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: ENST00000327790
Querying Taster for transcript #2: ENST00000434325
Querying Taster for transcript #3: ENST00000269812
MT speed 0.2 s - this script 2.596267 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
ENST00000434325(MANE Select)	PLPP2	Benign	18\|82	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000269812	PLPP2	Benign	21\|79	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000327790	PLPP2	Benign	31\|69	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed

MutationT@ster 2025

Variant:

19:281424G>C_2_ENST00000434325

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Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 18|82 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr19:281424G>C (GRCh38)

Gene symbol

PLPP2

Gene constraints

LOEUF: 1.11, LOF (oe): 0.81, misssense (oe): 0.96, synonymous (oe): 1.01 ? (gnomAD)

Ensembl transcript ID

ENST00000434325.7

Genbank transcript ID

NM_003712 (exact from MANE)

UniProt / AlphaMissense peptide

PLPP2_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.831C>G
g.9980C>G

AA changes

AAE:	D277E	?
Score:	45

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

	Not in dbSNP
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	0	2	2

Protein conservation

Species	Match	AA	Alignment
Human		277	S	L	S	L	T	L	T	L	G	E	A	D	H	N	H	Y	G	Y	P	H	S	S	S	*
mutated	all conserved	277	S	L	S	L	T	L	T	L	G	E	A	E	H	N	H	Y	G	Y	P	H	S	S	S
Ptroglodytes	all identical	298	S	L	S	L	T	L	T	L	G	E	A	D	H	N	H	Y	G	Y	P	H	S	S	S
Mmulatta	no homologue
Fcatus	all identical	277	S	L	S	L	T	L	T	L	G	E	A	D	R	N	H	Y	G
Mmusculus	no alignment	n/a
Ggallus	all identical	333	S	L	P	L	T	L	S	-	-	D	T	D	R	N	H	Y	S	Y
Trubripes	all identical	561	S	L	Q	-	-	-	-	I	A	D	S	D	HG	N	H	Y	N	Y	H	H	N
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	all identical	278	S	L	Q	L	S	-	-	-	-	E	S	D	Q	N	H	F	G	Y

Protein features

Start (aa)	End (aa)	Feature	Details
1	288	CHAIN		lost
248	288	TOPO_DOM	Cytoplasmic	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.225	0
	-0.494	0
(flanking)	1.731	0.027

?

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

19

Strand

-1

Original gDNA sequence snippet

TTGACCCTGGGCGAGGCTGACCACAACCACTATGGATACCC

Altered gDNA sequence snippet

TTGACCCTGGGCGAGGCTGAGCACAACCACTATGGATACCC

Original cDNA sequence snippet

TTGACCCTGGGCGAGGCTGACCACAACCACTATGGATACCC

Altered cDNA sequence snippet

TTGACCCTGGGCGAGGCTGAGCACAACCACTATGGATACCC

Wildtype AA sequence

MQRRWVFVLL DVLCLLVASL PFAILTLVNA PYKRGFYCGD DSIRYPYRPD TITHGLMAGV
TITATVILVS AGEAYLVYTD RLYSRSDFNN YVAAVYKVLG TFLFGAAVSQ SLTDLAKYMI
GRLRPNFLAV CDPDWSRVNC SVYVQLEKVC RGNPADVTEA RLSFYSGHSS FGMYCMVFLA
LYVQARLCWK WARLLRPTVQ FFLVAFALYV GYTRVSDYKH HWSDVLVGLL QGALVAALTV
CYISDFFKAR PPQHCLKEEE LERKPSLSLT LTLGEADHNH YGYPHSSS*

