MutationT @ ster 2025

Prediction:

DeleteriousPermalink

Summary:

Known as potential disease variant: ClinVar ID 90311 (likely pathogenic)
Splice site lost

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

Analysed issue

Analysis result

Variant

Chr3:37012100G>A (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.67, LOF (oe): 0.50, misssense (oe): 0.86, synonymous (oe): 0.95 ? (gnomAD)

Ensembl transcript ID

ENST00000673673.2

Genbank transcript ID

NM_001354630 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.677+1G>A
g.18875G>A

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Hereditary nonpolyposis colorectal neoplasms
Lynch syndrome
Hereditary cancer-predisposing syndrome
Colorectal cancer, hereditary nonpolyposis, type 2

likely pathogenic

Variant DBs

dbSNP ID	rs267607778
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	1	1

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	7.59	1
	7.324	1
(flanking)	5.642	1

?

Splice sites

alteration within used splice site, likely to disturb normal splicing

MaxEntScan:

effect	gDNA position	score	sequence	exon-intron border
Donor lost	18874	wt: 0.00 / mu: 0.00	-	wt: CTGTTAGTCG\|gtatgtcgat mu: CTGTTAGTCG\|atatgtcgat

Distance from splice site

1

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

3

Strand

1

Original gDNA sequence snippet

TTTGGAAATGCTGTTAGTCGGTATGTCGATAACCTATATAA

Altered gDNA sequence snippet

TTTGGAAATGCTGTTAGTCGATATGTCGATAACCTATATAA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MSFVAGVIRR LDETVVNRIA AGEVIQRPAN AIKEMIENCL DAKSTSIQVI VKEGGLKLIQ
IQDNGTGIRK EDLDIVCERF TTSKLQSFED LASISTYGFR GEALASISHV AHVTITTKTA
DGKCAYRASY SDGKLKAPPK PCAGNQGTQI TVEDLFYNIA TRRKALKNPS EEYGKILEVV
GRYSVHNAGI SFSVKKQGET VADVRTLPNA STVDNIRSIF GNAVSRELIE IGCEDKTLAF
KMNGYISNAN YSVKKCIFLL FINHRLVEST SLRKAIETVY AAYLPKNTHP FLYLSLEISP
QNVDVNVHPT KHEVHFLHEE SILERVQQHI ESKLLGSNSS RMYFTQTLLP GLAGPSGEMV
KSTTSLTSSS TSGSSDKVYA HQMVRTDSRE QKLDAFLQPL SKPLSSQPQA IVTEDKTDIS
SGRARQQDEE MLELPAPAEV AAKNQSLEGD TTKGTSEMSE KRGPTSSNPR KRHREDSDVE
MVEDDSRKEM TAACTPRRRI INLTSVLSLQ EEINEQGHEV LREMLHNHSF VGCVNPQWAL
AQHQTKLYLL NTTKLSEELF YQILIYDFAN FGVLRLSEGN LIGLPLLIDN YVPPLEGLPI
FILRLATEVN WDEEKECFES LSKECAMFYS IRKQYISEES TLSGQQSEVP GSIPNSWKWT
VEHIVYKALR SHILPPKHFT EDGNILQLAN LPDLYKVFER C*

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

323 / 323

Last intron/exon boundary

2260

Theoretical NMD boundary in CDS

1887

Length of CDS

2106

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

18875

Chromosomal position

37012100

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

MutationT@ster 2025

Variant:

3:37012100G>A_3_ENST00000616768

Prediction:

DeleteriousPermalink

Summary:

Known as potential disease variant: ClinVar ID 90311 (likely pathogenic)
Splice site lost

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

Analysed issue

Analysis result

Variant

Chr3:37012100G>A (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.60, LOF (oe): 0.39, misssense (oe): 0.87, synonymous (oe): 0.96 ? (gnomAD)

Ensembl transcript ID

ENST00000616768.6

Genbank transcript ID

NM_001354628 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.677+1G>A
g.18875G>A

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Hereditary nonpolyposis colorectal neoplasms
Lynch syndrome
Hereditary cancer-predisposing syndrome
Colorectal cancer, hereditary nonpolyposis, type 2

likely pathogenic

Variant DBs

dbSNP ID	rs267607778
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	1	1

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	7.59	1
	7.324	1
(flanking)	5.642	1

?

Splice sites

alteration within used splice site, likely to disturb normal splicing

MaxEntScan:

effect	gDNA position	score	sequence	exon-intron border
Donor lost	18874	wt: 0.00 / mu: 0.00	-	wt: CTGTTAGTCG\|gtatgtcgat mu: CTGTTAGTCG\|atatgtcgat

Distance from splice site

1

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

3

Strand

1

Original gDNA sequence snippet

TTTGGAAATGCTGTTAGTCGGTATGTCGATAACCTATATAA

Altered gDNA sequence snippet

TTTGGAAATGCTGTTAGTCGATATGTCGATAACCTATATAA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MSFVAGVIRR LDETVVNRIA AGEVIQRPAN AIKEMIENCL DAKSTSIQVI VKEGGLKLIQ
IQDNGTGIRK EDLDIVCERF TTSKLQSFED LASISTYGFR GEALASISHV AHVTITTKTA
DGKCAYRASY SDGKLKAPPK PCAGNQGTQI TVEDLFYNIA TRRKALKNPS EEYGKILEVV
GRYSVHNAGI SFSVKKQGET VADVRTLPNA STVDNIRSIF GNAVSRELIE IGCEDKTLAF
KMNGYISNAN YSVKKCIFLL FINHRLVEST SLRKAIETVY AAYLPKNTHP FLYLSLEISP
QNVDVNVHPT KHEVHFLHEE SILERVQQHI ESKLLGSNSS RMYFTQTLLP GLAGPSGEMV
KSTTSLTSSS TSGSSDKVYA HQMVRTDSRE QKLDAFLQPL SKPLSSQPQA IVTEDKTDIS
SGRARQQDEE MLELPAPAEV AAKNQSLEGD TTKGTSEMSE KRGPTSSNPR KRHREDSDVE
MVEDDSRKEM TAACTPRRRI INLTSVLSLQ EEINEQGHEV LREMLHNHSF VGCVNPQWAL
AQHQTKLYLL NTTKLSEELF YQILIYDFAN FGVLRLSEPA PLFDLAMLAL DSPESGWTEE
DGPKEGLAEY IVEFLKKKAE MLADYFSLEI DEVNWDEEKE CFESLSKECA MFYSIRKQYI
SEESTLSGQQ SEVPGSIPNS WKWTVEHIVY KALRSHILPP KHFTEDGNIL QLANLPDLYK
VFERC*

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

77 / 77

Last intron/exon boundary

2086

Theoretical NMD boundary in CDS

1959

Length of CDS

2178

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

18875

Chromosomal position

37012100

Speed

0.01 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

MutationT@ster 2025

Variant:

3:37012100G>A_4_ENST00000673899

Prediction:

DeleteriousPermalink

Summary:

Known as potential disease variant: ClinVar ID 90311 (likely pathogenic)
Splice site lost

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

Analysed issue

Analysis result

Variant

Chr3:37012100G>A (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.72, LOF (oe): 0.53, misssense (oe): 0.89, synonymous (oe): 0.96 ? (gnomAD)

Ensembl transcript ID

ENST00000673899.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.677+1G>A
g.18875G>A

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Hereditary nonpolyposis colorectal neoplasms
Lynch syndrome
Hereditary cancer-predisposing syndrome
Colorectal cancer, hereditary nonpolyposis, type 2

likely pathogenic

Variant DBs

dbSNP ID	rs267607778
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	1	1

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	7.59	1
	7.324	1
(flanking)	5.642	1

?

