MutationT@ster 2025

NEVER press reload or F5 - unless you want to start from the very beginning.
Input seems to be ok - now mapping the variant to the different transcripts...
Querying Taster for transcript #1: ENST00000233146
Querying Taster for transcript #2: ENST00000713919
Querying Taster for transcript #3: ENST00000406134
Querying Taster for transcript #4: ENST00000713854
Querying Taster for transcript #5: ENST00000645506
Querying Taster for transcript #6: ENST00000543555
MT speed 0.27 s - this script 2.704576 s

Transcript summary:

Permalink

Transcript	Gene symbol	Prediction	Tree vote	Model	Splice site change	Variant type	Protein length	Features at a glance
ENST00000233146(MANE Select)	MSH2	Deleterious	90\|10	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000543555	MSH2	Deleterious	94\|6	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000406134	MSH2	Deleterious	95\|5	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed
ENST00000645506	MSH2	Deleterious	95\|5	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed
ENST00000713919	MSH2	Deleterious	100\|0	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed
ENST00000713854	MSH2	Deleterious	100\|0	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed

MutationT@ster 2025

Variant:

2:47475260C>A_1_ENST00000233146

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 90|10 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr2:47475260C>A (GRCh38)

Gene symbol

MSH2

Gene constraints

LOEUF: 0.67, LOF (oe): 0.52, misssense (oe): 1.25, synonymous (oe): 1.12 ? (gnomAD)

Ensembl transcript ID

ENST00000233146.7

Genbank transcript ID

NM_000251 (exact from MANE), NM_001406638 (by similarity), NM_001406641 (by similarity), NM_001406648 (by similarity), NM_001406653 (by similarity), NM_001406655 (by similarity)

UniProt / AlphaMissense peptide

MSH2_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1995C>A
g.72194C>A

AA changes

AAE:	H665Q	?
Score:	24

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs1553368723
	Allele 'A' was not found in gnomAD

Protein conservation

Species	Match	AA	Alignment
Human		665	D	V	Y	F	E	K	D	K	Q	M	F	H	I	I	T	G	P	N	M	G	G	K	S	T
mutated	not conserved	665								K	Q	M	F	Q	I	I	T	G	P	N	M	G	G	K	S
Ptroglodytes	all identical	665								K	Q	M	F	H	I	I	T	G	P	N	M	G	G	K	S
Mmulatta	all identical	665								K	Q	M	F	H	I	I	T	G	P	N	M	G	G	K	S
Fcatus	all identical	665								K	Q	M	F	H	I	I	T	G	P	N	M	G	G	K	S
Mmusculus	all identical	665								K	Q	M	F	H	I	I	T	G	P	N	M	G	G	K	S
Ggallus	all identical	660								K	Q	M	F	H	I	I	T	G	P	N	M	G	G	K	S
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	not conserved	663							E	E	C	N	M	F	I	I	T	G	P	N	M	G	G	K	S
Celegans	not conserved	640	D	V	V	L	D	K	C	R	L	I	-	-	I	L	T	G	A	N	M
Xtropicalis	all identical	664								K	Q	M	F	H	I	I	T	G	P	N	M	G	G	K	S

Protein features

Start (aa)	End (aa)	Feature	Details
2	934	CHAIN		lost
601	671	REGION	Interaction with EXO1	lost
664	668	STRAND		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	8.655	1
	0.866	1
(flanking)	8.655	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