Mutated AA sequence

MQRRWVFVLL DVLCLLVASL PFAILTLVNA PYKRGFYCGD DSIRYPYRPD TITHGLMAGV
TITATVILVS AGEAYLVYTD RLYSRSDFNN YVAAVYKVLG TFLFGAAVSQ SLTDLAKYMI
GRLRPNFLAV CDPDWSRVNC SVYVQLEKVC RGNPADVTEA RLSFYSGHSS FGMYCMVFLA
LYVQARLCWK WARLLRPTVQ FFLVAFALYV GYTRVSDYKH HWSDVLVGLL QGALVAALTV
CYISDFFKAR PPQHCLKEEE LERKPSLSLT LTLGEAEHNH YGYPHSSS*

Position of stopcodon in wt / mu CDS

867 / 867

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

289 / 289

Position of stopcodon in wt / mu cDNA

934 / 934

Position of start ATG in wt / mu cDNA

68 / 68

Last intron/exon boundary

784

Theoretical NMD boundary in CDS

666

Length of CDS

867

Coding sequence (CDS) position

831

cDNA position

898

gDNA position

9980

Chromosomal position

281424

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

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MutationT@ster 2025

Variant:

19:281424G>C_3_ENST00000269812

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Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

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

Analysed issue

Analysis result

Variant

Chr19:281424G>C (GRCh38)

Gene symbol

PLPP2

Gene constraints

LOEUF: 1.10, LOF (oe): 0.77, misssense (oe): 1.00, synonymous (oe): 1.01 ? (gnomAD)

Ensembl transcript ID

ENST00000269812.7

Genbank transcript ID

NM_177526 (by similarity)

UniProt / AlphaMissense peptide

PLPP2_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.663C>G
g.9980C>G

AA changes

AAE:	D221E	?
Score:	45

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

	Not in dbSNP
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	0	2	2

Protein conservation

Species	Match	AA	Alignment
Human		221	S	L	S	L	T	L	T	L	G	E	A	D	H	N	H	Y	G	Y	P	H	S	S	S	*
mutated	all conserved	221	S	L	S	L	T	L	T	L	G	E	A	E	H	N	H	Y	G	Y	P	H	S	S	S
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	288	CHAIN		lost
213	224	REGION		lost
218	226	TOPO_DOM	Lumenal	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.225	0
	-0.494	0
(flanking)	1.731	0.027

?

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

19

Strand

-1

Original gDNA sequence snippet

TTGACCCTGGGCGAGGCTGACCACAACCACTATGGATACCC

Altered gDNA sequence snippet

TTGACCCTGGGCGAGGCTGAGCACAACCACTATGGATACCC

Original cDNA sequence snippet

TTGACCCTGGGCGAGGCTGACCACAACCACTATGGATACCC

Altered cDNA sequence snippet

TTGACCCTGGGCGAGGCTGAGCACAACCACTATGGATACCC

Wildtype AA sequence

MAGVTITATV ILVSAGEAYL VYTDRLYSRS DFNNYVAAVY KVLGTFLFGA AVSQSLTDLA
KYMIGRLRPN FLAVCDPDWS RVNCSVYVQL EKVCRGNPAD VTEARLSFYS GHSSFGMYCM
VFLALYVQAR LCWKWARLLR PTVQFFLVAF ALYVGYTRVS DYKHHWSDVL VGLLQGALVA
ALTVCYISDF FKARPPQHCL KEEELERKPS LSLTLTLGEA DHNHYGYPHS SS*

Mutated AA sequence

MAGVTITATV ILVSAGEAYL VYTDRLYSRS DFNNYVAAVY KVLGTFLFGA AVSQSLTDLA
KYMIGRLRPN FLAVCDPDWS RVNCSVYVQL EKVCRGNPAD VTEARLSFYS GHSSFGMYCM
VFLALYVQAR LCWKWARLLR PTVQFFLVAF ALYVGYTRVS DYKHHWSDVL VGLLQGALVA
ALTVCYISDF FKARPPQHCL KEEELERKPS LSLTLTLGEA EHNHYGYPHS SS*