Splice sites

alteration within used splice site, likely to disturb normal splicing

MaxEntScan:

effect	gDNA position	score	sequence	exon-intron border
Donor lost	18874	wt: 0.00 / mu: 0.00	-	wt: CTGTTAGTCG\|gtatgtcgat mu: CTGTTAGTCG\|atatgtcgat

Distance from splice site

1

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

3

Strand

1

Original gDNA sequence snippet

TTTGGAAATGCTGTTAGTCGGTATGTCGATAACCTATATAA

Altered gDNA sequence snippet

TTTGGAAATGCTGTTAGTCGATATGTCGATAACCTATATAA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MSFVAGVIRR LDETVVNRIA AGEVIQRPAN AIKEMIENCL DAKSTSIQVI VKEGGLKLIQ
IQDNGTGIRK EDLDIVCERF TTSKLQSFED LASISTYGFR GEALASISHV AHVTITTKTA
DGKCAYRASY SDGKLKAPPK PCAGNQGTQI TVEDLFYNIA TRRKALKNPS EEYGKILEVV
GRYSVHNAGI SFSVKKQGET VADVRTLPNA STVDNIRSIF GNAVSRKRHR EDSDVEMVED
DSRKEMTAAC TPRRRIINLT SVLSLQEEIN EQGHEVLREM LHNHSFVGCV NPQWALAQHQ
TKLYLLNTTK LSEELFYQIL IYDFANFGVL RLSEPAPLFD LAMLALDSPE SGWTEEDGPK
EGLAEYIVEF LKKKAEMLAD YFSLEIDEEG NLIGLPLLID NYVPPLEGLP IFILRLATEV
NWDEEKECFE SLSKECAMFY SIRKQYISEE STLSGQQSEV PGSIPNSWKW TVEHIVYKAL
RSHILPPKHF TEDGNILQLA NLPDLYKVFE RC*

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

60 / 60

Last intron/exon boundary

1430

Theoretical NMD boundary in CDS

1320

Length of CDS

1539

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

18875

Chromosomal position

37012100

Speed

0.01 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

MutationT@ster 2025

Variant:

3:37012100G>A_5_ENST00000673990

Prediction:

DeleteriousPermalink

Summary:

Known as potential disease variant: ClinVar ID 90311 (likely pathogenic)
Splice site lost

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

Analysed issue

Analysis result

Variant

Chr3:37012100G>A (GRCh38)

Gene symbol

Gene constraints

no data

Ensembl transcript ID

ENST00000673990.2

Genbank transcript ID

NM_001354622 (by similarity), NM_001354627 (by similarity), NM_001354621 (by similarity), NM_001354623 (by similarity), NM_001354624 (by similarity), NM_001354626 (by similarity), NM_001354625 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.-253+1G>A
g.18875G>A

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Hereditary nonpolyposis colorectal neoplasms
Lynch syndrome
Hereditary cancer-predisposing syndrome
Colorectal cancer, hereditary nonpolyposis, type 2

likely pathogenic

Variant DBs

dbSNP ID	rs267607778
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	1	1

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	7.59	1
	7.324	1
(flanking)	5.642	1

?

Splice sites

alteration within used splice site, likely to disturb normal splicing

MaxEntScan:

effect	gDNA position	score	sequence	exon-intron border
Donor lost	18874	wt: 0.00 / mu: 0.00	-	wt: CTGTTAGTCG\|gtatgtcgat mu: CTGTTAGTCG\|atatgtcgat

Distance from splice site

1

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

3

Strand

1

Original gDNA sequence snippet

TTTGGAAATGCTGTTAGTCGGTATGTCGATAACCTATATAA

Altered gDNA sequence snippet

TTTGGAAATGCTGTTAGTCGATATGTCGATAACCTATATAA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MYFTQTLLPG LAGPSGEMVK STTSLTSSST SGSSDKVYAH QMVRTDSREQ KLDAFLQPLS
KPLSSQPQAI VTEDKTDISS GRARQQDEEM LELPAPAEVA AKNQSLEGDT TKGTSEMSEK
RGPTSSNPRK RHREDSDVEM VEDDSRKEMT AACTPRRRII NLTSVLSLQE EINEQGHEVL
REMLHNHSFV GCVNPQWALA QHQTKLYLLN TTKLSEELFY QILIYDFANF GVLRLSEPAP
LFDLAMLALD SPESGWTEED GPKEGLAEYI VEFLKKKAEM LADYFSLEID EEGNLIGLPL
LIDNYVPPLE GLPIFILRLA TEVNWDEEKE CFESLSKECA MFYSIRKQYI SEESTLSGQQ
SEVPGSIPNS WKWTVEHIVY KALRSHILPP KHFTEDGNIL QLANLPDLYK VFERC*

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

915 / 915

Last intron/exon boundary

1994

Theoretical NMD boundary in CDS

1029

Length of CDS

1248

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

18875

Chromosomal position

37012100

Speed

0.01 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

MutationT@ster 2025

Variant:

3:37012100G>A_6_ENST00000492474

Prediction:

DeleteriousPermalink

Summary:

Known as potential disease variant: ClinVar ID 90311 (likely pathogenic)
Splice site lost

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

Analysed issue

Analysis result

Variant

Chr3:37012100G>A (GRCh38)

Gene symbol

Gene constraints

no data

Ensembl transcript ID

ENST00000492474.6

Genbank transcript ID

UniProt / AlphaMissense peptide

MLH1_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

intron

DNA changes

c.-47+1G>A
g.18875G>A

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Hereditary nonpolyposis colorectal neoplasms
Lynch syndrome
Hereditary cancer-predisposing syndrome
Colorectal cancer, hereditary nonpolyposis, type 2

likely pathogenic

Variant DBs

dbSNP ID	rs267607778
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	1	1

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	7.59	1
	7.324	1
(flanking)	5.642	1

?

Splice sites

alteration within used splice site, likely to disturb normal splicing

MaxEntScan:

effect	gDNA position	score	sequence	exon-intron border
Donor lost	18874	wt: 0.00 / mu: 0.00	-	wt: CTGTTAGTCG\|gtatgtcgat mu: CTGTTAGTCG\|atatgtcgat

Distance from splice site

1

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

3

Strand

1

Original gDNA sequence snippet

TTTGGAAATGCTGTTAGTCGGTATGTCGATAACCTATATAA

Altered gDNA sequence snippet

TTTGGAAATGCTGTTAGTCGATATGTCGATAACCTATATAA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MNGYISNANY SVKKCIFLLF INHRLVESTS LRKAIETVYA AYLPKNTHPF LYLSLEISPQ
NVDVNVHPTK HEVHFLHEES ILERVQQHIE SKLLGSNSSR MYFTQTLLPG LAGPSGEMVK
STTSLTSSST SGSSDKVYAH QMVRTDSREQ KLDAFLQPLS KPLSSQPQAI VTEDKTDISS
GRARQQDEEM LELPAPAEVA AKNQSLEGDT TKGTSEMSEK RGPTSSNPRK RHREDSDVEM
VEDDSRKEMT AACTPRRRII NLTSVLSLQE EINEQGHEVL REMLHNHSFV GCVNPQWALA
QHQTKLYLLN TTKLSEELFY QILIYDFANF GVLRLSEPAP LFDLAMLALD SPESGWTEED
GPKEGLAEYI VEFLKKKAEM LADYFSLEID EEGNLIGLPL LIDNYVPPLE GLPIFILRLA
TEVNWDEEKE CFESLSKECA MFYSIRKQYI SEESTLSGQQ SEVPGSIPNS WKWTVEHIVY
KALRSHILPP KHFTEDGNIL QLANLPDLYK VFERC*

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

782 / 782

Last intron/exon boundary

2161

Theoretical NMD boundary in CDS

1329

Length of CDS

1548

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

18875

Chromosomal position

37012100

Speed

0.01 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

MutationT@ster 2025

Variant:

3:37012100G>A_7_ENST00000455445

Prediction:

DeleteriousPermalink

Summary:

Known as potential disease variant: ClinVar ID 90311 (likely pathogenic)
Splice site lost

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

Analysed issue

Analysis result

Variant

Chr3:37012100G>A (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.68, LOF (oe): 0.48, misssense (oe): 0.87, synonymous (oe): 0.95 ? (gnomAD)

Ensembl transcript ID

ENST00000455445.6

Genbank transcript ID

NM_001354618 (by similarity), NM_001167618 (by similarity)

UniProt / AlphaMissense peptide

MLH1_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

intron

DNA changes

c.-47+1G>A
g.18875G>A

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Hereditary nonpolyposis colorectal neoplasms
Lynch syndrome
Hereditary cancer-predisposing syndrome
Colorectal cancer, hereditary nonpolyposis, type 2

likely pathogenic

Variant DBs

dbSNP ID	rs267607778
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	1	1

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	7.59	1
	7.324	1
(flanking)	5.642	1

?

