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: ENST00000640055
Querying Taster for transcript #2: ENST00000639958
Querying Taster for transcript #3: ENST00000548696
Querying Taster for transcript #4: ENST00000455697
Querying Taster for transcript #5: ENST00000640132
Querying Taster for transcript #6: ENST00000445766
Querying Taster for transcript #7: ENST00000639589
Querying Taster for transcript #8: ENST00000345127
MT speed 0.39 s - this script 2.826196 s

Transcript summary:

Permalink

Transcript	Gene symbol	Prediction	Tree vote	Model	Splice site change	Variant type	Protein length	Features at a glance
ENST00000640055	PRICKLE1	Benign	4\|96	3utr	No	Deletion	N/A	Homozygous in gnomAD Poly(A) signal changed
ENST00000639958	PRICKLE1	Benign	4\|96	3utr	No	Deletion	N/A	Homozygous in gnomAD Poly(A) signal changed
ENST00000548696	PRICKLE1	Benign	4\|96	3utr	No	Deletion	N/A	Homozygous in gnomAD Poly(A) signal changed
ENST00000455697	PRICKLE1	Benign	4\|96	3utr	No	Deletion	N/A	Homozygous in gnomAD Poly(A) signal changed
ENST00000640132	PRICKLE1	Benign	4\|96	3utr	No	Deletion	N/A	Homozygous in gnomAD Poly(A) signal changed
ENST00000445766	PRICKLE1	Benign	4\|96	3utr	No	Deletion	N/A	Homozygous in gnomAD Poly(A) signal changed
ENST00000639589	PRICKLE1	Benign	4\|96	3utr	No	Deletion	N/A	Homozygous in gnomAD Poly(A) signal changed
ENST00000345127(MANE Select)	PRICKLE1	Benign	4\|96	3utr	No	Deletion	N/A	Homozygous in gnomAD Poly(A) signal changed

MutationT@ster 2025

Variant:

12:42459256GT>G_1_ENST00000640055

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD
Poly(A) signal changed

Model: 3utr
Tree vote: 4|96 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr12:42459257delT (GRCh38)

Gene symbol

PRICKLE1

Gene constraints

LOEUF: 0.28, LOF (oe): 0.17, misssense (oe): 0.76, synonymous (oe): 0.89 ? (gnomAD)

Ensembl transcript ID

ENST00000640055.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Deletion

Gene region

3'UTR

DNA changes

cDNA.3346delA
g.131099delA

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	rs68074167
gnomAD	homozygous (-/-)	heterozygous	allele carriers
	>32000	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.328	0.314
	1.081	0.143
(flanking)	-0.442	0.051

?

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

unique in [sequence type]: position, polyA signal, score
unique in >mutated: 135578, AATAAA, 0.224256 unique in >mutated: 135579, AATAAA, 0.224256

