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: ENST00000698836
Querying Taster for transcript #2: ENST00000531066
MT speed 0.05 s - this script 2.430373 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
ENST00000698836	PLEKHA7	Benign	45\|155	without_aae		No				Single base exchange		Normal	Homozygous in gnomAD
ENST00000531066(MANE Select)	PLEKHA7	Benign	110\|90	without_aae		No				Single base exchange		Normal	Homozygous in gnomAD

MutationT@ster 2025

Variant:

11:16783795G>A_1_ENST00000698836

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Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 45|155 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr11:16783795G>A (GRCh38)

Gene symbol

PLEKHA7

Gene constraints

no data

Ensembl transcript ID

ENST00000698836.1

Genbank transcript ID

NM_001410960 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.3558C>T
g.230621C>T

AA changes

no AA changes

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs4757433
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	64	2677	2741

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.9	0.918
	-1.246	0.001
(flanking)	7.491	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

No

Chromosome

11

Strand

-1

Original gDNA sequence snippet

GTGTCAATCCCTGAGCGCTACGTGGAGCTAGATCCCGAAGA

Altered gDNA sequence snippet

GTGTCAATCCCTGAGCGCTATGTGGAGCTAGATCCCGAAGA

Original cDNA sequence snippet

GTGTCAATCCCTGAGCGCTACGTGGAGCTAGATCCCGAAGA

Altered cDNA sequence snippet

GTGTCAATCCCTGAGCGCTATGTGGAGCTAGATCCCGAAGA

Wildtype AA sequence

MAAATVGRDT LPEHWSYGVC RDGRVFFIND QLRCTTWLHP RTGEPVNSGH MIRSDLPRGW
EEGFTEEGAS YFIDHNQQTT AFRHPVTGQF SPENSEFILQ EEPNPHMSKQ DRNQRPSSMV
SETSTAGTAS TLEAKPGPKI IKSSSKVHSF GKRDQAIRRN PNVPVVVRGW LHKQDSSGMR
LWKRRWFVLA DYCLFYYKDS REEAVLGSIP LPSYVISPVA PEDRISRKYS FKAVHTGMRA
LIYNSSTAGS QAEQSGMRTY YFSADTQEDM NAWVRAMNQA AQVLSRSSLK RDMEKVERQA
VPQANHTESC HECGRVGPGH TRDCPHRGHD DIVNFERQEQ EGEQYRSQRD PLEGKRDRSK
ARSPYSPAEE DALFMDLPTG PRGQQAQPQR AEKNGMLPAS YGPGEQNGTG GYQRAFPPRT
NPEKHSQRKS NLAQVEHWAR AQKGDSRSLP LDQTLPRQGP GQSLSFPENY QTLPKSTRHP
SGGSSPPPRN LPSDYKYAQD RASHLKMSSE ERRAHRDGTV WQLYEWQQRQ QFRHGSPTAP
ICLGSPEFTD QGRSRSMLEV PRSISVPPSP SDIPPPGPPR VFPPRRPHTP AERVTVKPPD
QRRSVDISLG DSPRRARGHA VKNSSHVDRR SMPSMGYMTH TVSAPSLHGK SADDTYLQLK
KDLEYLDLKM TGRDLLKDRS LKPVKIAESD TDVKLSIFCE QDRVLQDLED KIRALKENKD
QLESVLEVLH RQMEQYRDQP QHLEKIAYQQ KLLQEDLVHI RAELSRESTE MENAWNEYLK
LENDVEQLKQ TLQEQHRRAF FFQEKSQIQK DLWRIEDVTA GLSANKENFR ILVESVKNPE
RKTVPLFPHP PVPSLSTSES KPPPQPSPPT SPVRTPLEVR LFPQLQTYVP YRPHPPQLRK
VTSPLQSPTK AKPKVQEDEA PPRPPLPELY SPEDQPPAVP PLPREATIIR HTSVRGLKRQ
SDERKRDREL GQCVNGDSRV ELRSYVSEPE LATLSGDMAQ PSLGLVGPES RYQTLPGRGL
SGSTSRLQQS STIAPYVTLR RGLNAESSKA TFPRPKSALE RLYSGDHQRG KMSAEEQLER
MKRHQKALVR ERKRTLGQGE RTGLPSSRYL SRPLPGDLGS WKREQDFDLQ LLERVVQGEK
KDKEENGWLK VQAMPVTELD LEPQDYDLDI SRELSKPEKV SIPERYVELD PEEPPSLEEL
QARYRKAEKI RNILARSSMC NLQPTSGQDQ NSVADLDLQL QEQERIINIS YALASEASQR
SKQVAAQAVT DP*