Splice sites

alteration within used splice site, likely to disturb normal splicing

MaxEntScan:

effect	gDNA position	score	sequence	exon-intron border
Donor lost	18874	wt: 0.00 / mu: 0.00	-	wt: CTGTTAGTCG\|gtatgtcgat mu: CTGTTAGTCG\|atatgtcgat

Distance from splice site

1

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

3

Strand

1

Original gDNA sequence snippet

TTTGGAAATGCTGTTAGTCGGTATGTCGATAACCTATATAA

Altered gDNA sequence snippet

TTTGGAAATGCTGTTAGTCGATATGTCGATAACCTATATAA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MNGYISNANY SVKKCIFLLF INHRLVESTS LRKAIETVYA AYLPKNTHPF LYLSLEISPQ
NVDVNVHPTK HEVHFLHEES ILERVQQHIE SKLLGSNSSR MYFTQTLLPG LAGPSGEMVK
STTSLTSSST SGSSDKVYAH QMVRTDSREQ KLDAFLQPLS KPLSSQPQAI VTEDKTDISS
GRARQQDEEM LELPAPAEVA AKNQSLEGDT TKGTSEMSEK RGPTSSNPRK RHREDSDVEM
VEDDSRKEMT AACTPRRRII NLTSVLSLQE EINEQGHEVL REMLHNHSFV GCVNPQWALA
QHQTKLYLLN TTKLSEELFY QILIYDFANF GVLRLSEPAP LFDLAMLALD SPESGWTEED
GPKEGLAEYI VEFLKKKAEM LADYFSLEID EEGNLIGLPL LIDNYVPPLE GLPIFILRLA
TEVNWDEEKE CFESLSKECA MFYSIRKQYI SEESTLSGQQ SEVPGSIPNS WKWTVEHIVY
KALRSHILPP KHFTEDGNIL QLANLPDLYK VFERC*

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

696 / 696

Last intron/exon boundary

2075

Theoretical NMD boundary in CDS

1329

Length of CDS

1548

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

18875

Chromosomal position

37012100

Speed

0.01 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

MutationT@ster 2025

Variant:

3:37012100G>A_8_ENST00000539477

Prediction:

DeleteriousPermalink

Summary:

Known as potential disease variant: ClinVar ID 90311 (likely pathogenic)
Splice site lost

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

Analysed issue

Analysis result

Variant

Chr3:37012100G>A (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.68, LOF (oe): 0.48, misssense (oe): 0.87, synonymous (oe): 0.95 ? (gnomAD)

Ensembl transcript ID

ENST00000539477.6

Genbank transcript ID

NM_001167619 (by similarity), NM_001354615 (by similarity), NM_001354616 (by similarity)

UniProt / AlphaMissense peptide

MLH1_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

intron

DNA changes

c.-47+1G>A
g.18875G>A

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Hereditary nonpolyposis colorectal neoplasms
Lynch syndrome
Hereditary cancer-predisposing syndrome
Colorectal cancer, hereditary nonpolyposis, type 2

likely pathogenic

Variant DBs

dbSNP ID	rs267607778
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	1	1

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	7.59	1
	7.324	1
(flanking)	5.642	1

?

Splice sites

alteration within used splice site, likely to disturb normal splicing

MaxEntScan:

effect	gDNA position	score	sequence	exon-intron border
Donor lost	18874	wt: 0.00 / mu: 0.00	-	wt: CTGTTAGTCG\|gtatgtcgat mu: CTGTTAGTCG\|atatgtcgat

Distance from splice site

1

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

3

Strand

1

Original gDNA sequence snippet

TTTGGAAATGCTGTTAGTCGGTATGTCGATAACCTATATAA

Altered gDNA sequence snippet

TTTGGAAATGCTGTTAGTCGATATGTCGATAACCTATATAA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MNGYISNANY SVKKCIFLLF INHRLVESTS LRKAIETVYA AYLPKNTHPF LYLSLEISPQ
NVDVNVHPTK HEVHFLHEES ILERVQQHIE SKLLGSNSSR MYFTQTLLPG LAGPSGEMVK
STTSLTSSST SGSSDKVYAH QMVRTDSREQ KLDAFLQPLS KPLSSQPQAI VTEDKTDISS
GRARQQDEEM LELPAPAEVA AKNQSLEGDT TKGTSEMSEK RGPTSSNPRK RHREDSDVEM
VEDDSRKEMT AACTPRRRII NLTSVLSLQE EINEQGHEVL REMLHNHSFV GCVNPQWALA
QHQTKLYLLN TTKLSEELFY QILIYDFANF GVLRLSEPAP LFDLAMLALD SPESGWTEED
GPKEGLAEYI VEFLKKKAEM LADYFSLEID EEGNLIGLPL LIDNYVPPLE GLPIFILRLA
TEVNWDEEKE CFESLSKECA MFYSIRKQYI SEESTLSGQQ SEVPGSIPNS WKWTVEHIVY
KALRSHILPP KHFTEDGNIL QLANLPDLYK VFERC*

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

603 / 603

Last intron/exon boundary

1982

Theoretical NMD boundary in CDS

1329

Length of CDS

1548

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

18875

Chromosomal position

37012100

Speed

0.01 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

MutationT@ster 2025

Variant:

3:37012100G>A_9_ENST00000435176

Prediction:

DeleteriousPermalink

Summary:

Known as potential disease variant: ClinVar ID 90311 (likely pathogenic)
Splice site lost

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

Analysed issue

Analysis result

Variant

Chr3:37012100G>A (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.70, LOF (oe): 0.52, misssense (oe): 0.88, synonymous (oe): 0.96 ? (gnomAD)

Ensembl transcript ID

ENST00000435176.5

Genbank transcript ID

NM_001167617 (by similarity), NM_001354620 (by similarity)

UniProt / AlphaMissense peptide

MLH1_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

intron

DNA changes

c.383+1G>A
g.18875G>A

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Hereditary nonpolyposis colorectal neoplasms
Lynch syndrome
Hereditary cancer-predisposing syndrome
Colorectal cancer, hereditary nonpolyposis, type 2

likely pathogenic

Variant DBs

dbSNP ID	rs267607778
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	1	1

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	7.59	1
	7.324	1
(flanking)	5.642	1

?