11

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

2

Strand

1

Original gDNA sequence snippet

AAAGATAAACAGATGTTCCACATCATTACTGGTAAAAAACC

Altered gDNA sequence snippet

AAAGATAAACAGATGTTCCAAATCATTACTGGTAAAAAACC

Original cDNA sequence snippet

AAAGATAAACAGATGTTCCACATCATTACTGGCCCCAATAT

Altered cDNA sequence snippet

AAAGATAAACAGATGTTCCAAATCATTACTGGCCCCAATAT

Wildtype AA sequence

MAVQPKETLQ LESAAEVGFV RFFQGMPEKP TTTVRLFDRG DFYTAHGEDA LLAAREVFKT
QGVIKYMGPA GAKNLQSVVL SKMNFESFVK DLLLVRQYRV EVYKNRAGNK ASKENDWYLA
YKASPGNLSQ FEDILFGNND MSASIGVVGV KMSAVDGQRQ VGVGYVDSIQ RKLGLCEFPD
NDQFSNLEAL LIQIGPKECV LPGGETAGDM GKLRQIIQRG GILITERKKA DFSTKDIYQD
LNRLLKGKKG EQMNSAVLPE MENQVAVSSL SAVIKFLELL SDDSNFGQFE LTTFDFSQYM
KLDIAAVRAL NLFQGSVEDT TGSQSLAALL NKCKTPQGQR LVNQWIKQPL MDKNRIEERL
NLVEAFVEDA ELRQTLQEDL LRRFPDLNRL AKKFQRQAAN LQDCYRLYQG INQLPNVIQA
LEKHEGKHQK LLLAVFVTPL TDLRSDFSKF QEMIETTLDM DQVENHEFLV KPSFDPNLSE
LREIMNDLEK KMQSTLISAA RDLGLDPGKQ IKLDSSAQFG YYFRVTCKEE KVLRNNKNFS
TVDIQKNGVK FTNSKLTSLN EEYTKNKTEY EEAQDAIVKE IVNISSGYVE PMQTLNDVLA
QLDAVVSFAH VSNGAPVPYV RPAILEKGQG RIILKASRHA CVEVQDEIAF IPNDVYFEKD
KQMFHIITGP NMGGKSTYIR QTGVIVLMAQ IGCFVPCESA EVSIVDCILA RVGAGDSQLK
GVSTFMAEML ETASILRSAT KDSLIIIDEL GRGTSTYDGF GLAWAISEYI ATKIGAFCMF
ATHFHELTAL ANQIPTVNNL HVTALTTEET LTMLYQVKKG VCDQSFGIHV AELANFPKHV
IECAKQKALE LEEFQYIGES QGYDIMEPAA KKCYLEREQG EKIIQEFLSK VKQMPFTEMS
EENITIKLKQ LKAEVIAKNN SFVNEIISRI KVTT*

Mutated AA sequence

MAVQPKETLQ LESAAEVGFV RFFQGMPEKP TTTVRLFDRG DFYTAHGEDA LLAAREVFKT
QGVIKYMGPA GAKNLQSVVL SKMNFESFVK DLLLVRQYRV EVYKNRAGNK ASKENDWYLA
YKASPGNLSQ FEDILFGNND MSASIGVVGV KMSAVDGQRQ VGVGYVDSIQ RKLGLCEFPD
NDQFSNLEAL LIQIGPKECV LPGGETAGDM GKLRQIIQRG GILITERKKA DFSTKDIYQD
LNRLLKGKKG EQMNSAVLPE MENQVAVSSL SAVIKFLELL SDDSNFGQFE LTTFDFSQYM
KLDIAAVRAL NLFQGSVEDT TGSQSLAALL NKCKTPQGQR LVNQWIKQPL MDKNRIEERL
NLVEAFVEDA ELRQTLQEDL LRRFPDLNRL AKKFQRQAAN LQDCYRLYQG INQLPNVIQA
LEKHEGKHQK LLLAVFVTPL TDLRSDFSKF QEMIETTLDM DQVENHEFLV KPSFDPNLSE
LREIMNDLEK KMQSTLISAA RDLGLDPGKQ IKLDSSAQFG YYFRVTCKEE KVLRNNKNFS
TVDIQKNGVK FTNSKLTSLN EEYTKNKTEY EEAQDAIVKE IVNISSGYVE PMQTLNDVLA
QLDAVVSFAH VSNGAPVPYV RPAILEKGQG RIILKASRHA CVEVQDEIAF IPNDVYFEKD
KQMFQIITGP NMGGKSTYIR QTGVIVLMAQ IGCFVPCESA EVSIVDCILA RVGAGDSQLK
GVSTFMAEML ETASILRSAT KDSLIIIDEL GRGTSTYDGF GLAWAISEYI ATKIGAFCMF
ATHFHELTAL ANQIPTVNNL HVTALTTEET LTMLYQVKKG VCDQSFGIHV AELANFPKHV
IECAKQKALE LEEFQYIGES QGYDIMEPAA KKCYLEREQG EKIIQEFLSK VKQMPFTEMS
EENITIKLKQ LKAEVIAKNN SFVNEIISRI KVTT*

Position of stopcodon in wt / mu CDS

2805 / 2805

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

935 / 935

Position of stopcodon in wt / mu cDNA

2841 / 2841

Position of start ATG in wt / mu cDNA

37 / 37

Last intron/exon boundary

2670

Theoretical NMD boundary in CDS

2583

Length of CDS

2805

Coding sequence (CDS) position

1995

cDNA position

2031

gDNA position

72194

Chromosomal position

47475260

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:

2:47475260C>A_6_ENST00000543555

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 94|6 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr2:47475260C>A (GRCh38)

