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: ENST00000601723
Querying Taster for transcript #2: ENST00000340093
Querying Taster for transcript #3: ENST00000221264
Querying Taster for transcript #4: ENST00000339082
MT speed 0.86 s - this script 3.217293 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
ENST00000221264	PLAUR	Benign	3\|197	without_aae	No	Single base exchange	N/A
ENST00000340093(MANE Select)	PLAUR	Benign	33\|67	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000339082	PLAUR	Benign	38\|62	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000601723	PLAUR	Benign	39\|61	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed

MutationT@ster 2025

Variant:

19:43655510T>C_3_ENST00000221264

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Prediction:

BenignPermalink

Summary:

Model: without_aae
Tree vote: 3|197 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr19:43655510T>C (GRCh38)

Gene symbol

PLAUR

Gene constraints

LOEUF: 0.91, LOF (oe): 0.60, misssense (oe): 0.90, synonymous (oe): 0.84 ? (gnomAD)

Ensembl transcript ID

ENST00000221264.8

Genbank transcript ID

NM_001005377 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.472+969A>G
g.15038A>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

dbSNP ID	rs138306315
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	1	292	293

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-2.587	0
	0.915	0.023
(flanking)	-0.132	0.028

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

19

Strand

-1

Original gDNA sequence snippet

TCCCGGCTGCCCGGGCTCCAATGGTTTCCACAACAACGACA

Altered gDNA sequence snippet

TCCCGGCTGCCCGGGCTCCAGTGGTTTCCACAACAACGACA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MGHPPLLPLL LLLHTCVPAS WGLRCMQCKT NGDCRVEECA LGQDLCRTTI VRLWEEGEEL
ELVEKSCTHS EKTNRTLSYR TGLKITSLTE VVCGLDLCNQ GNSGRAVTYS RSRYLECISC
GSSDMSCERG RHQSLQCRSP EEQCLDVVTH WIQEGEEVLE LENLPQNGRQ CYSCKGNSTH
GCSSEETFLI DCRGPMNQCL VATGTHEPKN QSYMVRGCAT ASMCQHAHLG DAFSMNHIDV
SCCTKSGCNH PDLDVQYRSG AAPQPGPAHL SLTITLLMTA RLWGGTLLWT *

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

428 / 428

Last intron/exon boundary

1046

Theoretical NMD boundary in CDS

568

Length of CDS

873

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

15038

Chromosomal position

43655510

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

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MutationT@ster 2025

Variant:

19:43655510T>C_2_ENST00000340093

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Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 33|67 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr19:43655510T>C (GRCh38)

Gene symbol

PLAUR

Gene constraints

LOEUF: 0.91, LOF (oe): 0.63, misssense (oe): 0.90, synonymous (oe): 0.84 ? (gnomAD)

Ensembl transcript ID

ENST00000340093.8

Genbank transcript ID

NM_002659 (exact from MANE)

UniProt / AlphaMissense peptide

UPAR_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.536A>G
g.15038A>G

AA changes

AAE:	N179S	?
Score:	46

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs138306315
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	1	292	293

Protein conservation

Species	Match	AA	Alignment
Human		179	G	C	G	Y	L	P	G	C	P	G	S	N	G	F	H	N	N	D	T	F	H	F	L	K
mutated	all conserved	179	G	C	G	Y	L	P	G	C	P	G	S	S	G	F	H	N	N	D	T	F	H	F	L
Ptroglodytes	all identical	179	G	C	G	Y	L	P	G	C	P	G	S	N	G	F	H	N	N	D	T	F	H	F	L
Mmulatta	all conserved	180						P	S	C	P	G	S	S	G	F	H	N	N	D	T	F	H	F	L
Fcatus	not conserved	179											P	T	G	F	H	N	N	H	T	F	H	F	L
Mmusculus	not conserved	178												A	G	F	H	S	N	Q	T	F	H	F	L
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	not conserved	502	G	C	G	T	G	N	L	C	N	R	S	L	E	Y	NSG	N	G

Protein features

Start (aa)	End (aa)	Feature	Details
23	305	CHAIN		lost
115	213	DOMAIN	UPAR/Ly6	lost
176	183	STRAND		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-2.587	0
	0.915	0.023
(flanking)	-0.132	0.028

?

