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: ENST00000268613
Querying Taster for transcript #2: ENST00000567109
Querying Taster for transcript #3: ENST00000565636
Querying Taster for transcript #4: ENST00000431540
Querying Taster for transcript #5: ENST00000428848
MT speed 0.18 s - this script 2.606317 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
ENST00000268613	CDH13	Benign	0\|200	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000567109(MANE Select)	CDH13	Benign	0\|200	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000428848	CDH13	Benign	0\|200	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000565636	CDH13	Benign	1\|199	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000431540	CDH13	Benign	1\|199	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD

MutationT@ster 2025

Variant:

16:83034409G>C_1_ENST00000268613

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Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 0|200 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr16:83034409G>C (GRCh38)

Gene symbol

CDH13

Gene constraints

LOEUF: 0.54, LOF (oe): 0.38, misssense (oe): 1.11, synonymous (oe): 1.33 ? (gnomAD)

Ensembl transcript ID

ENST00000268613.14

Genbank transcript ID

NM_001220488 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.507+2191G>C
g.407445G>C

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	rs4366698
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	>32000	27102	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.852	0.205
	-0.021	0.006
(flanking)	0.342	0.005

?

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

16

Strand

1

Original gDNA sequence snippet

ACGTCAGTCATGTTTCAGAGGAAACTGGATATTGGTGAATT

Altered gDNA sequence snippet

ACGTCAGTCATGTTTCAGAGCAAACTGGATATTGGTGAATT

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MKTPPGASSR TKCSRELRSF CAFSCPRAKQ PTCTAWFPQQ EHPSENGPQM PGRDPPAAST
MQVLLLTSAE DLDCTPGFQQ KVFHINQPAE FIEDQSILNL TFSDCKGNDK LRYEVSSPYF
KVNSDGGLVA LRNITAVGKT LFVHARTPHA EDMAELVIVG GKDIQGSLQD IFKFARTSPV
PRQKRSIVVS PILIPENQRQ PFPRDVGKVV DSDRPERSKF RLTGKGVDQE PKGIFRINEN
TGSVSVTRTL DREVIAVYQL FVETTDVNGK TLEGPVPLEV IVIDQNDNRP IFREGPYIGH
VMEGSPTGTT VMRMTAFDAD DPATDNALLR YNIRQQTPDK PSPNMFYIDP EKGDIVTVVS
PALLDRETLE NPKYELIIEA QDMAGLDVGL TGTATATIMI DDKNDHSPKF TKKEFQATVE
EGAVGVIVNL TVEDKDDPTT GAWRAAYTII NGNPGQSFEI HTNPQTNEGM LSVVKPLDYE
ISAFHTLLIK VENEDPLVPD VSYGPSSTAT VHITVLDVNE GPVFYPDPMM VTRQEDLSVG
SVLLTVNATD PDSLQHQTIR YSVYKDPAGW LNINPINGTV DTTAVLDRES PFVDNSVYTA
LFLAIDSGNP PATGTGTLLI TLEDVNDNAP FIYPTVAEVC DDAKNLSVVI LGASDKDLHP
NTDPFKFEIH KQAVPDKVWK ISKINNTHAL VSLLQNLNKA NYNLPIMVTD SGKPPMTNIT
DLRVQVCSCR NSKVDCNAAG ALRFSLPSVL LLSLFSLACL *

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

94 / 94

Last intron/exon boundary

2368

Theoretical NMD boundary in CDS

2224

Length of CDS

2283

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

407445

Chromosomal position

83034409

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:

16:83034409G>C_2_ENST00000567109

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 0|200 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr16:83034409G>C (GRCh38)

Gene symbol

CDH13

Gene constraints

LOEUF: 0.46, LOF (oe): 0.30, misssense (oe): 1.09, synonymous (oe): 1.32 ? (gnomAD)

Ensembl transcript ID

ENST00000567109.6

Genbank transcript ID

NM_001257 (exact from MANE)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.366+2191G>C
g.407445G>C

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	rs4366698
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	>32000	27102	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.852	0.205
	-0.021	0.006
(flanking)	0.342	0.005

?