Mutated AA sequence

MAAATVGRDT LPEHWSYGVC RDGRVFFIND QLRCTTWLHP RTGEPVNSGH MIRSDLPRGW
EEGFTEEGAS YFIDHNQQTT AFRHPVTGQF SPENSEFILQ EEPNPHMSKQ DRNQRPSSMV
SETSTAGTAS TLEAKPGPKI IKSSSKVHSF GKRDQAIRRN PNVPVVVRGW LHKQDSSGMR
LWKRRWFVLA DYCLFYYKDS REEAVLGSIP LPSYVISPVA PEDRISRKYS FKAVHTGMRA
LIYNSSTAGS QAEQSGMRTY YFSADTQEDM NAWVRAMNQA AQVLSRSSLK RDMEKVERQA
VPQANHTESC HECGRVGPGH TRDCPHRGHD DIVNFERQEQ EGEQYRSQRD PLEGKRDRSK
ARSPYSPAEE DALFMDLPTG PRGQQAQPQR AEKNGMLPAS YGPGEQNGTG GYQRAFPPRT
NPEKHSQRKS NLAQVEHWAR AQKGDSRSLP LDQTLPRQGP GQSLSFPENY QTLPKSTRHP
SGGSSPPPRN LPSDYKYAQD RASHLKMSSE ERRAHRDGTV WQLYEWQQRQ QFRHGSPTAP
ICLGSPEFTD QGRSRSMLEV PRSISVPPSP SDIPPPGPPR VFPPRRPHTP AERVTVKPPD
QRRSVDISLG DSPRRARGHA VKNSSHVDRR SMPSMGYMTH TVSAPSLHGK SADDTYLQLK
KDLEYLDLKM TGRDLLKDRS LKPVKIAESD TDVKLSIFCE QDRVLQDLED KIRALKENKD
QLESVLEVLH RQMEQYRDQP QHLEKIAYQQ KLLQEDLVHI RAELSRESTE MENAWNEYLK
LENDVEQLKQ TLQEQHRRAF FFQEKSQIQK DLWRIEDVTA GLSANKENFR ILVESVKNPE
RKTVPLFPHP PVPSLSTSES KPPPQPSPPT SPVRTPLEVR LFPQLQTYVP YRPHPPQLRK
VTSPLQSPTK AKPKVQEDEA PPRPPLPELY SPEDQPPAVP PLPREATIIR HTSVRGLKRQ
SDERKRDREL GQCVNGDSRV ELRSYVSEPE LATLSGDMAQ PSLGLVGPES RYQTLPGRGL
SGSTSRLQQS STIAPYVTLR RGLNAESSKA TFPRPKSALE RLYSGDHQRG KMSAEEQLER
MKRHQKALVR ERKRTLGQGE RTGLPSSRYL SRPLPGDLGS WKREQDFDLQ LLERVVQGEK
KDKEENGWLK VQAMPVTELD LEPQDYDLDI SRELSKPEKV SIPERYVELD PEEPPSLEEL
QARYRKAEKI RNILARSSMC NLQPTSGQDQ NSVADLDLQL QEQERIINIS YALASEASQR
SKQVAAQAVT DP*

Position of stopcodon in wt / mu CDS

3819 / 3819

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

1273 / 1273

Position of stopcodon in wt / mu cDNA

3833 / 3833

Position of start ATG in wt / mu cDNA

15 / 15

Last intron/exon boundary

3810

Theoretical NMD boundary in CDS

3745

Length of CDS

3819

Coding sequence (CDS) position

3558

cDNA position

3572

gDNA position

230621

Chromosomal position

16783795

Speed

0.03 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:

11:16783795G>A_2_ENST00000531066

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Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 110|90 (del | benign) ?
Automatic classification due to gnomAD,
tree vote conflicts with the automatic classification ?