AA sequence altered

N/A

Chromosome

12

Strand

-1

Original gDNA sequence snippet

CTACAGATTGAAAAAAAAAAACAAAAAACATTGCTATTTAT

Altered gDNA sequence snippet

CTACAGATTGAAAAAAAAAACAAAAAACATTGCTATTTAT

Original cDNA sequence snippet

CTACAGATTGAAAAAAAAAAACAAAAAACATTGCTATTTAT

Altered cDNA sequence snippet

CTACAGATTGAAAAAAAAAACAAAAAACATTGCTATTTAT

Wildtype AA sequence

MPLEMEPKMS KLAFGCQRSS TSDDDSGCAL EEYAWVPPGL RPEQIQLYFA CLPEEKVPYV
NSPGEKHRIK QLLYQLPPHD NEVRYCQSLS EEEKKELQVF SAQRKKEALG RGTIKLLSRA
VMHAVCEQCG LKINGGEVAV FASRAGPGVC WHPSCFVCFT CNELLVDLIY FYQDGKIHCG
RHHAELLKPR CSACDEIIFA DECTEAEGRH WHMKHFCCLE CETVLGGQRY IMKDGRPFCC
GCFESLYAEY CETCGEHIGV DHAQMTYDGQ HWHATEACFS CAQCKASLLG CPFLPKQGQI
YCSKTCSLGE DVHASDSSDS AFQSARSRDS RRSVRMGKSS RSADQCRQSL LLSPALNYKF
PGLSGNADDT LSRKLDDLSL SRQGTSFASE EFWKGRVEQE TPEDPEEWAD HEDYMTQLLL
KFGDKSLFQP QPNEMDIRAS EHWISDNMVK SKTELKQNNQ SLASKKYQSD MYWAQSQDGL
GDSAYGSHPG PASSRRLQEL ELDHGASGYN HDETQWYEDS LECLSDLKPE QSVRDSMDSL
ALSNITGASV DGENKPRPSL YSLQNFEEME TEDCEKMSNM GTLNSSMLHR SAESLKSLSS
ELCPEKILPE EKPVHLPVLR RSKSQSRPQQ VKFSDDVIDN GNYDIEIRQP PMSERTRRRV
YNFEERGSRS HHHRRRRSRK SRSDNALNLV TERKYSPKDR LRLYTPDNYE KFIQNKSARE
IQAYIQNADL YGQYAHATSD YGLQNPGMNR FLGLYGEDDD SWCSSSSSSS DSEEEGYFLG
QPIPQPRPQR FAYYTDDLSS PPSALPTPQF GQRTTKSKKK KGHKGKNCII S*

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

299 / 299

Last intron/exon boundary

1937

Theoretical NMD boundary in CDS

1588

Length of CDS

2496

Coding sequence (CDS) position

N/A

cDNA position

3345 / 3347

gDNA position

131098 / 131100

Chromosomal position

42459256 / 42459258

Speed

0.04 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:

12:42459256GT>G_2_ENST00000639958

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD
Poly(A) signal changed

Model: 3utr
Tree vote: 4|96 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr12:42459257delT (GRCh38)

Gene symbol

PRICKLE1

Gene constraints

LOEUF: 0.28, LOF (oe): 0.17, misssense (oe): 0.76, synonymous (oe): 0.89 ? (gnomAD)

Ensembl transcript ID

ENST00000639958.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Deletion

Gene region

3'UTR

DNA changes

cDNA.3375delA
g.131099delA

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	rs68074167
gnomAD	homozygous (-/-)	heterozygous	allele carriers
	>32000	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.328	0.314
	1.081	0.143
(flanking)	-0.442	0.051

?

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

unique in [sequence type]: position, polyA signal, score
unique in >mutated: 135578, AATAAA, 0.224256 unique in >mutated: 135579, AATAAA, 0.224256