Splice sites

alteration within used splice site, likely to disturb normal splicing

MaxEntScan:

effect	gDNA position	score	sequence	exon-intron border
Donor lost	18874	wt: 0.00 / mu: 0.00	-	wt: CTGTTAGTCG\|gtatgtcgat mu: CTGTTAGTCG\|atatgtcgat

Distance from splice site

1

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

3

Strand

1

Original gDNA sequence snippet

TTTGGAAATGCTGTTAGTCGGTATGTCGATAACCTATATAA

Altered gDNA sequence snippet

TTTGGAAATGCTGTTAGTCGATATGTCGATAACCTATATAA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MAFEALASIS HVAHVTITTK TADGKCAYRA SYSDGKLKAP PKPCAGNQGT QITVEDLFYN
IATRRKALKN PSEEYGKILE VVGRYSVHNA GISFSVKKQG ETVADVRTLP NASTVDNIRS
IFGNAVSREL IEIGCEDKTL AFKMNGYISN ANYSVKKCIF LLFINHRLVE STSLRKAIET
VYAAYLPKNT HPFLYLSLEI SPQNVDVNVH PTKHEVHFLH EESILERVQQ HIESKLLGSN
SSRMYFTQTL LPGLAGPSGE MVKSTTSLTS SSTSGSSDKV YAHQMVRTDS REQKLDAFLQ
PLSKPLSSQP QAIVTEDKTD ISSGRARQQD EEMLELPAPA EVAAKNQSLE GDTTKGTSEM
SEKRGPTSSN PRKRHREDSD VEMVEDDSRK EMTAACTPRR RIINLTSVLS LQEEINEQGH
EVLREMLHNH SFVGCVNPQW ALAQHQTKLY LLNTTKLSEE LFYQILIYDF ANFGVLRLSE
PAPLFDLAML ALDSPESGWT EEDGPKEGLA EYIVEFLKKK AEMLADYFSL EIDEEGNLIG
LPLLIDNYVP PLEGLPIFIL RLATEVNWDE EKECFESLSK ECAMFYSIRK QYISEESTLS
GQQSEVPGSI PNSWKWTVEH IVYKALRSHI LPPKHFTEDG NILQLANLPD LYKVFERC*

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

261 / 261

Last intron/exon boundary

2069

Theoretical NMD boundary in CDS

1758

Length of CDS

1977

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

18875

Chromosomal position

37012100

Speed

0.01 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

MutationT@ster 2025

Variant:

3:37012100G>A_10_ENST00000441265

Prediction:

DeleteriousPermalink

Summary:

Known as potential disease variant: ClinVar ID 90311 (likely pathogenic)
Splice site lost

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

Analysed issue

Analysis result

Variant

Chr3:37012100G>A (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.65, LOF (oe): 0.40, misssense (oe): 0.87, synonymous (oe): 0.99 ? (gnomAD)

Ensembl transcript ID

ENST00000441265.6

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.-47+1G>A
g.18875G>A

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Hereditary nonpolyposis colorectal neoplasms
Lynch syndrome
Hereditary cancer-predisposing syndrome
Colorectal cancer, hereditary nonpolyposis, type 2

likely pathogenic

Variant DBs

dbSNP ID	rs267607778
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	1	1

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	7.59	1
	7.324	1
(flanking)	5.642	1

?

Splice sites

alteration within used splice site, likely to disturb normal splicing

MaxEntScan:

effect	gDNA position	score	sequence	exon-intron border
Donor lost	18874	wt: 0.00 / mu: 0.00	-	wt: CTGTTAGTCG\|gtatgtcgat mu: CTGTTAGTCG\|atatgtcgat

Distance from splice site

1

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

3

Strand

1

Original gDNA sequence snippet

TTTGGAAATGCTGTTAGTCGGTATGTCGATAACCTATATAA

Altered gDNA sequence snippet

TTTGGAAATGCTGTTAGTCGATATGTCGATAACCTATATAA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MNGYISNANY SVKKCIFLLF INHRLVESTS LRKAIETVYA AYLPKNTHPF LYLSLEISPQ
NVDVNVHPTK HEVHFLHEES ILERVQQHIE SKLLGSNSSR MYFTQTLLPG LAGPSGEMVK
STTSLTSSST SGSSDKVYAH QMVRTDSREQ KLDAFLQPLS KPLSSQPQAI VTEDKTDISS
GRARQQDEEM LELPAPAEVA AKNQSLEGDT TKGTSEMSEK RGPTSSNPRK RHREDSDVEM
VEDDSRKEMT AACTPRRRII NLTSVLSLQE EINEQGHEVL REMLHNHSFV GCVNPQWALA
QHQTKLYLLN TTKLRSQHRS LTLPCLP*

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

820 / 820

Last intron/exon boundary

1763

Theoretical NMD boundary in CDS

893

Length of CDS

984

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

18875

Chromosomal position

37012100

Speed

0.01 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

MutationT@ster 2025

Variant:

3:37012100G>A_11_ENST00000429117

Prediction:

DeleteriousPermalink

Summary:

Known as potential disease variant: ClinVar ID 90311 (likely pathogenic)
Splice site lost

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

Analysed issue

Analysis result

Variant

Chr3:37012100G>A (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.61, LOF (oe): 0.13, misssense (oe): 0.92, synonymous (oe): 1.07 ? (gnomAD)

Ensembl transcript ID

ENST00000429117.6

Genbank transcript ID

UniProt / AlphaMissense peptide

MLH1_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

intron

DNA changes

c.383+1G>A
g.18875G>A

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Hereditary nonpolyposis colorectal neoplasms
Lynch syndrome
Hereditary cancer-predisposing syndrome
Colorectal cancer, hereditary nonpolyposis, type 2

likely pathogenic

Variant DBs

dbSNP ID	rs267607778
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	1	1

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	7.59	1
	7.324	1
(flanking)	5.642	1

?

Splice sites

alteration within used splice site, likely to disturb normal splicing

MaxEntScan:

effect	gDNA position	score	sequence	exon-intron border
Donor lost	18874	wt: 0.00 / mu: 0.00	-	wt: CTGTTAGTCG\|gtatgtcgat mu: CTGTTAGTCG\|atatgtcgat

Distance from splice site

1

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

3

Strand

1

Original gDNA sequence snippet

TTTGGAAATGCTGTTAGTCGGTATGTCGATAACCTATATAA

Altered gDNA sequence snippet

TTTGGAAATGCTGTTAGTCGATATGTCGATAACCTATATAA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MAFEALASIS HVAHVTITTK TADGKCAYRA SYSDGKLKAP PKPCAGNQGT QITVEDLFYN
IATRRKALKN PSEEYGKILE VVGRYSVHNA GISFSVKKQG ETVADVRTLP NASTVDNIRS
IFGNAVSREL IEIGCEDKTL AFKMNGYISN ANYSVKKCIF LLFINHRLVE STSLRKAIET
VYAAYLPKNT HPFLYLSLEI SPQNVDVNVH PTKHEVHFLH EESILERVQQ HIESKLLGSN
SSRMYFTQTL LPGLAGPSGE MVKSTTSLTS SSTSGSSDKV YAHQMVRTDS REQKLDAFLQ
PLSKPLSSQP QAIVTEDKTD ISSGRARQQD EEMLELPAPA EVAAKNQSLE GDTTKGTSEM
SEKRGPTSSN PRKRHREDSD VEMVEDDSRK EMTAACTPRR RIINLTSVLS LQEEINEQGH
EVLREMLHNH SFVGCVNPQW ALAQHQTKLY LLNTTKLSEE LFYQILIYDF ANFGVLRLSE
PAPLFDLAML ALDSPESGWT EEDGPKEGLA EYIVEFLKKK AEMLADYFSL EIDEEGNLIG
LPLLIDNYVP PLEGLPIFIL RLATEVNWDE EKECFESLSK ECAMFYSIRK QYISEESTLS
GQQSEVPGSI PNSWKWTVEH IVYKALRSHI LPPKHFTEDG NILQLANLPD LYKVFERC*

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

313 / 313

Last intron/exon boundary

2121

Theoretical NMD boundary in CDS

1758

Length of CDS

1977

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

18875

Chromosomal position

37012100

Speed

0.01 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

MutationT@ster 2025

Variant:

3:37012100G>A_12_ENST00000485889

Prediction:

DeleteriousPermalink

Summary:

Known as potential disease variant: ClinVar ID 90311 (likely pathogenic)
Splice site lost

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

Analysed issue

Analysis result

Variant

Chr3:37012100G>A (GRCh38)

Gene symbol

Gene constraints

no data

Ensembl transcript ID

ENST00000485889.2

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.-47+1G>A
g.18875G>A

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Hereditary nonpolyposis colorectal neoplasms
Lynch syndrome
Hereditary cancer-predisposing syndrome
Colorectal cancer, hereditary nonpolyposis, type 2

likely pathogenic

Variant DBs

dbSNP ID	rs267607778
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	1	1

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	7.59	1
	7.324	1
(flanking)	5.642	1

?