Gene symbol

MSH2

Gene constraints

LOEUF: 0.62, LOF (oe): 0.47, misssense (oe): 1.21, synonymous (oe): 1.07 ? (gnomAD)

Ensembl transcript ID

ENST00000543555.6

Genbank transcript ID

NM_001258281 (by similarity)

UniProt / AlphaMissense peptide

MSH2_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1797C>A
g.72194C>A

AA changes

AAE:	H599Q	?
Score:	24

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs1553368723
	Allele 'A' was not found in gnomAD

Protein conservation

Species	Match	AA	Alignment
Human		599	D	V	Y	F	E	K	D	K	Q	M	F	H	I	I	T	G	P	N	M	G	G	K	S	T
mutated	not conserved	599	D	V	Y	F	E	K	D	K	Q	M	F	Q	I	I	T	G	P	N	M	G	G	K	S
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

Start (aa)	End (aa)	Feature	Details
2	934	CHAIN		lost
589	613	HELIX		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	8.655	1
	0.866	1
(flanking)	8.655	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

11

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

2

Strand

1

Original gDNA sequence snippet

AAAGATAAACAGATGTTCCACATCATTACTGGTAAAAAACC

Altered gDNA sequence snippet

AAAGATAAACAGATGTTCCAAATCATTACTGGTAAAAAACC

Original cDNA sequence snippet

AAAGATAAACAGATGTTCCACATCATTACTGGCCCCAATAT

Altered cDNA sequence snippet

AAAGATAAACAGATGTTCCAAATCATTACTGGCCCCAATAT

Wildtype AA sequence

MGPAGAKNLQ SVVLSKMNFE SFVKDLLLVR QYRVEVYKNR AGNKASKEND WYLAYKASPG
NLSQFEDILF GNNDMSASIG VVGVKMSAVD GQRQVGVGYV DSIQRKLGLC EFPDNDQFSN
LEALLIQIGP KECVLPGGET AGDMGKLRQI IQRGGILITE RKKADFSTKD IYQDLNRLLK
GKKGEQMNSA VLPEMENQVA VSSLSAVIKF LELLSDDSNF GQFELTTFDF SQYMKLDIAA
VRALNLFQGS VEDTTGSQSL AALLNKCKTP QGQRLVNQWI KQPLMDKNRI EERLNLVEAF
VEDAELRQTL QEDLLRRFPD LNRLAKKFQR QAANLQDCYR LYQGINQLPN VIQALEKHEG
KHQKLLLAVF VTPLTDLRSD FSKFQEMIET TLDMDQVENH EFLVKPSFDP NLSELREIMN
DLEKKMQSTL ISAARDLGLD PGKQIKLDSS AQFGYYFRVT CKEEKVLRNN KNFSTVDIQK
NGVKFTNSKL TSLNEEYTKN KTEYEEAQDA IVKEIVNISS GYVEPMQTLN DVLAQLDAVV
SFAHVSNGAP VPYVRPAILE KGQGRIILKA SRHACVEVQD EIAFIPNDVY FEKDKQMFHI
ITGPNMGGKS TYIRQTGVIV LMAQIGCFVP CESAEVSIVD CILARVGAGD SQLKGVSTFM
AEMLETASIL RSATKDSLII IDELGRGTST YDGFGLAWAI SEYIATKIGA FCMFATHFHE
LTALANQIPT VNNLHVTALT TEETLTMLYQ VKKGVCDQSF GIHVAELANF PKHVIECAKQ
KALELEEFQY IGESQGYDIM EPAAKKCYLE REQGEKIIQE FLSKVKQMPF TEMSEENITI
KLKQLKAEVI AKNNSFVNEI ISRIKVTT*