AA sequence altered

N/A

Chromosome

12

Strand

-1

Original gDNA sequence snippet

CTACAGATTGAAAAAAAAAAACAAAAAACATTGCTATTTAT

Altered gDNA sequence snippet

CTACAGATTGAAAAAAAAAACAAAAAACATTGCTATTTAT

Original cDNA sequence snippet

CTACAGATTGAAAAAAAAAAACAAAAAACATTGCTATTTAT

Altered cDNA sequence snippet

CTACAGATTGAAAAAAAAAACAAAAAACATTGCTATTTAT

Wildtype AA sequence

MPLEMEPKMS KLAFGCQRSS TSDDDSGCAL EEYAWVPPGL RPEQIQLYFA CLPEEKVPYV
NSPGEKHRIK QLLYQLPPHD NEVRYCQSLS EEEKKELQVF SAQRKKEALG RGTIKLLSRA
VMHAVCEQCG LKINGGEVAV FASRAGPGVC WHPSCFVCFT CNELLVDLIY FYQDGKIHCG
RHHAELLKPR CSACDEIIFA DECTEAEGRH WHMKHFCCLE CETVLGGQRY IMKDGRPFCC
GCFESLYAEY CETCGEHIGV DHAQMTYDGQ HWHATEACFS CAQCKASLLG CPFLPKQGQI
YCSKTCSLGE DVHASDSSDS AFQSARSRDS RRSVRMGKSS RSADQCRQSL LLSPALNYKF
PGLSGNADDT LSRKLDDLSL SRQGTSFASE EFWKGRVEQE TPEDPEEWAD HEDYMTQLLL
KFGDKSLFQP QPNEMDIRAS EHWISDNMVK SKTELKQNNQ SLASKKYQSD MYWAQSQDGL
GDSAYGSHPG PASSRRLQEL ELDHGASGYN HDETQWYEDS LECLSDLKPE QSVRDSMDSL
ALSNITGASV DGENKPRPSL YSLQNFEEME TEDCEKMSNM GTLNSSMLHR SAESLKSLSS
ELCPEKILPE EKPVHLPVLR RSKSQSRPQQ VKFSDDVIDN GNYDIEIRQP PMSERTRRRV
YNFEERGSRS HHHRRRRSRK SRSDNALNLV TERKYSPKDR LRLYTPDNYE KFIQNKSARE
IQAYIQNADL YGQYAHATSD YGLQNPGMNR FLGLYGEDDD SWCSSSSSSS DSEEEGYFLG
QPIPQPRPQR FAYYTDDLSS PPSALPTPQF GQRTTKSKKK KGHKGKNCII S*

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

328 / 328

Last intron/exon boundary

1966

Theoretical NMD boundary in CDS

1588

Length of CDS

2496

Coding sequence (CDS) position

N/A

cDNA position

3374 / 3376

gDNA position

131098 / 131100

Chromosomal position

42459256 / 42459258

Speed

0.04 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:

12:42459256GT>G_3_ENST00000548696

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD
Poly(A) signal changed

Model: 3utr
Tree vote: 4|96 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr12:42459257delT (GRCh38)

Gene symbol

PRICKLE1

Gene constraints

LOEUF: 0.28, LOF (oe): 0.17, misssense (oe): 0.76, synonymous (oe): 0.89 ? (gnomAD)

Ensembl transcript ID

ENST00000548696.6

Genbank transcript ID

NM_001144883 (by similarity), NM_001144882 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Deletion

Gene region

3'UTR

DNA changes

cDNA.3329delA
g.131099delA

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	rs68074167
gnomAD	homozygous (-/-)	heterozygous	allele carriers
	>32000	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.328	0.314
	1.081	0.143
(flanking)	-0.442	0.051

?

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

unique in [sequence type]: position, polyA signal, score
unique in >mutated: 135578, AATAAA, 0.224256 unique in >mutated: 135579, AATAAA, 0.224256

AA sequence altered

N/A

Chromosome

12

Strand

-1

Original gDNA sequence snippet

CTACAGATTGAAAAAAAAAAACAAAAAACATTGCTATTTAT

Altered gDNA sequence snippet

CTACAGATTGAAAAAAAAAACAAAAAACATTGCTATTTAT

Original cDNA sequence snippet

CTACAGATTGAAAAAAAAAAACAAAAAACATTGCTATTTAT

Altered cDNA sequence snippet

CTACAGATTGAAAAAAAAAACAAAAAACATTGCTATTTAT

Wildtype AA sequence

MPLEMEPKMS KLAFGCQRSS TSDDDSGCAL EEYAWVPPGL RPEQIQLYFA CLPEEKVPYV
NSPGEKHRIK QLLYQLPPHD NEVRYCQSLS EEEKKELQVF SAQRKKEALG RGTIKLLSRA
VMHAVCEQCG LKINGGEVAV FASRAGPGVC WHPSCFVCFT CNELLVDLIY FYQDGKIHCG
RHHAELLKPR CSACDEIIFA DECTEAEGRH WHMKHFCCLE CETVLGGQRY IMKDGRPFCC
GCFESLYAEY CETCGEHIGV DHAQMTYDGQ HWHATEACFS CAQCKASLLG CPFLPKQGQI
YCSKTCSLGE DVHASDSSDS AFQSARSRDS RRSVRMGKSS RSADQCRQSL LLSPALNYKF
PGLSGNADDT LSRKLDDLSL SRQGTSFASE EFWKGRVEQE TPEDPEEWAD HEDYMTQLLL
KFGDKSLFQP QPNEMDIRAS EHWISDNMVK SKTELKQNNQ SLASKKYQSD MYWAQSQDGL
GDSAYGSHPG PASSRRLQEL ELDHGASGYN HDETQWYEDS LECLSDLKPE QSVRDSMDSL
ALSNITGASV DGENKPRPSL YSLQNFEEME TEDCEKMSNM GTLNSSMLHR SAESLKSLSS
ELCPEKILPE EKPVHLPVLR RSKSQSRPQQ VKFSDDVIDN GNYDIEIRQP PMSERTRRRV
YNFEERGSRS HHHRRRRSRK SRSDNALNLV TERKYSPKDR LRLYTPDNYE KFIQNKSARE
IQAYIQNADL YGQYAHATSD YGLQNPGMNR FLGLYGEDDD SWCSSSSSSS DSEEEGYFLG
QPIPQPRPQR FAYYTDDLSS PPSALPTPQF GQRTTKSKKK KGHKGKNCII S*