Splice sites

alteration within used splice site, likely to disturb normal splicing

MaxEntScan:

effect	gDNA position	score	sequence	exon-intron border
Donor lost	18874	wt: 0.00 / mu: 0.00	-	wt: CTGTTAGTCG\|gtatgtcgat mu: CTGTTAGTCG\|atatgtcgat

Distance from splice site

1

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

3

Strand

1

Original gDNA sequence snippet

TTTGGAAATGCTGTTAGTCGGTATGTCGATAACCTATATAA

Altered gDNA sequence snippet

TTTGGAAATGCTGTTAGTCGATATGTCGATAACCTATATAA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MNGYISNANY SVKKCIFLLF INHRLVESTS LRKAIETVYA AYLPKNTHPF LYLSLEISPQ
NVDVNVHPTK HEVHFLHEES ILERVQQHIE SKLLGSNSSR MYFTQTLLPG LAGPSGEMVK
STTSLTSSST SGSSDKVYAH QMVRTDSREQ KLDAFLQPLS KPLSSQPQAI VTEDKTDISS
GRARQQDEEM LELPAPAEVA AKNQSLEGDT TKGTSEMSEK RGPTSSNPRK RHREDSDVEM
VEDDSRKEMT AACTPRRRII NLTSVLSLQE EINEQGHEVL REMLHNHSFV GCVNPQWALA
QHQTKLYLLN TTKLSEELFY QILIYDFANF GVLRLSEPAP LFDLAMLALD SPESGWTEED
GPKEGLAEYI VEFLKKKAEM LADYFSLEID EEGNLIGLPL LIDNYVPPLE GLPIFILRLA
TEVNWDEEKE CFESLSKECA MFYSIRKQYI SEESTLSGQQ SEVPGSIPNS WKWTVEHIVY
KALRSHILPP KHFTEDGNIL QLANLPDLYK VFERC*

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

779 / 779

Last intron/exon boundary

2158

Theoretical NMD boundary in CDS

1329

Length of CDS

1548

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

18875

Chromosomal position

37012100

Speed

0.01 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

MutationT@ster 2025

Variant:

3:37012100G>A_13_ENST00000466900

Prediction:

DeleteriousPermalink

Summary:

Known as potential disease variant: ClinVar ID 90311 (likely pathogenic)
Splice site lost

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

Analysed issue

Analysis result

Variant

Chr3:37012100G>A (GRCh38)

Gene symbol

Gene constraints

no data

Ensembl transcript ID

ENST00000466900.6

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.-47+1G>A
g.18875G>A

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Hereditary nonpolyposis colorectal neoplasms
Lynch syndrome
Hereditary cancer-predisposing syndrome
Colorectal cancer, hereditary nonpolyposis, type 2

likely pathogenic

Variant DBs

dbSNP ID	rs267607778
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	1	1

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	7.59	1
	7.324	1
(flanking)	5.642	1

?

Splice sites

alteration within used splice site, likely to disturb normal splicing

MaxEntScan:

effect	gDNA position	score	sequence	exon-intron border
Donor lost	18874	wt: 0.00 / mu: 0.00	-	wt: CTGTTAGTCG\|gtatgtcgat mu: CTGTTAGTCG\|atatgtcgat

Distance from splice site

1

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

3

Strand

1

Original gDNA sequence snippet

TTTGGAAATGCTGTTAGTCGGTATGTCGATAACCTATATAA

Altered gDNA sequence snippet

TTTGGAAATGCTGTTAGTCGATATGTCGATAACCTATATAA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MNGYISNANY SVKKCIFLLF INHRLVESTS LRKAIETVYA AYLPKNTHPF LYLSLEISPQ
NVDVNVHPTK HEVHFLHEES ILERVQQHIE SKLLGSNSSR MYFTQTLLPG LAGPSGEMVK
STTSLTSSST SGSSDKVYAH QMVRTDSREQ KLDAFLQPLS KPLSSQPQAI VTEDKTDISS
GRARQQDEEM LELPAPAEVA AKNQSLEGDT TKGTSEMSEK RGPTSSNPRK RHREDSDVEM
VEDDSRKEMT AACTPRRRII NLTSVLSLQE EINEQGHEVL REMLHNHSFV GCVNPQWALA
QHQTKLYLLN TTKLSEELFY QILIYDFANF GVLRLSEPAP LFDLAMLALD SPESGWTEED
GPKEGLAEYI VEFLKKKAEM LADYFSLEID EEGNLIGLPL LIDNYVPPLE GLPIFILRLA
TEVNWDEEKE CFESLSKECA MFYSIRKQYI SEESTLSGQQ SEVPGSIPNS WKWTVEHIVY
KALRSHILPP KHFTEDGNIL QLANLPDLYK VFERC*

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

757 / 757

Last intron/exon boundary

2136

Theoretical NMD boundary in CDS

1329

Length of CDS

1548

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

18875

Chromosomal position

37012100

Speed

0.01 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

MutationT@ster 2025

Variant:

3:37012100G>A_14_ENST00000458205

Prediction:

DeleteriousPermalink

Summary:

Known as potential disease variant: ClinVar ID 90311 (likely pathogenic)
Splice site lost

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

Analysed issue

Analysis result

Variant

Chr3:37012100G>A (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.68, LOF (oe): 0.48, misssense (oe): 0.87, synonymous (oe): 0.95 ? (gnomAD)

Ensembl transcript ID

ENST00000458205.6

Genbank transcript ID

NM_001258274 (by similarity)

UniProt / AlphaMissense peptide

MLH1_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

intron

DNA changes

c.-47+1G>A
g.18875G>A

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Hereditary nonpolyposis colorectal neoplasms
Lynch syndrome
Hereditary cancer-predisposing syndrome
Colorectal cancer, hereditary nonpolyposis, type 2

likely pathogenic

Variant DBs

dbSNP ID	rs267607778
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	1	1

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	7.59	1
	7.324	1
(flanking)	5.642	1

?

Splice sites

alteration within used splice site, likely to disturb normal splicing

MaxEntScan:

effect	gDNA position	score	sequence	exon-intron border
Donor lost	18874	wt: 0.00 / mu: 0.00	-	wt: CTGTTAGTCG\|gtatgtcgat mu: CTGTTAGTCG\|atatgtcgat

Distance from splice site

1

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

3

Strand

1

Original gDNA sequence snippet

TTTGGAAATGCTGTTAGTCGGTATGTCGATAACCTATATAA

Altered gDNA sequence snippet

TTTGGAAATGCTGTTAGTCGATATGTCGATAACCTATATAA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MNGYISNANY SVKKCIFLLF INHRLVESTS LRKAIETVYA AYLPKNTHPF LYLSLEISPQ
NVDVNVHPTK HEVHFLHEES ILERVQQHIE SKLLGSNSSR MYFTQTLLPG LAGPSGEMVK
STTSLTSSST SGSSDKVYAH QMVRTDSREQ KLDAFLQPLS KPLSSQPQAI VTEDKTDISS
GRARQQDEEM LELPAPAEVA AKNQSLEGDT TKGTSEMSEK RGPTSSNPRK RHREDSDVEM
VEDDSRKEMT AACTPRRRII NLTSVLSLQE EINEQGHEVL REMLHNHSFV GCVNPQWALA
QHQTKLYLLN TTKLSEELFY QILIYDFANF GVLRLSEPAP LFDLAMLALD SPESGWTEED
GPKEGLAEYI VEFLKKKAEM LADYFSLEID EEGNLIGLPL LIDNYVPPLE GLPIFILRLA
TEVNWDEEKE CFESLSKECA MFYSIRKQYI SEESTLSGQQ SEVPGSIPNS WKWTVEHIVY
KALRSHILPP KHFTEDGNIL QLANLPDLYK VFERC*

