

AA changes

AAE:	R385Q	?
Score:	43

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs34762805
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	308	308

Protein conservation

Species	Match	AA	Alignment
Human		385	R	R	N	Y	V	C	S	F	P	G	C	R	K	T	Y	F	K	S	S	H	L	K	A	H
mutated	all conserved	385	R	R	N	Y	V	C	S	F	P	G	C	Q	K	T	Y	F	K	S	S	H	L	K	A
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	512	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	2.41	1
	2.952	1
(flanking)	3.828	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

2

Strand

1

Original gDNA sequence snippet

ATGCAGCTTCCCAGGTTGCCGGAAGACCTACTTCAAAAGTT

Altered gDNA sequence snippet

ATGCAGCTTCCCAGGTTGCCAGAAGACCTACTTCAAAAGTT

Original cDNA sequence snippet

ATGCAGCTTCCCAGGTTGCCGGAAGACCTACTTCAAAAGTT

Altered cDNA sequence snippet

ATGCAGCTTCCCAGGTTGCCAGAAGACCTACTTCAAAAGTT

Wildtype AA sequence

MDICESILER KRHDSERSTC SILEQTDMEA VEALVCMSSW GQRSQKGDLL RIRPLTPVSD
SGDVTTTVHM DAATPELPKD FHSLSTLCIT PPQSPDLVEP STRTPVSPQV TDSKACTATD
VLQSSAVVAR ALSGGAERGL LGLEPVPSSP CRAKGTSVIR HTGESPAACF PTIQTPDCRL
SDSREGEEQL LGHFETLQDT HLTDSLLSTN LVSCQPCLHK SGGLLLTDKG QQAGWPGAVQ
TCSPKNYEND LPRKTTPLIS VSVPAPPVLC QMIPVTGQSS MLPAFLKPPP QLSVGTVRPI
LAQAAPAPQP VFVGPAVPQG AVMLVLPQGA LPPPAPCAAN VMAAGNTKLL PLAPAPVFIT
SSQNCVPQVD FSRRRNYVCS FPGCRKTYFK SSHLKAHLRT HTGEKPFNCS WDGCDKKFAR
SDELSRHRRT HTGEKKFVCP VCDRRFMRSD HLTKHARRHM TTKKIPGWQA EVGKLNRIAS
AESPGSPLVS MPASA*

Mutated AA sequence

MDICESILER KRHDSERSTC SILEQTDMEA VEALVCMSSW GQRSQKGDLL RIRPLTPVSD
SGDVTTTVHM DAATPELPKD FHSLSTLCIT PPQSPDLVEP STRTPVSPQV TDSKACTATD
VLQSSAVVAR ALSGGAERGL LGLEPVPSSP CRAKGTSVIR HTGESPAACF PTIQTPDCRL
SDSREGEEQL LGHFETLQDT HLTDSLLSTN LVSCQPCLHK SGGLLLTDKG QQAGWPGAVQ
TCSPKNYEND LPRKTTPLIS VSVPAPPVLC QMIPVTGQSS MLPAFLKPPP QLSVGTVRPI
LAQAAPAPQP VFVGPAVPQG AVMLVLPQGA LPPPAPCAAN VMAAGNTKLL PLAPAPVFIT
SSQNCVPQVD FSRRRNYVCS FPGCQKTYFK SSHLKAHLRT HTGEKPFNCS WDGCDKKFAR
SDELSRHRRT HTGEKKFVCP VCDRRFMRSD HLTKHARRHM TTKKIPGWQA EVGKLNRIAS
AESPGSPLVS MPASA*

Position of stopcodon in wt / mu CDS

1488 / 1488

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

496 / 496

Position of stopcodon in wt / mu cDNA

1556 / 1556

Position of start ATG in wt / mu cDNA

69 / 69

Last intron/exon boundary

1275

Theoretical NMD boundary in CDS

1156

Length of CDS

1488

Coding sequence (CDS) position

1154

cDNA position

1222

gDNA position

5694

Chromosomal position

10048542

Speed

0.07 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:

2:10048542G>A_3_ENST00000535335

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 88|12 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr2:10048542G>A (GRCh38)

Gene symbol

KLF11

Gene constraints

LOEUF: 1.07, LOF (oe): 0.76, misssense (oe): 1.09, synonymous (oe): 1.17 ? (gnomAD)