Mutated AA sequence

MGPAGAKNLQ SVVLSKMNFE SFVKDLLLVR QYRVEVYKNR AGNKASKEND WYLAYKASPG
NLSQFEDILF GNNDMSASIG VVGVKMSAVD GQRQVGVGYV DSIQRKLGLC EFPDNDQFSN
LEALLIQIGP KECVLPGGET AGDMGKLRQI IQRGGILITE RKKADFSTKD IYQDLNRLLK
GKKGEQMNSA VLPEMENQVA VSSLSAVIKF LELLSDDSNF GQFELTTFDF SQYMKLDIAA
VRALNLFQGS VEDTTGSQSL AALLNKCKTP QGQRLVNQWI KQPLMDKNRI EERLNLVEAF
VEDAELRQTL QEDLLRRFPD LNRLAKKFQR QAANLQDCYR LYQGINQLPN VIQALEKHEG
KHQKLLLAVF VTPLTDLRSD FSKFQEMIET TLDMDQVENH EFLVKPSFDP NLSELREIMN
DLEKKMQSTL ISAARDLGLD PGKQIKLDSS AQFGYYFRVT CKEEKVLRNN KNFSTVDIQK
NGVKFTNSKL TSLNEEYTKN KTEYEEAQDA IVKEIVNISS GYVEPMQTLN DVLAQLDAVV
SFAHVSNGAP VPYVRPAILE KGQGRIILKA SRHACVEVQD EIAFIPNDVY FEKDKQMFQI
ITGPNMGGKS TYIRQTGVIV LMAQIGCFVP CESAEVSIVD CILARVGAGD SQLKGVSTFM
AEMLETASIL RSATKDSLII IDELGRGTST YDGFGLAWAI SEYIATKIGA FCMFATHFHE
LTALANQIPT VNNLHVTALT TEETLTMLYQ VKKGVCDQSF GIHVAELANF PKHVIECAKQ
KALELEEFQY IGESQGYDIM EPAAKKCYLE REQGEKIIQE FLSKVKQMPF TEMSEENITI
KLKQLKAEVI AKNNSFVNEI ISRIKVTT*

Position of stopcodon in wt / mu CDS

2607 / 2607

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

869 / 869

Position of stopcodon in wt / mu cDNA

2746 / 2746

Position of start ATG in wt / mu cDNA

140 / 140

Last intron/exon boundary

2575

Theoretical NMD boundary in CDS

2385

Length of CDS

2607

Coding sequence (CDS) position

1797

cDNA position

1936

gDNA position

72194

Chromosomal position

47475260

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:

2:47475260C>A_3_ENST00000406134

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed

Model: simple_aae
Tree vote: 95|5 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr2:47475260C>A (GRCh38)

Gene symbol

MSH2

Gene constraints

LOEUF: 0.65, LOF (oe): 0.49, misssense (oe): 1.24, synonymous (oe): 1.14 ? (gnomAD)

Ensembl transcript ID

ENST00000406134.5

Genbank transcript ID

NM_001406637 (by similarity), NM_001406633 (by similarity), NM_001406632 (by similarity), NM_001406631 (by similarity), NM_001406639 (by similarity), NM_001406647 (by similarity), NM_001406646 (by similarity), NM_001406643 (by similarity), NM_001406635 (by similarity), NM_001406640 (by similarity), NM_001406642 (by similarity), NM_001406636 (by similarity), NM_001406674 (by similarity), NM_001406634 (by similarity), NM_001406656 (by similarity), NM_001406669 (by similarity), NM_001406645 (by similarity), NM_001406652 (by similarity), NM_001406654 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1995C>A
g.72194C>A

AA changes

AAE:	H665Q	?
Score:	24

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs1553368723
	Allele 'A' was not found in gnomAD

Protein conservation

Species	Match	AA	Alignment
Human		665	D	V	Y	F	E	K	D	K	Q	M	F	H	I	I	T	G	P	N	M	G	G	K	S	T
mutated	not conserved	665								K	Q	M	F	Q	I	I	T	G	P	N	M	G	G	K	S
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	8.655	1
	0.866	1
(flanking)	8.655	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