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

282 / 282

Last intron/exon boundary

1920

Theoretical NMD boundary in CDS

1588

Length of CDS

2496

Coding sequence (CDS) position

N/A

cDNA position

3328 / 3330

gDNA position

131098 / 131100

Chromosomal position

42459256 / 42459258

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

Back to summary table

MutationT@ster 2025

Variant:

12:42459256GT>G_4_ENST00000455697

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD
Poly(A) signal changed

Model: 3utr
Tree vote: 4|96 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr12:42459257delT (GRCh38)

Gene symbol

PRICKLE1

Gene constraints

LOEUF: 0.28, LOF (oe): 0.17, misssense (oe): 0.76, synonymous (oe): 0.89 ? (gnomAD)

Ensembl transcript ID

ENST00000455697.6

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Deletion

Gene region

3'UTR

DNA changes

cDNA.3392delA
g.131099delA

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	rs68074167
gnomAD	homozygous (-/-)	heterozygous	allele carriers
	>32000	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.328	0.314
	1.081	0.143
(flanking)	-0.442	0.051

?

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

unique in [sequence type]: position, polyA signal, score
unique in >mutated: 135578, AATAAA, 0.224256 unique in >mutated: 135579, AATAAA, 0.224256

AA sequence altered

N/A

Chromosome

12

Strand

-1

Original gDNA sequence snippet

CTACAGATTGAAAAAAAAAAACAAAAAACATTGCTATTTAT

Altered gDNA sequence snippet

CTACAGATTGAAAAAAAAAACAAAAAACATTGCTATTTAT

Original cDNA sequence snippet

CTACAGATTGAAAAAAAAAAACAAAAAACATTGCTATTTAT

Altered cDNA sequence snippet

CTACAGATTGAAAAAAAAAACAAAAAACATTGCTATTTAT

Wildtype AA sequence

MPLEMEPKMS KLAFGCQRSS TSDDDSGCAL EEYAWVPPGL RPEQIQLYFA CLPEEKVPYV
NSPGEKHRIK QLLYQLPPHD NEVRYCQSLS EEEKKELQVF SAQRKKEALG RGTIKLLSRA
VMHAVCEQCG LKINGGEVAV FASRAGPGVC WHPSCFVCFT CNELLVDLIY FYQDGKIHCG
RHHAELLKPR CSACDEIIFA DECTEAEGRH WHMKHFCCLE CETVLGGQRY IMKDGRPFCC
GCFESLYAEY CETCGEHIGV DHAQMTYDGQ HWHATEACFS CAQCKASLLG CPFLPKQGQI
YCSKTCSLGE DVHASDSSDS AFQSARSRDS RRSVRMGKSS RSADQCRQSL LLSPALNYKF
PGLSGNADDT LSRKLDDLSL SRQGTSFASE EFWKGRVEQE TPEDPEEWAD HEDYMTQLLL
KFGDKSLFQP QPNEMDIRAS EHWISDNMVK SKTELKQNNQ SLASKKYQSD MYWAQSQDGL
GDSAYGSHPG PASSRRLQEL ELDHGASGYN HDETQWYEDS LECLSDLKPE QSVRDSMDSL
ALSNITGASV DGENKPRPSL YSLQNFEEME TEDCEKMSNM GTLNSSMLHR SAESLKSLSS
ELCPEKILPE EKPVHLPVLR RSKSQSRPQQ VKFSDDVIDN GNYDIEIRQP PMSERTRRRV
YNFEERGSRS HHHRRRRSRK SRSDNALNLV TERKYSPKDR LRLYTPDNYE KFIQNKSARE
IQAYIQNADL YGQYAHATSD YGLQNPGMNR FLGLYGEDDD SWCSSSSSSS DSEEEGYFLG
QPIPQPRPQR FAYYTDDLSS PPSALPTPQF GQRTTKSKKK KGHKGKNCII S*