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

868 / 868

Last intron/exon boundary

2247

Theoretical NMD boundary in CDS

1329

Length of CDS

1548

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

18875

Chromosomal position

37012100

Speed

0.01 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

MutationT@ster 2025

Variant:

3:37012100G>A_16_ENST00000713802

Prediction:

DeleteriousPermalink

Summary:

Known as potential disease variant: ClinVar ID 90311 (likely pathogenic)
Splice site lost

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

Analysed issue

Analysis result

Variant

Chr3:37012100G>A (GRCh38)

Gene symbol

Gene constraints

no data

Ensembl transcript ID

ENST00000713802.1

Genbank transcript ID

NM_001354629 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.578+1G>A
g.18875G>A

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Hereditary nonpolyposis colorectal neoplasms
Lynch syndrome
Hereditary cancer-predisposing syndrome
Colorectal cancer, hereditary nonpolyposis, type 2

likely pathogenic

Variant DBs

dbSNP ID	rs267607778
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	1	1

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	7.59	1
	7.324	1
(flanking)	5.642	1

?

Splice sites

alteration within used splice site, likely to disturb normal splicing

MaxEntScan:

effect	gDNA position	score	sequence	exon-intron border
Donor lost	18874	wt: 0.00 / mu: 0.00	-	wt: CTGTTAGTCG\|gtatgtcgat mu: CTGTTAGTCG\|atatgtcgat

Distance from splice site

1

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

3

Strand

1

Original gDNA sequence snippet

TTTGGAAATGCTGTTAGTCGGTATGTCGATAACCTATATAA

Altered gDNA sequence snippet

TTTGGAAATGCTGTTAGTCGATATGTCGATAACCTATATAA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MSFVAGVIRR LDETVVNRIA AGEVIQRPAN AIKEMIENCL DAKSTSIQVI VKEGGLKLIQ
IQDNGTGIRA LASISHVAHV TITTKTADGK CAYRASYSDG KLKAPPKPCA GNQGTQITVE
DLFYNIATRR KALKNPSEEY GKILEVVGRY SVHNAGISFS VKKQGETVAD VRTLPNASTV
DNIRSIFGNA VSRELIEIGC EDKTLAFKMN GYISNANYSV KKCIFLLFIN HRLVESTSLR
KAIETVYAAY LPKNTHPFLY LSLEISPQNV DVNVHPTKHE VHFLHEESIL ERVQQHIESK
LLGSNSSRMY FTQTLLPGLA GPSGEMVKST TSLTSSSTSG SSDKVYAHQM VRTDSREQKL
DAFLQPLSKP LSSQPQAIVT EDKTDISSGR ARQQDEEMLE LPAPAEVAAK NQSLEGDTTK
GTSEMSEKRG PTSSNPRKRH REDSDVEMVE DDSRKEMTAA CTPRRRIINL TSVLSLQEEI
NEQGHEVLRE MLHNHSFVGC VNPQWALAQH QTKLYLLNTT KLSEELFYQI LIYDFANFGV
LRLSEPAPLF DLAMLALDSP ESGWTEEDGP KEGLAEYIVE FLKKKAEMLA DYFSLEIDEE
GNLIGLPLLI DNYVPPLEGL PIFILRLATE VNWDEEKECF ESLSKECAMF YSIRKQYISE
ESTLSGQQSE VPGSIPNSWK WTVEHIVYKA LRSHILPPKH FTEDGNILQL ANLPDLYKVF
ERC*

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

7 / 7

Last intron/exon boundary

2010

Theoretical NMD boundary in CDS

1953

Length of CDS

2172

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

18875

Chromosomal position

37012100

Speed

0.01 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

MutationT@ster 2025

Variant:

3:37012100G>A_15_ENST00000674019

Prediction:

DeleteriousPermalink

Summary:

Known as potential disease variant: ClinVar ID 90311 (likely pathogenic)
Splice site lost

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

Analysed issue

Analysis result

Variant

Chr3:37012100G>A (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.68, LOF (oe): 0.48, misssense (oe): 0.87, synonymous (oe): 0.95 ? (gnomAD)

Ensembl transcript ID

ENST00000674019.1

Genbank transcript ID

NM_001354619 (by similarity)

UniProt / AlphaMissense peptide

MLH1_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

intron

DNA changes

c.-47+1G>A
g.18875G>A

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Hereditary nonpolyposis colorectal neoplasms
Lynch syndrome
Hereditary cancer-predisposing syndrome
Colorectal cancer, hereditary nonpolyposis, type 2

likely pathogenic

Variant DBs

dbSNP ID	rs267607778
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	1	1

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	7.59	1
	7.324	1
(flanking)	5.642	1

?

Splice sites

alteration within used splice site, likely to disturb normal splicing

MaxEntScan:

effect	gDNA position	score	sequence	exon-intron border
Donor lost	18874	wt: 0.00 / mu: 0.00	-	wt: CTGTTAGTCG\|gtatgtcgat mu: CTGTTAGTCG\|atatgtcgat

Distance from splice site

1

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

3

Strand

1

Original gDNA sequence snippet

TTTGGAAATGCTGTTAGTCGGTATGTCGATAACCTATATAA

Altered gDNA sequence snippet

TTTGGAAATGCTGTTAGTCGATATGTCGATAACCTATATAA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MNGYISNANY SVKKCIFLLF INHRLVESTS LRKAIETVYA AYLPKNTHPF LYLSLEISPQ
NVDVNVHPTK HEVHFLHEES ILERVQQHIE SKLLGSNSSR MYFTQTLLPG LAGPSGEMVK
STTSLTSSST SGSSDKVYAH QMVRTDSREQ KLDAFLQPLS KPLSSQPQAI VTEDKTDISS
GRARQQDEEM LELPAPAEVA AKNQSLEGDT TKGTSEMSEK RGPTSSNPRK RHREDSDVEM
VEDDSRKEMT AACTPRRRII NLTSVLSLQE EINEQGHEVL REMLHNHSFV GCVNPQWALA
QHQTKLYLLN TTKLSEELFY QILIYDFANF GVLRLSEPAP LFDLAMLALD SPESGWTEED
GPKEGLAEYI VEFLKKKAEM LADYFSLEID EEGNLIGLPL LIDNYVPPLE GLPIFILRLA
TEVNWDEEKE CFESLSKECA MFYSIRKQYI SEESTLSGQQ SEVPGSIPNS WKWTVEHIVY
KALRSHILPP KHFTEDGNIL QLANLPDLYK VFERC*

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

859 / 859

Last intron/exon boundary

2238

Theoretical NMD boundary in CDS

1329

Length of CDS

1548

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

18875

Chromosomal position

37012100

Speed

0.01 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

MutationT@ster 2025

Variant:

3:37012100G>A_17_ENST00000673715

Prediction:

DeleteriousPermalink

Summary:

Known as potential disease variant: ClinVar ID 90311 (likely pathogenic)
Splice site lost

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

Analysed issue

Analysis result

Variant

Chr3:37012100G>A (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.60, LOF (oe): 0.42, misssense (oe): 0.92, synonymous (oe): 1.00 ? (gnomAD)

Ensembl transcript ID

ENST00000673715.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.677+1G>A
g.18875G>A

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Hereditary nonpolyposis colorectal neoplasms
Lynch syndrome
Hereditary cancer-predisposing syndrome
Colorectal cancer, hereditary nonpolyposis, type 2

likely pathogenic

Variant DBs

dbSNP ID	rs267607778
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	1	1

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	7.59	1
	7.324	1
(flanking)	5.642	1

?