Analysed issue

Analysis result

Variant

Chr11:16783795G>A (GRCh38)

Gene symbol

PLEKHA7

Gene constraints

LOEUF: 0.73, LOF (oe): 0.61, misssense (oe): 0.96, synonymous (oe): 0.98 ? (gnomAD)

Ensembl transcript ID

ENST00000531066.6

Genbank transcript ID

NM_001329630 (exact from MANE)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.3555C>T
g.230621C>T

AA changes

no AA changes

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs4757433
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	64	2677	2741

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.9	0.918
	-1.246	0.001
(flanking)	7.491	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

No

Chromosome

11

Strand

-1

Original gDNA sequence snippet

GTGTCAATCCCTGAGCGCTACGTGGAGCTAGATCCCGAAGA

Altered gDNA sequence snippet

GTGTCAATCCCTGAGCGCTATGTGGAGCTAGATCCCGAAGA

Original cDNA sequence snippet

GTGTCAATCCCTGAGCGCTACGTGGAGCTAGATCCCGAAGA

Altered cDNA sequence snippet

GTGTCAATCCCTGAGCGCTATGTGGAGCTAGATCCCGAAGA

Wildtype AA sequence

MAAATVGRDT LPEHWSYGVC RDGRVFFIND QLRCTTWLHP RTGEPVNSGH MIRSDLPRGW
EEGFTEEGAS YFIDHNQQTT AFRHPVTGQF SPENSEFILQ EEPNPHMSKQ DRNQRPSSMV
SETSTAGTAS TLEAKPGPKI IKSSSKVHSF GKRDQAIRRN PNVPVVVRGW LHKQDSSGMR
LWKRRWFVLA DYCLFYYKDS REEAVLGSIP LPSYVISPVA PEDRISRKYS FKAVHTGMRA
LIYNSSTAGS QAEQSGMRTY YFSADTQEDM NAWVRAMNQA AQVLSRSSLK RDMEKVERQA
VPQANHTESC HECGRVGPGH TRDCPHRGHD DIVNFERQEQ EGEQYRSQRD PLEGKRDRSK
ARSPYSPAEE DALFMDLPTG PRGQQAQPQR AEKNGMLPAS YGPGEQNGTG GYQRAFPPRT
NPEKHSQRKS NLAQVEHWAR AQKGDSRSLP LDQTLPRQGP GQSLSFPENY QTLPKSTRHP
SGGSSPPPRN LPSDYKYAQD RASHLKMSSE ERRAHRDGTV WQLYEWQQRQ QFRHGSPTAP
ICLGSPEFTD QGRSRSMLEV PRSISVPPSP SDIPPPGPPR VFPPRRPHTP AERVTVKPPD
QRRSVDISLG DSPRRARGHA VKNSSHVDRR SMPSMGYMTH TVSAPSLHGK SADDTYLQLK
KDLEYLDLKM TGRDLLKDRS LKPVKIAESD TDVKLSIFCE QDRVLQDLED KIRALKENKD
QLESVLEVLH RQMEQYRDQP QHLEKIAYQQ KLLQEDLVHI RAELSRESTE MENAWNEYLK
LENDVEQLKQ TLQEQHRRAF FFQEKSQIQK DLWRIEDVTA GLSANKENFR ILVESVKNPE
RKTVPLFPHP PVPSLSTSES KPPPQPSPPT SPVRTPLEVR LFPQLQTYVP YRPHPPQLRK
VTSPLQSPTK AKPKVEDEAP PRPPLPELYS PEDQPPAVPP LPREATIIRH TSVRGLKRQS
DERKRDRELG QCVNGDSRVE LRSYVSEPEL ATLSGDMAQP SLGLVGPESR YQTLPGRGLS
GSTSRLQQSS TIAPYVTLRR GLNAESSKAT FPRPKSALER LYSGDHQRGK MSAEEQLERM
KRHQKALVRE RKRTLGQGER TGLPSSRYLS RPLPGDLGSW KREQDFDLQL LERVVQGEKK
DKEENGWLKV QAMPVTELDL EPQDYDLDIS RELSKPEKVS IPERYVELDP EEPPSLEELQ
ARYRKAEKIR NILARSSMCN LQPTSGQDQN SVADLDLQLQ EQERIINISY ALASEASQRS
KQVAAQAVTD P*