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

345 / 345

Last intron/exon boundary

1983

Theoretical NMD boundary in CDS

1588

Length of CDS

2496

Coding sequence (CDS) position

N/A

cDNA position

3391 / 3393

gDNA position

131098 / 131100

Chromosomal position

42459256 / 42459258

Speed

0.04 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:

12:42459256GT>G_5_ENST00000640132

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD
Poly(A) signal changed

Model: 3utr
Tree vote: 4|96 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr12:42459257delT (GRCh38)

Gene symbol

PRICKLE1

Gene constraints

LOEUF: 0.28, LOF (oe): 0.17, misssense (oe): 0.76, synonymous (oe): 0.89 ? (gnomAD)

Ensembl transcript ID

ENST00000640132.1

Genbank transcript ID

NM_001144881 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Deletion

Gene region

3'UTR

DNA changes

cDNA.3393delA
g.131099delA

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	rs68074167
gnomAD	homozygous (-/-)	heterozygous	allele carriers
	>32000	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.328	0.314
	1.081	0.143
(flanking)	-0.442	0.051

?

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

unique in [sequence type]: position, polyA signal, score
unique in >mutated: 135578, AATAAA, 0.224256 unique in >mutated: 135579, AATAAA, 0.224256

AA sequence altered

N/A

Chromosome

12

Strand

-1

Original gDNA sequence snippet

CTACAGATTGAAAAAAAAAAACAAAAAACATTGCTATTTAT

Altered gDNA sequence snippet

CTACAGATTGAAAAAAAAAACAAAAAACATTGCTATTTAT

Original cDNA sequence snippet

CTACAGATTGAAAAAAAAAAACAAAAAACATTGCTATTTAT

Altered cDNA sequence snippet

CTACAGATTGAAAAAAAAAACAAAAAACATTGCTATTTAT

Wildtype AA sequence

MPLEMEPKMS KLAFGCQRSS TSDDDSGCAL EEYAWVPPGL RPEQIQLYFA CLPEEKVPYV
NSPGEKHRIK QLLYQLPPHD NEVRYCQSLS EEEKKELQVF SAQRKKEALG RGTIKLLSRA
VMHAVCEQCG LKINGGEVAV FASRAGPGVC WHPSCFVCFT CNELLVDLIY FYQDGKIHCG
RHHAELLKPR CSACDEIIFA DECTEAEGRH WHMKHFCCLE CETVLGGQRY IMKDGRPFCC
GCFESLYAEY CETCGEHIGV DHAQMTYDGQ HWHATEACFS CAQCKASLLG CPFLPKQGQI
YCSKTCSLGE DVHASDSSDS AFQSARSRDS RRSVRMGKSS RSADQCRQSL LLSPALNYKF
PGLSGNADDT LSRKLDDLSL SRQGTSFASE EFWKGRVEQE TPEDPEEWAD HEDYMTQLLL
KFGDKSLFQP QPNEMDIRAS EHWISDNMVK SKTELKQNNQ SLASKKYQSD MYWAQSQDGL
GDSAYGSHPG PASSRRLQEL ELDHGASGYN HDETQWYEDS LECLSDLKPE QSVRDSMDSL
ALSNITGASV DGENKPRPSL YSLQNFEEME TEDCEKMSNM GTLNSSMLHR SAESLKSLSS
ELCPEKILPE EKPVHLPVLR RSKSQSRPQQ VKFSDDVIDN GNYDIEIRQP PMSERTRRRV
YNFEERGSRS HHHRRRRSRK SRSDNALNLV TERKYSPKDR LRLYTPDNYE KFIQNKSARE
IQAYIQNADL YGQYAHATSD YGLQNPGMNR FLGLYGEDDD SWCSSSSSSS DSEEEGYFLG
QPIPQPRPQR FAYYTDDLSS PPSALPTPQF GQRTTKSKKK KGHKGKNCII S*