Splice sites

alteration within used splice site, likely to disturb normal splicing

MaxEntScan:

effect	gDNA position	score	sequence	exon-intron border
Donor lost	18874	wt: 0.00 / mu: 0.00	-	wt: CTGTTAGTCG\|gtatgtcgat mu: CTGTTAGTCG\|atatgtcgat

Distance from splice site

1

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

3

Strand

1

Original gDNA sequence snippet

TTTGGAAATGCTGTTAGTCGGTATGTCGATAACCTATATAA

Altered gDNA sequence snippet

TTTGGAAATGCTGTTAGTCGATATGTCGATAACCTATATAA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MSFVAGVIRR LDETVVNRIA AGEVIQRPAN AIKEMIENCL DAKSTSIQVI VKEGGLKLIQ
IQDNGTGIRK EDLDIVCERF TTSKLQSFED LASISTYGFR GEALASISHV AHVTITTKTA
DGKCAYRASY SDGKLKAPPK PCAGNQGTQI TVEDLFYNIA TRRKALKNPS EEYGKILEVV
GRYSVHNAGI SFSVKKQGET VADVRTLPNA STVDNIRSIF GNAVSRELIE IGCEDKTLAF
KMNGYISNAN YSVKKCIFLL FINHRLVEST SLRKAIETVY AAYLPKNTHP FLYLSLEISP
QNVDVNVHPT KHEVHFLHEE SILERVQQHI ESKLLGSNSS RMYFTQTLLP GLAGPSGEMV
KSTTSLTSSS TSGSSDKVYA HQMVRTDSRE QKLDAFLQPL SKPLSSQPQA IVTEDKTDIS
SGRARQQDEE MLELPAPAEV AAKNQSLEGD TTKGTSEMSE KRGPTSSNPR KRHREDSDVE
MVEDDSRKEM TAACTPRRRI INLTSVLSLQ EEINEQGHEV LREMLHNHSF VGCVNPQWAL
AQHQTKLYLL NTTKLSEELF YQILIYDFAN FGVLRLSEPA PLFDLAMLAL DSPESGWTEE
DGPKEGLAEY IVEFLKKKAE MLADYFSLEI DEV*

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

26 / 26

Last intron/exon boundary

1756

Theoretical NMD boundary in CDS

1680

Length of CDS

1902

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

18875

Chromosomal position

37012100

Speed

0.01 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

MutationT@ster 2025

Variant:

3:37012100G>A_18_ENST00000231790

Prediction:

DeleteriousPermalink

Summary:

Known as potential disease variant: ClinVar ID 90311 (likely pathogenic)
Splice site lost

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

Analysed issue

Analysis result

Variant

Chr3:37012100G>A (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.64, LOF (oe): 0.48, misssense (oe): 0.90, synonymous (oe): 0.98 ? (gnomAD)

Ensembl transcript ID

ENST00000231790.8

Genbank transcript ID

NM_000249 (exact from MANE)

UniProt / AlphaMissense peptide

MLH1_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

intron

DNA changes

c.677+1G>A
g.18875G>A

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Hereditary nonpolyposis colorectal neoplasms
Lynch syndrome
Hereditary cancer-predisposing syndrome
Colorectal cancer, hereditary nonpolyposis, type 2

likely pathogenic

Variant DBs

dbSNP ID	rs267607778
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	1	1

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	7.59	1
	7.324	1
(flanking)	5.642	1

?

Splice sites

alteration within used splice site, likely to disturb normal splicing

MaxEntScan:

effect	gDNA position	score	sequence	exon-intron border
Donor lost	18874	wt: 0.00 / mu: 0.00	-	wt: CTGTTAGTCG\|gtatgtcgat mu: CTGTTAGTCG\|atatgtcgat

Distance from splice site

1

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

3

Strand

1

Original gDNA sequence snippet

TTTGGAAATGCTGTTAGTCGGTATGTCGATAACCTATATAA

Altered gDNA sequence snippet

TTTGGAAATGCTGTTAGTCGATATGTCGATAACCTATATAA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MSFVAGVIRR LDETVVNRIA AGEVIQRPAN AIKEMIENCL DAKSTSIQVI VKEGGLKLIQ
IQDNGTGIRK EDLDIVCERF TTSKLQSFED LASISTYGFR GEALASISHV AHVTITTKTA
DGKCAYRASY SDGKLKAPPK PCAGNQGTQI TVEDLFYNIA TRRKALKNPS EEYGKILEVV
GRYSVHNAGI SFSVKKQGET VADVRTLPNA STVDNIRSIF GNAVSRELIE IGCEDKTLAF
KMNGYISNAN YSVKKCIFLL FINHRLVEST SLRKAIETVY AAYLPKNTHP FLYLSLEISP
QNVDVNVHPT KHEVHFLHEE SILERVQQHI ESKLLGSNSS RMYFTQTLLP GLAGPSGEMV
KSTTSLTSSS TSGSSDKVYA HQMVRTDSRE QKLDAFLQPL SKPLSSQPQA IVTEDKTDIS
SGRARQQDEE MLELPAPAEV AAKNQSLEGD TTKGTSEMSE KRGPTSSNPR KRHREDSDVE
MVEDDSRKEM TAACTPRRRI INLTSVLSLQ EEINEQGHEV LREMLHNHSF VGCVNPQWAL
AQHQTKLYLL NTTKLSEELF YQILIYDFAN FGVLRLSEPA PLFDLAMLAL DSPESGWTEE
DGPKEGLAEY IVEFLKKKAE MLADYFSLEI DEEGNLIGLP LLIDNYVPPL EGLPIFILRL
ATEVNWDEEK ECFESLSKEC AMFYSIRKQY ISEESTLSGQ QSEVPGSIPN SWKWTVEHIV
YKALRSHILP PKHFTEDGNI LQLANLPDLY KVFERC*

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

31 / 31

Last intron/exon boundary

2133

Theoretical NMD boundary in CDS

2052

Length of CDS

2271

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

18875

Chromosomal position

37012100

Speed

0.01 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

MutationT@ster 2025

Variant:

3:37012100G>A_19_ENST00000456676

Prediction:

DeleteriousPermalink

Summary:

Known as potential disease variant: ClinVar ID 90311 (likely pathogenic)
Splice site lost

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

Analysed issue

Analysis result

Variant

Chr3:37012100G>A (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.60, LOF (oe): 0.43, misssense (oe): 0.90, synonymous (oe): 0.97 ? (gnomAD)

Ensembl transcript ID

ENST00000456676.7

Genbank transcript ID

NM_001258271 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.677+1G>A
g.18875G>A

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Hereditary nonpolyposis colorectal neoplasms
Lynch syndrome
Hereditary cancer-predisposing syndrome
Colorectal cancer, hereditary nonpolyposis, type 2

likely pathogenic

Variant DBs

dbSNP ID	rs267607778
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	1	1

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	7.59	1
	7.324	1
(flanking)	5.642	1

?