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

16

Strand

1

Original gDNA sequence snippet

ACGTCAGTCATGTTTCAGAGGAAACTGGATATTGGTGAATT

Altered gDNA sequence snippet

ACGTCAGTCATGTTTCAGAGCAAACTGGATATTGGTGAATT

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MQPRTPLVLC VLLSQVLLLT SAEDLDCTPG FQQKVFHINQ PAEFIEDQSI LNLTFSDCKG
NDKLRYEVSS PYFKVNSDGG LVALRNITAV GKTLFVHART PHAEDMAELV IVGGKDIQGS
LQDIFKFART SPVPRQKRSI VVSPILIPEN QRQPFPRDVG KVVDSDRPER SKFRLTGKGV
DQEPKGIFRI NENTGSVSVT RTLDREVIAV YQLFVETTDV NGKTLEGPVP LEVIVIDQND
NRPIFREGPY IGHVMEGSPT GTTVMRMTAF DADDPATDNA LLRYNIRQQT PDKPSPNMFY
IDPEKGDIVT VVSPALLDRE TLENPKYELI IEAQDMAGLD VGLTGTATAT IMIDDKNDHS
PKFTKKEFQA TVEEGAVGVI VNLTVEDKDD PTTGAWRAAY TIINGNPGQS FEIHTNPQTN
EGMLSVVKPL DYEISAFHTL LIKVENEDPL VPDVSYGPSS TATVHITVLD VNEGPVFYPD
PMMVTRQEDL SVGSVLLTVN ATDPDSLQHQ TIRYSVYKDP AGWLNINPIN GTVDTTAVLD
RESPFVDNSV YTALFLAIDS GNPPATGTGT LLITLEDVND NAPFIYPTVA EVCDDAKNLS
VVILGASDKD LHPNTDPFKF EIHKQAVPDK VWKISKINNT HALVSLLQNL NKANYNLPIM
VTDSGKPPMT NITDLRVQVC SCRNSKVDCN AAGALRFSLP SVLLLSLFSL ACL*

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

125 / 125

Last intron/exon boundary

2258

Theoretical NMD boundary in CDS

2083

Length of CDS

2142

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

407445

Chromosomal position

83034409

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

MutationT@ster 2025

Variant:

16:83034409G>C_5_ENST00000428848

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 0|200 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr16:83034409G>C (GRCh38)

Gene symbol

CDH13

Gene constraints

LOEUF: 0.46, LOF (oe): 0.30, misssense (oe): 1.09, synonymous (oe): 1.32 ? (gnomAD)

Ensembl transcript ID

ENST00000428848.7

Genbank transcript ID

NM_001220489 (by similarity), NM_001220490 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.366+2191G>C
g.407445G>C

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	rs4366698
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	>32000	27102	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.852	0.205
	-0.021	0.006
(flanking)	0.342	0.005

?