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

TCCCGGCTGCCCGGGCTCCAATGGTTTCCACAACAACGACA

Altered gDNA sequence snippet

TCCCGGCTGCCCGGGCTCCAGTGGTTTCCACAACAACGACA

Original cDNA sequence snippet

TCCCGGCTGCCCGGGCTCCAATGGTTTCCACAACAACGACA

Altered cDNA sequence snippet

TCCCGGCTGCCCGGGCTCCAGTGGTTTCCACAACAACGACA

Wildtype AA sequence

MGHPPLLPLL LLLHTCVPAS WGLRCMQCKT NGDCRVEECA LGQDLCRTTI VRLWEEGEEL
ELVEKSCTHS EKTNRTLSYR TGLKITSLTE VVCGLDLCNQ GNSGRAVTYS RSRYLECISC
GSSDMSCERG RHQSLQCRSP EEQCLDVVTH WIQEGEEGRP KDDRHLRGCG YLPGCPGSNG
FHNNDTFHFL KCCNTTKCNE GPILELENLP QNGRQCYSCK GNSTHGCSSE ETFLIDCRGP
MNQCLVATGT HEPKNQSYMV RGCATASMCQ HAHLGDAFSM NHIDVSCCTK SGCNHPDLDV
QYRSGAAPQP GPAHLSLTIT LLMTARLWGG TLLWT*

Mutated AA sequence

MGHPPLLPLL LLLHTCVPAS WGLRCMQCKT NGDCRVEECA LGQDLCRTTI VRLWEEGEEL
ELVEKSCTHS EKTNRTLSYR TGLKITSLTE VVCGLDLCNQ GNSGRAVTYS RSRYLECISC
GSSDMSCERG RHQSLQCRSP EEQCLDVVTH WIQEGEEGRP KDDRHLRGCG YLPGCPGSSG
FHNNDTFHFL KCCNTTKCNE GPILELENLP QNGRQCYSCK GNSTHGCSSE ETFLIDCRGP
MNQCLVATGT HEPKNQSYMV RGCATASMCQ HAHLGDAFSM NHIDVSCCTK SGCNHPDLDV
QYRSGAAPQP GPAHLSLTIT LLMTARLWGG TLLWT*

Position of stopcodon in wt / mu CDS

1008 / 1008

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

336 / 336

Position of stopcodon in wt / mu cDNA

1057 / 1057

Position of start ATG in wt / mu cDNA

50 / 50

Last intron/exon boundary

803

Theoretical NMD boundary in CDS

703

Length of CDS

1008

Coding sequence (CDS) position

536

cDNA position

585

gDNA position

15038

Chromosomal position

43655510

Speed

0.37 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:

19:43655510T>C_4_ENST00000339082

Back to summary table

Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 38|62 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr19:43655510T>C (GRCh38)

Gene symbol

PLAUR

Gene constraints

LOEUF: 0.96, LOF (oe): 0.66, misssense (oe): 0.90, synonymous (oe): 0.83 ? (gnomAD)

Ensembl transcript ID

ENST00000339082.7

Genbank transcript ID

NM_001005376 (by similarity)

UniProt / AlphaMissense peptide

UPAR_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.536A>G
g.15038A>G

AA changes

AAE:	N179S	?
Score:	46

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs138306315
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	1	292	293

Protein conservation

Species	Match	AA	Alignment
Human		179	G	C	G	Y	L	P	G	C	P	G	S	N	G	F	H	N	N	D	T	F	H	F	L	K
mutated	all conserved	179	G	C	G	Y	L	P	G	C	P	G	S	S	G	F	H	N	N	D	T	F	H	F	L
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
23	305	CHAIN		lost
115	213	DOMAIN	UPAR/Ly6	lost
176	183	STRAND		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-2.587	0
	0.915	0.023
(flanking)	-0.132	0.028

?

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

TCCCGGCTGCCCGGGCTCCAATGGTTTCCACAACAACGACA

Altered gDNA sequence snippet

TCCCGGCTGCCCGGGCTCCAGTGGTTTCCACAACAACGACA

Original cDNA sequence snippet

TCCCGGCTGCCCGGGCTCCAATGGTTTCCACAACAACGACA

Altered cDNA sequence snippet

TCCCGGCTGCCCGGGCTCCAGTGGTTTCCACAACAACGACA

Wildtype AA sequence

MGHPPLLPLL LLLHTCVPAS WGLRCMQCKT NGDCRVEECA LGQDLCRTTI VRLWEEGEEL
ELVEKSCTHS EKTNRTLSYR TGLKITSLTE VVCGLDLCNQ GNSGRAVTYS RSRYLECISC
GSSDMSCERG RHQSLQCRSP EEQCLDVVTH WIQEGEEGRP KDDRHLRGCG YLPGCPGSNG
FHNNDTFHFL KCCNTTKCNE GPILELENLP QNGRQCYSCK GNSTHGCSSE ETFLIDCRGP
MNQCLVATGT HERSLWGSWL PCKSTTALRP PCCEEAQATH V*