Ensembl transcript ID

ENST00000535335.1

Genbank transcript ID

NM_001177718 (by similarity)

UniProt / AlphaMissense peptide

KLF11_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1154G>A
g.5694G>A

AA changes

AAE:	R385Q	?
Score:	43

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs34762805
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	308	308

Protein conservation

Species	Match	AA	Alignment
Human		385	R	R	N	Y	V	C	S	F	P	G	C	R	K	T	Y	F	K	S	S	H	L	K	A	H
mutated	all conserved	385	R	R	N	Y	V	C	S	F	P	G	C	Q	K	T	Y	F	K	S	S	H	L	K	A
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	512	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	2.41	1
	2.952	1
(flanking)	3.828	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

2

Strand

1

Original gDNA sequence snippet

ATGCAGCTTCCCAGGTTGCCGGAAGACCTACTTCAAAAGTT

Altered gDNA sequence snippet

ATGCAGCTTCCCAGGTTGCCAGAAGACCTACTTCAAAAGTT

Original cDNA sequence snippet

ATGCAGCTTCCCAGGTTGCCGGAAGACCTACTTCAAAAGTT

Altered cDNA sequence snippet

ATGCAGCTTCCCAGGTTGCCAGAAGACCTACTTCAAAAGTT

Wildtype AA sequence

MDICESILER KRHDSERSTC SILEQTDMEA VEALVCMSSW GQRSQKGDLL RIRPLTPVSD
SGDVTTTVHM DAATPELPKD FHSLSTLCIT PPQSPDLVEP STRTPVSPQV TDSKACTATD
VLQSSAVVAR ALSGGAERGL LGLEPVPSSP CRAKGTSVIR HTGESPAACF PTIQTPDCRL
SDSREGEEQL LGHFETLQDT HLTDSLLSTN LVSCQPCLHK SGGLLLTDKG QQAGWPGAVQ
TCSPKNYEND LPRKTTPLIS VSVPAPPVLC QMIPVTGQSS MLPAFLKPPP QLSVGTVRPI
LAQAAPAPQP VFVGPAVPQG AVMLVLPQGA LPPPAPCAAN VMAAGNTKLL PLAPAPVFIT
SSQNCVPQVD FSRRRNYVCS FPGCRKTYFK SSHLKAHLRT HTGEKPFNCS WDGCDKKFAR
SDELSRHRRT HTGEKKFVCP VCDRRFMRSD HLTKHARRHM TTKKIPGWQA EVGKLNRIAS
AESPGSPLVS MPASA*

Mutated AA sequence

MDICESILER KRHDSERSTC SILEQTDMEA VEALVCMSSW GQRSQKGDLL RIRPLTPVSD
SGDVTTTVHM DAATPELPKD FHSLSTLCIT PPQSPDLVEP STRTPVSPQV TDSKACTATD
VLQSSAVVAR ALSGGAERGL LGLEPVPSSP CRAKGTSVIR HTGESPAACF PTIQTPDCRL
SDSREGEEQL LGHFETLQDT HLTDSLLSTN LVSCQPCLHK SGGLLLTDKG QQAGWPGAVQ
TCSPKNYEND LPRKTTPLIS VSVPAPPVLC QMIPVTGQSS MLPAFLKPPP QLSVGTVRPI
LAQAAPAPQP VFVGPAVPQG AVMLVLPQGA LPPPAPCAAN VMAAGNTKLL PLAPAPVFIT
SSQNCVPQVD FSRRRNYVCS FPGCQKTYFK SSHLKAHLRT HTGEKPFNCS WDGCDKKFAR
SDELSRHRRT HTGEKKFVCP VCDRRFMRSD HLTKHARRHM TTKKIPGWQA EVGKLNRIAS
AESPGSPLVS MPASA*

Position of stopcodon in wt / mu CDS

1488 / 1488

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

496 / 496

Position of stopcodon in wt / mu cDNA

1704 / 1704

Position of start ATG in wt / mu cDNA

217 / 217

Last intron/exon boundary

1423

Theoretical NMD boundary in CDS

1156

Length of CDS

1488

Coding sequence (CDS) position

1154

cDNA position

1370

gDNA position

5694

Chromosomal position

10048542

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