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

346 / 346

Last intron/exon boundary

1984

Theoretical NMD boundary in CDS

1588

Length of CDS

2496

Coding sequence (CDS) position

N/A

cDNA position

3392 / 3394

gDNA position

131098 / 131100

Chromosomal position

42459256 / 42459258

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:

12:42459256GT>G_6_ENST00000445766

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD
Poly(A) signal changed

Model: 3utr
Tree vote: 4|96 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr12:42459257delT (GRCh38)

Gene symbol

PRICKLE1

Gene constraints

LOEUF: 0.28, LOF (oe): 0.17, misssense (oe): 0.76, synonymous (oe): 0.89 ? (gnomAD)

Ensembl transcript ID

ENST00000445766.7

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Deletion

Gene region

3'UTR

DNA changes

cDNA.3178delA
g.131099delA

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	rs68074167
gnomAD	homozygous (-/-)	heterozygous	allele carriers
	>32000	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.328	0.314
	1.081	0.143
(flanking)	-0.442	0.051

?

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

unique in [sequence type]: position, polyA signal, score
unique in >mutated: 135578, AATAAA, 0.224256 unique in >mutated: 135579, AATAAA, 0.224256

AA sequence altered

N/A

Chromosome

12

Strand

-1

Original gDNA sequence snippet

CTACAGATTGAAAAAAAAAAACAAAAAACATTGCTATTTAT

Altered gDNA sequence snippet

CTACAGATTGAAAAAAAAAACAAAAAACATTGCTATTTAT

Original cDNA sequence snippet

CTACAGATTGAAAAAAAAAAACAAAAAACATTGCTATTTAT

Altered cDNA sequence snippet

CTACAGATTGAAAAAAAAAACAAAAAACATTGCTATTTAT

Wildtype AA sequence

MPLEMEPKMS KLAFGCQRSS TSDDDSGCAL EEYAWVPPGL RPEQIQLYFA CLPEEKVPYV
NSPGEKHRIK QLLYQLPPHD NEVRYCQSLS EEEKKELQVF SAQRKKEALG RGTIKLLSRA
VMHAVCEQCG LKINGGEVAV FASRAGPGVC WHPSCFVCFT CNELLVDLIY FYQDGKIHCG
RHHAELLKPR CSACDEIIFA DECTEAEGRH WHMKHFCCLE CETVLGGQRY IMKDGRPFCC
GCFESLYAEY CETCGEHIGV DHAQMTYDGQ HWHATEACFS CAQCKASLLG CPFLPKQGQI
YCSKTCSLGE DVHASDSSDS AFQSARSRDS RRSVRMGKSS RSADQCRQSL LLSPALNYKF
PGLSGNADDT LSRKLDDLSL SRQGTSFASE EFWKGRVEQE TPEDPEEWAD HEDYMTQLLL
KFGDKSLFQP QPNEMDIRAS EHWISDNMVK SKTELKQNNQ SLASKKYQSD MYWAQSQDGL
GDSAYGSHPG PASSRRLQEL ELDHGASGYN HDETQWYEDS LECLSDLKPE QSVRDSMDSL
ALSNITGASV DGENKPRPSL YSLQNFEEME TEDCEKMSNM GTLNSSMLHR SAESLKSLSS
ELCPEKILPE EKPVHLPVLR RSKSQSRPQQ VKFSDDVIDN GNYDIEIRQP PMSERTRRRV
YNFEERGSRS HHHRRRRSRK SRSDNALNLV TERKYSPKDR LRLYTPDNYE KFIQNKSARE
IQAYIQNADL YGQYAHATSD YGLQNPGMNR FLGLYGEDDD SWCSSSSSSS DSEEEGYFLG
QPIPQPRPQR FAYYTDDLSS PPSALPTPQF GQRTTKSKKK KGHKGKNCII S*