Mutated AA sequence

MAAATVGRDT LPEHWSYGVC RDGRVFFIND QLRCTTWLHP RTGEPVNSGH MIRSDLPRGW
EEGFTEEGAS YFIDHNQQTT AFRHPVTGQF SPENSEFILQ EEPNPHMSKQ DRNQRPSSMV
SETSTAGTAS TLEAKPGPKI IKSSSKVHSF GKRDQAIRRN PNVPVVVRGW LHKQDSSGMR
LWKRRWFVLA DYCLFYYKDS REEAVLGSIP LPSYVISPVA PEDRISRKYS FKAVHTGMRA
LIYNSSTAGS QAEQSGMRTY YFSADTQEDM NAWVRAMNQA AQVLSRSSLK RDMEKVERQA
VPQANHTESC HECGRVGPGH TRDCPHRGHD DIVNFERQEQ EGEQYRSQRD PLEGKRDRSK
ARSPYSPAEE DALFMDLPTG PRGQQAQPQR AEKNGMLPAS YGPGEQNGTG GYQRAFPPRT
NPEKHSQRKS NLAQVEHWAR AQKGDSRSLP LDQTLPRQGP GQSLSFPENY QTLPKSTRHP
SGGSSPPPRN LPSDYKYAQD RASHLKMSSE ERRAHRDGTV WQLYEWQQRQ QFRHGSPTAP
ICLGSPEFTD QGRSRSMLEV PRSISVPPSP SDIPPPGPPR VFPPRRPHTP AERVTVKPPD
QRRSVDISLG DSPRRARGHA VKNSSHVDRR SMPSMGYMTH TVSAPSLHGK SADDTYLQLK
KDLEYLDLKM TGRDLLKDRS LKPVKIAESD TDVKLSIFCE QDRVLQDLED KIRALKENKD
QLESVLEVLH RQMEQYRDQP QHLEKIAYQQ KLLQEDLVHI RAELSRESTE MENAWNEYLK
LENDVEQLKQ TLQEQHRRAF FFQEKSQIQK DLWRIEDVTA GLSANKENFR ILVESVKNPE
RKTVPLFPHP PVPSLSTSES KPPPQPSPPT SPVRTPLEVR LFPQLQTYVP YRPHPPQLRK
VTSPLQSPTK AKPKVEDEAP PRPPLPELYS PEDQPPAVPP LPREATIIRH TSVRGLKRQS
DERKRDRELG QCVNGDSRVE LRSYVSEPEL ATLSGDMAQP SLGLVGPESR YQTLPGRGLS
GSTSRLQQSS TIAPYVTLRR GLNAESSKAT FPRPKSALER LYSGDHQRGK MSAEEQLERM
KRHQKALVRE RKRTLGQGER TGLPSSRYLS RPLPGDLGSW KREQDFDLQL LERVVQGEKK
DKEENGWLKV QAMPVTELDL EPQDYDLDIS RELSKPEKVS IPERYVELDP EEPPSLEELQ
ARYRKAEKIR NILARSSMCN LQPTSGQDQN SVADLDLQLQ EQERIINISY ALASEASQRS
KQVAAQAVTD P*

Position of stopcodon in wt / mu CDS

3816 / 3816

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

1272 / 1272

Position of stopcodon in wt / mu cDNA

3829 / 3829

Position of start ATG in wt / mu cDNA

14 / 14

Last intron/exon boundary

3806

Theoretical NMD boundary in CDS

3742

Length of CDS

3816

Coding sequence (CDS) position

3555

cDNA position

3568

gDNA position

230621

Chromosomal position

16783795

Speed

0.02 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