Mutated AA sequence

MGHPPLLPLL LLLHTCVPAS WGLRCMQCKT NGDCRVEECA LGQDLCRTTI VRLWEEGEEL
ELVEKSCTHS EKTNRTLSYR TGLKITSLTE VVCGLDLCNQ GNSGRAVTYS RSRYLECISC
GSSDMSCERG RHQSLQCRSP EEQCLDVVTH WIQEGEEGRP KDDRHLRGCG YLPGCPGSSG
FHNNDTFHFL KCCNTTKCNE GPILELENLP QNGRQCYSCK GNSTHGCSSE ETFLIDCRGP
MNQCLVATGT HERSLWGSWL PCKSTTALRP PCCEEAQATH V*

Position of stopcodon in wt / mu CDS

846 / 846

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

282 / 282

Position of stopcodon in wt / mu cDNA

892 / 892

Position of start ATG in wt / mu cDNA

47 / 47

Last intron/exon boundary

800

Theoretical NMD boundary in CDS

703

Length of CDS

846

Coding sequence (CDS) position

536

cDNA position

582

gDNA position

15038

Chromosomal position

43655510

Speed

0.35 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:

19:43655510T>C_1_ENST00000601723

Back to summary table

Prediction:

BenignPermalink

Summary:

Amino acid sequence changed

Model: simple_aae
Tree vote: 39|61 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr19:43655510T>C (GRCh38)

Gene symbol

PLAUR

Gene constraints

LOEUF: 0.84, LOF (oe): 0.54, misssense (oe): 0.88, synonymous (oe): 0.89 ? (gnomAD)

Ensembl transcript ID

ENST00000601723.5

Genbank transcript ID

NM_001301037 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.536A>G
g.15038A>G

AA changes

AAE:	N179S	?
Score:	46

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs138306315
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	1	292	293

Protein conservation

Species	Match	AA	Alignment
Human		179	G	C	G	Y	L	P	G	C	P	G	S	N	G	F	H	N	N	D	T	F	H	F	L	K
mutated	all conserved	179	G	C	G	Y	L	P	G	C	P	G	S	S	G	F	H	N	N	D	T	F	H	F	L
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)	-2.587	0
	0.915	0.023
(flanking)	-0.132	0.028

?

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

TCCCGGCTGCCCGGGCTCCAATGGTTTCCACAACAACGACA

Altered gDNA sequence snippet

TCCCGGCTGCCCGGGCTCCAGTGGTTTCCACAACAACGACA

Original cDNA sequence snippet

TCCCGGCTGCCCGGGCTCCAATGGTTTCCACAACAACGACA

Altered cDNA sequence snippet

TCCCGGCTGCCCGGGCTCCAGTGGTTTCCACAACAACGACA

Wildtype AA sequence

MGHPPLLPLL LLLHTCVPAS WGLRCMQCKT NGDCRVEECA LGQDLCRTTI VRLWEEGEEL
ELVEKSCTHS EKTNRTLSYR TGLKITSLTE VVCGLDLCNQ GNSGRAVTYS RSRYLECISC
GSSDMSCERG RHQSLQCRSP EEQCLDVVTH WIQEGEEGRP KDDRHLRGCG YLPGCPGSNG
FHNNDTFHFL KCCNTTKCNE GPKPKNQSYM VRGCATASMC QHAHLGDAFS MNHIDVSCCT
KSGCNHPDLD VQYRSGAAPQ PGPAHLSLTI TLLMTARLWG GTLLWT*

Mutated AA sequence

MGHPPLLPLL LLLHTCVPAS WGLRCMQCKT NGDCRVEECA LGQDLCRTTI VRLWEEGEEL
ELVEKSCTHS EKTNRTLSYR TGLKITSLTE VVCGLDLCNQ GNSGRAVTYS RSRYLECISC
GSSDMSCERG RHQSLQCRSP EEQCLDVVTH WIQEGEEGRP KDDRHLRGCG YLPGCPGSSG
FHNNDTFHFL KCCNTTKCNE GPKPKNQSYM VRGCATASMC QHAHLGDAFS MNHIDVSCCT
KSGCNHPDLD VQYRSGAAPQ PGPAHLSLTI TLLMTARLWG GTLLWT*

Position of stopcodon in wt / mu CDS

861 / 861

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

287 / 287

Position of stopcodon in wt / mu cDNA

894 / 894

Position of start ATG in wt / mu cDNA

34 / 34

Last intron/exon boundary

640

Theoretical NMD boundary in CDS

556

Length of CDS

861

Coding sequence (CDS) position

536

cDNA position

569

gDNA position

15038

Chromosomal position

43655510

Speed

0.12 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