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

16

Strand

1

Original gDNA sequence snippet

ACGTCAGTCATGTTTCAGAGGAAACTGGATATTGGTGAATT

Altered gDNA sequence snippet

ACGTCAGTCATGTTTCAGAGCAAACTGGATATTGGTGAATT

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MQPRTPLVLC VLLSQVLLLT SAEDLDCTPG FQQKVFHINQ PAEFIEDQSI LNLTFSDCKG
NDKLRYEVSS PYFKVNSDGG LVALRNITAV GKTLFVHART PHAEDMAELV IVGGKDIQGS
LQVVDSDRPE RSKFRLTGKG VDQEPKGIFR INENTGSVSV TRTLDREVIA VYQLFVETTD
VNGKTLEGPV PLEVIVIDQN DNRPIFREGP YIGHVMEGSP TGTTVMRMTA FDADDPATDN
ALLRYNIRQQ TPDKPSPNMF YIDPEKGDIV TVVSPALLDR ETLENPKYEL IIEAQDMAGL
DVGLTGTATA TIMIDDKNDH SPKFTKKEFQ ATVEEGAVGV IVNLTVEDKD DPTTGAWRAA
YTIINGNPGQ SFEIHTNPQT NEGMLSVVKP LDYEISAFHT LLIKVENEDP LVPDVSYGPS
STATVHITVL DVNEGPVFYP DPMMVTRQED LSVGSVLLTV NATDPDSLQH QTIRYSVYKD
PAGWLNINPI NGTVDTTAVL DRESPFVDNS VYTALFLAID SGNPPATGTG TLLITLEDVN
DNAPFIYPTV AEVCDDAKNL SVVILGASDK DLHPNTDPFK FEIHKQAVPD KVWKISKINN
THALVSLLQN LNKANYNLPI MVTDSGKPPM TNITDLRVQV CSCRNSKVDC NAAGALRFSL
PSVLLLSLFS LACL*

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

124 / 124

Last intron/exon boundary

2140

Theoretical NMD boundary in CDS

1966

Length of CDS

2025

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

407445

Chromosomal position

83034409

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

Back to summary table

MutationT@ster 2025

Variant:

16:83034409G>C_3_ENST00000565636

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 1|199 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr16:83034409G>C (GRCh38)

Gene symbol

CDH13

Gene constraints

LOEUF: 1.30, LOF (oe): 0.72, misssense (oe): 1.57, synonymous (oe): 1.59 ? (gnomAD)

Ensembl transcript ID

ENST00000565636.5

Genbank transcript ID

NM_001220492 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.366+2191G>C
g.407445G>C

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	rs4366698
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	>32000	27102	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.852	0.205
	-0.021	0.006
(flanking)	0.342	0.005

?

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

16

Strand

1

Original gDNA sequence snippet

ACGTCAGTCATGTTTCAGAGGAAACTGGATATTGGTGAATT

Altered gDNA sequence snippet

ACGTCAGTCATGTTTCAGAGCAAACTGGATATTGGTGAATT

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MQPRTPLVLC VLLSQVLLLT SAEDLDCTPG FQQKVFHINQ PAEFIEDQSI LNLTFSDCKG
NDKLRYEVSS PYFKVNSDGG LVALRNITAV GKTLFVHART PHAEDMAELV IVGGKDIQGS
LQDIFKFART SPVPRQKRSI VVSPILIPEN QRQPFPRDVG KMKIWQVLCL ARWLT*

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

124 / 124

Last intron/exon boundary

656

Theoretical NMD boundary in CDS

482

Length of CDS

528

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

407445

Chromosomal position

83034409

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:

16:83034409G>C_4_ENST00000431540

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 1|199 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr16:83034409G>C (GRCh38)

Gene symbol

CDH13

Gene constraints

LOEUF: 0.94, LOF (oe): 0.30, misssense (oe): 1.56, synonymous (oe): 1.60 ? (gnomAD)

Ensembl transcript ID

ENST00000431540.7

Genbank transcript ID

NM_001220491 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.366+2191G>C
g.407445G>C

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	rs4366698
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	>32000	27102	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.852	0.205
	-0.021	0.006
(flanking)	0.342	0.005

?

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

16

Strand

1

Original gDNA sequence snippet

ACGTCAGTCATGTTTCAGAGGAAACTGGATATTGGTGAATT

Altered gDNA sequence snippet

ACGTCAGTCATGTTTCAGAGCAAACTGGATATTGGTGAATT

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MQPRTPLVLC VLLSQVLLLT SAEDLDCTPG FQQKVFHINQ PAEFIEDQSI LNLTFSDCKG
NDKLRYEVSS PYFKVNSDGG LVALRNITAV GKTLFVHART PHAEDMAELV IVGGKDIQGS
LQDIFKFART SPVPRQKRSI VVSPILIPEN QRQPFPRDVG KRTHNPINSE LLLNEGITAD
LNPCITILAI *

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

124 / 124

Last intron/exon boundary

606

Theoretical NMD boundary in CDS

432

Length of CDS

573

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

407445

Chromosomal position

83034409

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