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

131 / 131

Last intron/exon boundary

1769

Theoretical NMD boundary in CDS

1588

Length of CDS

2496

Coding sequence (CDS) position

N/A

cDNA position

3177 / 3179

gDNA position

131098 / 131100

Chromosomal position

42459256 / 42459258

Speed

0.04 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:

12:42459256GT>G_7_ENST00000639589

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Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD
Poly(A) signal changed

Model: 3utr
Tree vote: 4|96 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr12:42459257delT (GRCh38)

Gene symbol

PRICKLE1

Gene constraints

LOEUF: 0.28, LOF (oe): 0.17, misssense (oe): 0.76, synonymous (oe): 0.89 ? (gnomAD)

Ensembl transcript ID

ENST00000639589.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Deletion

Gene region

3'UTR

DNA changes

cDNA.3267delA
g.131099delA

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	rs68074167
gnomAD	homozygous (-/-)	heterozygous	allele carriers
	>32000	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.328	0.314
	1.081	0.143
(flanking)	-0.442	0.051

?

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

unique in [sequence type]: position, polyA signal, score
unique in >mutated: 135578, AATAAA, 0.224256 unique in >mutated: 135579, AATAAA, 0.224256

AA sequence altered

N/A

Chromosome

12

Strand

-1

Original gDNA sequence snippet

CTACAGATTGAAAAAAAAAAACAAAAAACATTGCTATTTAT

Altered gDNA sequence snippet

CTACAGATTGAAAAAAAAAACAAAAAACATTGCTATTTAT

Original cDNA sequence snippet

CTACAGATTGAAAAAAAAAAACAAAAAACATTGCTATTTAT

Altered cDNA sequence snippet

CTACAGATTGAAAAAAAAAACAAAAAACATTGCTATTTAT

Wildtype AA sequence

MPLEMEPKMS KLAFGCQRSS TSDDDSGCAL EEYAWVPPGL RPEQIQLYFA CLPEEKVPYV
NSPGEKHRIK QLLYQLPPHD NEVRYCQSLS EEEKKELQVF SAQRKKEALG RGTIKLLSRA
VMHAVCEQCG LKINGGEVAV FASRAGPGVC WHPSCFVCFT CNELLVDLIY FYQDGKIHCG
RHHAELLKPR CSACDEIIFA DECTEAEGRH WHMKHFCCLE CETVLGGQRY IMKDGRPFCC
GCFESLYAEY CETCGEHIGV DHAQMTYDGQ HWHATEACFS CAQCKASLLG CPFLPKQGQI
YCSKTCSLGE DVHASDSSDS AFQSARSRDS RRSVRMGKSS RSADQCRQSL LLSPALNYKF
PGLSGNADDT LSRKLDDLSL SRQGTSFASE EFWKGRVEQE TPEDPEEWAD HEDYMTQLLL
KFGDKSLFQP QPNEMDIRAS EHWISDNMVK SKTELKQNNQ SLASKKYQSD MYWAQSQDGL
GDSAYGSHPG PASSRRLQEL ELDHGASGYN HDETQWYEDS LECLSDLKPE QSVRDSMDSL
ALSNITGASV DGENKPRPSL YSLQNFEEME TEDCEKMSNM GTLNSSMLHR SAESLKSLSS
ELCPEKILPE EKPVHLPVLR RSKSQSRPQQ VKFSDDVIDN GNYDIEIRQP PMSERTRRRV
YNFEERGSRS HHHRRRRSRK SRSDNALNLV TERKYSPKDR LRLYTPDNYE KFIQNKSARE
IQAYIQNADL YGQYAHATSD YGLQNPGMNR FLGLYGEDDD SWCSSSSSSS DSEEEGYFLG
QPIPQPRPQR FAYYTDDLSS PPSALPTPQF GQRTTKSKKK KGHKGKNCII S*

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

220 / 220

Last intron/exon boundary

1858

Theoretical NMD boundary in CDS

1588

Length of CDS

2496

Coding sequence (CDS) position

N/A

cDNA position

3266 / 3268

gDNA position

131098 / 131100

Chromosomal position

42459256 / 42459258

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

MutationT@ster 2025

Variant:

12:42459256GT>G_8_ENST00000345127

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD
Poly(A) signal changed

Model: 3utr
Tree vote: 4|96 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr12:42459257delT (GRCh38)

Gene symbol

PRICKLE1

Gene constraints

LOEUF: 0.28, LOF (oe): 0.17, misssense (oe): 0.76, synonymous (oe): 0.89 ? (gnomAD)

Ensembl transcript ID

ENST00000345127.9

Genbank transcript ID

NM_153026 (exact from MANE)

UniProt / AlphaMissense peptide

N/A

Variant type

Deletion

Gene region

3'UTR

DNA changes

cDNA.3378delA
g.131099delA

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	rs68074167
gnomAD	homozygous (-/-)	heterozygous	allele carriers
	>32000	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.328	0.314
	1.081	0.143
(flanking)	-0.442	0.051

?

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

unique in [sequence type]: position, polyA signal, score
unique in >mutated: 135578, AATAAA, 0.224256 unique in >mutated: 135579, AATAAA, 0.224256

AA sequence altered

N/A

Chromosome

12

Strand

-1

Original gDNA sequence snippet

CTACAGATTGAAAAAAAAAAACAAAAAACATTGCTATTTAT

Altered gDNA sequence snippet

CTACAGATTGAAAAAAAAAACAAAAAACATTGCTATTTAT

Original cDNA sequence snippet

CTACAGATTGAAAAAAAAAAACAAAAAACATTGCTATTTAT

Altered cDNA sequence snippet

CTACAGATTGAAAAAAAAAACAAAAAACATTGCTATTTAT

Wildtype AA sequence

MPLEMEPKMS KLAFGCQRSS TSDDDSGCAL EEYAWVPPGL RPEQIQLYFA CLPEEKVPYV
NSPGEKHRIK QLLYQLPPHD NEVRYCQSLS EEEKKELQVF SAQRKKEALG RGTIKLLSRA
VMHAVCEQCG LKINGGEVAV FASRAGPGVC WHPSCFVCFT CNELLVDLIY FYQDGKIHCG
RHHAELLKPR CSACDEIIFA DECTEAEGRH WHMKHFCCLE CETVLGGQRY IMKDGRPFCC
GCFESLYAEY CETCGEHIGV DHAQMTYDGQ HWHATEACFS CAQCKASLLG CPFLPKQGQI
YCSKTCSLGE DVHASDSSDS AFQSARSRDS RRSVRMGKSS RSADQCRQSL LLSPALNYKF
PGLSGNADDT LSRKLDDLSL SRQGTSFASE EFWKGRVEQE TPEDPEEWAD HEDYMTQLLL
KFGDKSLFQP QPNEMDIRAS EHWISDNMVK SKTELKQNNQ SLASKKYQSD MYWAQSQDGL
GDSAYGSHPG PASSRRLQEL ELDHGASGYN HDETQWYEDS LECLSDLKPE QSVRDSMDSL
ALSNITGASV DGENKPRPSL YSLQNFEEME TEDCEKMSNM GTLNSSMLHR SAESLKSLSS
ELCPEKILPE EKPVHLPVLR RSKSQSRPQQ VKFSDDVIDN GNYDIEIRQP PMSERTRRRV
YNFEERGSRS HHHRRRRSRK SRSDNALNLV TERKYSPKDR LRLYTPDNYE KFIQNKSARE
IQAYIQNADL YGQYAHATSD YGLQNPGMNR FLGLYGEDDD SWCSSSSSSS DSEEEGYFLG
QPIPQPRPQR FAYYTDDLSS PPSALPTPQF GQRTTKSKKK KGHKGKNCII S*

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

331 / 331

Last intron/exon boundary

1969

Theoretical NMD boundary in CDS

1588

Length of CDS

2496

Coding sequence (CDS) position

N/A

cDNA position

3377 / 3379

gDNA position

131098 / 131100

Chromosomal position

42459256 / 42459258

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

Back to summary table