Position of stopcodon in wt / mu CDS

699 / 699

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

233 / 233

Position of stopcodon in wt / mu cDNA

883 / 883

Position of start ATG in wt / mu cDNA

185 / 185

Last intron/exon boundary

733

Theoretical NMD boundary in CDS

498

Length of CDS

699

Coding sequence (CDS) position

663

cDNA position

847

gDNA position

9980

Chromosomal position

281424

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:

19:281424G>C_1_ENST00000327790

Back to summary table

Prediction:

BenignPermalink

Summary:

Amino acid sequence changed

Model: simple_aae
Tree vote: 31|69 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr19:281424G>C (GRCh38)

Gene symbol

PLPP2

Gene constraints

LOEUF: 1.12, LOF (oe): 0.82, misssense (oe): 1.04, synonymous (oe): 1.11 ? (gnomAD)

Ensembl transcript ID

ENST00000327790.7

Genbank transcript ID

NM_177543 (by similarity)

UniProt / AlphaMissense peptide

PLPP2_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.894C>G
g.9980C>G

AA changes

AAE:	D298E	?
Score:	45

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

	Not in dbSNP
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	0	2	2

Protein conservation

Species	Match	AA	Alignment
Human		298	S	L	S	L	T	L	T	L	G	E	A	D	H	N	H	Y	G	Y	P	H	S	S	S	*
mutated	all conserved	298	S	L	S	L	T	L	T	L	G	E	A	E	H	N
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

No protein features affected

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.225	0
	-0.494	0
(flanking)	1.731	0.027

?

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

19

Strand

-1

Original gDNA sequence snippet

TTGACCCTGGGCGAGGCTGACCACAACCACTATGGATACCC

Altered gDNA sequence snippet

TTGACCCTGGGCGAGGCTGAGCACAACCACTATGGATACCC

Original cDNA sequence snippet

TTGACCCTGGGCGAGGCTGACCACAACCACTATGGATACCC

Altered cDNA sequence snippet

TTGACCCTGGGCGAGGCTGAGCACAACCACTATGGATACCC

Wildtype AA sequence

MGVARGPGSR GQHPPPRQQE VCAEGPRARL HPAPPGLGAS LPFAILTLVN APYKRGFYCG
DDSIRYPYRP DTITHGLMAG VTITATVILV SAGEAYLVYT DRLYSRSDFN NYVAAVYKVL
GTFLFGAAVS QSLTDLAKYM IGRLRPNFLA VCDPDWSRVN CSVYVQLEKV CRGNPADVTE
ARLSFYSGHS SFGMYCMVFL ALYVQARLCW KWARLLRPTV QFFLVAFALY VGYTRVSDYK
HHWSDVLVGL LQGALVAALT VCYISDFFKA RPPQHCLKEE ELERKPSLSL TLTLGEADHN
HYGYPHSSS*

Mutated AA sequence

MGVARGPGSR GQHPPPRQQE VCAEGPRARL HPAPPGLGAS LPFAILTLVN APYKRGFYCG
DDSIRYPYRP DTITHGLMAG VTITATVILV SAGEAYLVYT DRLYSRSDFN NYVAAVYKVL
GTFLFGAAVS QSLTDLAKYM IGRLRPNFLA VCDPDWSRVN CSVYVQLEKV CRGNPADVTE
ARLSFYSGHS SFGMYCMVFL ALYVQARLCW KWARLLRPTV QFFLVAFALY VGYTRVSDYK
HHWSDVLVGL LQGALVAALT VCYISDFFKA RPPQHCLKEE ELERKPSLSL TLTLGEAEHN
HYGYPHSSS*

Position of stopcodon in wt / mu CDS

930 / 930

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

310 / 310

Position of stopcodon in wt / mu cDNA

1049 / 1049

Position of start ATG in wt / mu cDNA

120 / 120

Last intron/exon boundary

899

Theoretical NMD boundary in CDS

729

Length of CDS

930

Coding sequence (CDS) position

894

cDNA position

1013

gDNA position

9980

Chromosomal position

281424

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