Splice sites

alteration within used splice site, likely to disturb normal splicing

MaxEntScan:

effect	gDNA position	score	sequence	exon-intron border
Donor lost	18874	wt: 0.00 / mu: 0.00	-	wt: CTGTTAGTCG\|gtatgtcgat mu: CTGTTAGTCG\|atatgtcgat

Distance from splice site

1

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

3

Strand

1

Original gDNA sequence snippet

TTTGGAAATGCTGTTAGTCGGTATGTCGATAACCTATATAA

Altered gDNA sequence snippet

TTTGGAAATGCTGTTAGTCGATATGTCGATAACCTATATAA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MSFVAGVIRR LDETVVNRIA AGEVIQRPAN AIKEMIENCL DAKSTSIQVI VKEGGLKLIQ
IQDNGTGIRK EDLDIVCERF TTSKLQSFED LASISTYGFR GEALASISHV AHVTITTKTA
DGKCAYRASY SDGKLKAPPK PCAGNQGTQI TVEDLFYNIA TRRKALKNPS EEYGKILEVV
GRYSVHNAGI SFSVKKQGET VADVRTLPNA STVDNIRSIF GNAVSRELIE IGCEDKTLAF
KMNGYISNAN YSVKKCIFLL FINHRLVEST SLRKAIETVY AAYLPKNTHP FLYLSLEISP
QNVDVNVHPT KHEVHFLHEE SILERVQQHI ESKLLGSNSS RMYFTQTLLP GLAGPSGEMV
KSTTSLTSSS TSGSSDKVYA HQMVRTDSRE QKLDAFLQPL SKPLSSQPQA IVTEDKTDIS
SGRARQQDEE MLELPAPAEV AAKNQSLEGD TTKGTSEMSE KRGPTSSNPR KRHREDSDVE
MVEDDSRKEM TAACTPRRRI INLTSVLSLQ EEINEQGHEV LREMLHNHSF VGCVNPQWAL
AQHQTKLYLL NTTKLSEELF YQILIYDFAN FGVLRLSEPA PLFDLAMLAL DSPESGWTEE
DGPKEGLAEY IVEFLKKKAE MLADYFSLEI DESEVPGSIP NSWKWTVEHI VYKALRSHIL
PPKHFTEDGN ILQLANLPDL YKVFERC*

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

31 / 31

Last intron/exon boundary

1926

Theoretical NMD boundary in CDS

1845

Length of CDS

2064

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

18875

Chromosomal position

37012100

Speed

0.01 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

MutationT@ster 2025

Variant:

3:37012100G>A_20_ENST00000450420

Prediction:

DeleteriousPermalink

Summary:

Known as potential disease variant: ClinVar ID 90311 (likely pathogenic)
Splice site lost

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

Analysed issue

Analysis result

Variant

Chr3:37012100G>A (GRCh38)

Gene symbol

Gene constraints

LOEUF: 1.25, LOF (oe): 0.64, misssense (oe): 0.84, synonymous (oe): 0.93 ? (gnomAD)

Ensembl transcript ID

ENST00000450420.6

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.677+1G>A
g.18875G>A

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Hereditary nonpolyposis colorectal neoplasms
Lynch syndrome
Hereditary cancer-predisposing syndrome
Colorectal cancer, hereditary nonpolyposis, type 2

likely pathogenic

Variant DBs

dbSNP ID	rs267607778
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	1	1

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	7.59	1
	7.324	1
(flanking)	5.642	1

?

Splice sites

alteration within used splice site, likely to disturb normal splicing

MaxEntScan:

effect	gDNA position	score	sequence	exon-intron border
Donor lost	18874	wt: 0.00 / mu: 0.00	-	wt: CTGTTAGTCG\|gtatgtcgat mu: CTGTTAGTCG\|atatgtcgat

Distance from splice site

1

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

3

Strand

1

Original gDNA sequence snippet

TTTGGAAATGCTGTTAGTCGGTATGTCGATAACCTATATAA

Altered gDNA sequence snippet

TTTGGAAATGCTGTTAGTCGATATGTCGATAACCTATATAA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MSFVAGVIRR LDETVVNRIA AGEVIQRPAN AIKEMIENCL DAKSTSIQVI VKEGGLKLIQ
IQDNGTGIRK EDLDIVCERF TTSKLQSFED LASISTYGFR GEALASISHV AHVTITTKTA
DGKCAYRASY SDGKLKAPPK PCAGNQGTQI TVEDLFYNIA TRRKALKNPS EEYGKILEVV
GRYSVHNAGI SFSVKKQGET VADVRTLPNA STVDNIRSIF GNAVSRELIE IGCEDKTLAF
KMNGYISNAN YSVKKCIFLL FINHRLVEST SLRKAIETVY AAYLPKNTHP FLYLSLEISP
QNVDVNVHPT KHEVHFLHEE SILERVQQHI ESKLLGSNSS RMYFTQTLLP GLAGPSGEMV
KSTTSLTSSS TSGSSDKVYA HQMVRTDSRE QKLDAFLQPL SKPLSSQPQA IVTEDKTDIS
SGRARQQDEE MLELPAPAEV AAKNQSLEGD TTKGTSEMSE KRGPTSSNPR KRHREDSDVE
MVEDDSRKEM TAACTPRRRI INLTSVLSLQ EEINEQGHEE *

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

31 / 31

Last intron/exon boundary

1588

Theoretical NMD boundary in CDS

1507

Length of CDS

1563

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

18875

Chromosomal position

37012100

Speed

0.01 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

MutationT@ster 2025

Variant:

3:37012100G>A_21_ENST00000536378

Prediction:

DeleteriousPermalink

Summary:

Known as potential disease variant: ClinVar ID 90311 (likely pathogenic)
Splice site lost

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

Analysed issue

Analysis result

Variant

Chr3:37012100G>A (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.68, LOF (oe): 0.48, misssense (oe): 0.87, synonymous (oe): 0.95 ? (gnomAD)

Ensembl transcript ID

ENST00000536378.5

Genbank transcript ID

NM_001354617 (by similarity), NM_001258273 (by similarity)

UniProt / AlphaMissense peptide

MLH1_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

intron

DNA changes

c.-47+1G>A
g.18875G>A

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Hereditary nonpolyposis colorectal neoplasms
Lynch syndrome
Hereditary cancer-predisposing syndrome
Colorectal cancer, hereditary nonpolyposis, type 2

likely pathogenic

Variant DBs

dbSNP ID	rs267607778
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	1	1

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	7.59	1
	7.324	1
(flanking)	5.642	1

?

Splice sites

alteration within used splice site, likely to disturb normal splicing

MaxEntScan:

effect	gDNA position	score	sequence	exon-intron border
Donor lost	18874	wt: 0.00 / mu: 0.00	-	wt: CTGTTAGTCG\|gtatgtcgat mu: CTGTTAGTCG\|atatgtcgat

Distance from splice site

1

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

3

Strand

1

Original gDNA sequence snippet

TTTGGAAATGCTGTTAGTCGGTATGTCGATAACCTATATAA

Altered gDNA sequence snippet

TTTGGAAATGCTGTTAGTCGATATGTCGATAACCTATATAA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MNGYISNANY SVKKCIFLLF INHRLVESTS LRKAIETVYA AYLPKNTHPF LYLSLEISPQ
NVDVNVHPTK HEVHFLHEES ILERVQQHIE SKLLGSNSSR MYFTQTLLPG LAGPSGEMVK
STTSLTSSST SGSSDKVYAH QMVRTDSREQ KLDAFLQPLS KPLSSQPQAI VTEDKTDISS
GRARQQDEEM LELPAPAEVA AKNQSLEGDT TKGTSEMSEK RGPTSSNPRK RHREDSDVEM
VEDDSRKEMT AACTPRRRII NLTSVLSLQE EINEQGHEVL REMLHNHSFV GCVNPQWALA
QHQTKLYLLN TTKLSEELFY QILIYDFANF GVLRLSEPAP LFDLAMLALD SPESGWTEED
GPKEGLAEYI VEFLKKKAEM LADYFSLEID EEGNLIGLPL LIDNYVPPLE GLPIFILRLA
TEVNWDEEKE CFESLSKECA MFYSIRKQYI SEESTLSGQQ SEVPGSIPNS WKWTVEHIVY
KALRSHILPP KHFTEDGNIL QLANLPDLYK VFERC*

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

831 / 831

Last intron/exon boundary

2210

Theoretical NMD boundary in CDS

1329

Length of CDS

1548

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

18875

Chromosomal position

37012100

Speed

0.01 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

Problem:

1

MutationT@ster 2025

annotation problem

The chosen transcript ENST00000413740 on chromosome 3 has no correct in-frame stop codon (TGA, TAA or TAG) annotated
This is likely to cause a false prediction. You should choose another transcript.