11

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

2

Strand

1

Original gDNA sequence snippet

AAAGATAAACAGATGTTCCACATCATTACTGGTAAAAAACC

Altered gDNA sequence snippet

AAAGATAAACAGATGTTCCAAATCATTACTGGTAAAAAACC

Original cDNA sequence snippet

AAAGATAAACAGATGTTCCACATCATTACTGGCCCCAATAT

Altered cDNA sequence snippet

AAAGATAAACAGATGTTCCAAATCATTACTGGCCCCAATAT

Wildtype AA sequence

MAVQPKETLQ LESAAEVGFV RFFQGMPEKP TTTVRLFDRG DFYTAHGEDA LLAAREVFKT
QGVIKYMGPA GAKNLQSVVL SKMNFESFVK DLLLVRQYRV EVYKNRAGNK ASKENDWYLA
YKASPGNLSQ FEDILFGNND MSASIGVVGV KMSAVDGQRQ VGVGYVDSIQ RKLGLCEFPD
NDQFSNLEAL LIQIGPKECV LPGGETAGDM GKLRQIIQRG GILITERKKA DFSTKDIYQD
LNRLLKGKKG EQMNSAVLPE MENQVAVSSL SAVIKFLELL SDDSNFGQFE LTTFDFSQYM
KLDIAAVRAL NLFQGSVEDT TGSQSLAALL NKCKTPQGQR LVNQWIKQPL MDKNRIEERL
NLVEAFVEDA ELRQTLQEDL LRRFPDLNRL AKKFQRQAAN LQDCYRLYQG INQLPNVIQA
LEKHEGKHQK LLLAVFVTPL TDLRSDFSKF QEMIETTLDM DQVENHEFLV KPSFDPNLSE
LREIMNDLEK KMQSTLISAA RDLGLDPGKQ IKLDSSAQFG YYFRVTCKEE KVLRNNKNFS
TVDIQKNGVK FTNSKLTSLN EEYTKNKTEY EEAQDAIVKE IVNISSGYVE PMQTLNDVLA
QLDAVVSFAH VSNGAPVPYV RPAILEKGQG RIILKASRHA CVEVQDEIAF IPNDVYFEKD
KQMFHIITGP NMGGKSTYIR QTGVIVLMAQ IGCFVPCESA EVSIVDCILA RVGAGDSQLK
GVSTFMAEML ETASILRSAT KDSLIIIDEL GRGTSTYDGF GLAWAISEYI ATKIGAFCMF
ATHFHELTAL ANQIPTVNNL HVTALTTEET LTMLYQVKKG VCDQSFGIHV AELANFPKHV
IECAKQKALE LEEFQYIGES QGYDIMEPAA KKCYLERENL RVTEPKDQCL ILLTWKRKLR
GGKRSACSRP ERQNQGSGEL S*

Mutated AA sequence

MAVQPKETLQ LESAAEVGFV RFFQGMPEKP TTTVRLFDRG DFYTAHGEDA LLAAREVFKT
QGVIKYMGPA GAKNLQSVVL SKMNFESFVK DLLLVRQYRV EVYKNRAGNK ASKENDWYLA
YKASPGNLSQ FEDILFGNND MSASIGVVGV KMSAVDGQRQ VGVGYVDSIQ RKLGLCEFPD
NDQFSNLEAL LIQIGPKECV LPGGETAGDM GKLRQIIQRG GILITERKKA DFSTKDIYQD
LNRLLKGKKG EQMNSAVLPE MENQVAVSSL SAVIKFLELL SDDSNFGQFE LTTFDFSQYM
KLDIAAVRAL NLFQGSVEDT TGSQSLAALL NKCKTPQGQR LVNQWIKQPL MDKNRIEERL
NLVEAFVEDA ELRQTLQEDL LRRFPDLNRL AKKFQRQAAN LQDCYRLYQG INQLPNVIQA
LEKHEGKHQK LLLAVFVTPL TDLRSDFSKF QEMIETTLDM DQVENHEFLV KPSFDPNLSE
LREIMNDLEK KMQSTLISAA RDLGLDPGKQ IKLDSSAQFG YYFRVTCKEE KVLRNNKNFS
TVDIQKNGVK FTNSKLTSLN EEYTKNKTEY EEAQDAIVKE IVNISSGYVE PMQTLNDVLA
QLDAVVSFAH VSNGAPVPYV RPAILEKGQG RIILKASRHA CVEVQDEIAF IPNDVYFEKD
KQMFQIITGP NMGGKSTYIR QTGVIVLMAQ IGCFVPCESA EVSIVDCILA RVGAGDSQLK
GVSTFMAEML ETASILRSAT KDSLIIIDEL GRGTSTYDGF GLAWAISEYI ATKIGAFCMF
ATHFHELTAL ANQIPTVNNL HVTALTTEET LTMLYQVKKG VCDQSFGIHV AELANFPKHV
IECAKQKALE LEEFQYIGES QGYDIMEPAA KKCYLERENL RVTEPKDQCL ILLTWKRKLR
GGKRSACSRP ERQNQGSGEL S*

Position of stopcodon in wt / mu CDS

2766 / 2766

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

922 / 922

Position of stopcodon in wt / mu cDNA

2828 / 2828

Position of start ATG in wt / mu cDNA

63 / 63

Last intron/exon boundary

2696

Theoretical NMD boundary in CDS

2583

Length of CDS

2766

Coding sequence (CDS) position

1995

cDNA position

2057

gDNA position

72194

Chromosomal position

47475260

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:

2:47475260C>A_5_ENST00000645506

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed

Model: simple_aae
Tree vote: 95|5 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr2:47475260C>A (GRCh38)

Gene symbol

MSH2

Gene constraints

LOEUF: 0.66, LOF (oe): 0.51, misssense (oe): 1.24, synonymous (oe): 1.14 ? (gnomAD)

Ensembl transcript ID

ENST00000645506.1

Genbank transcript ID

NM_001406644 (by similarity), NM_001406651 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1995C>A
g.72194C>A

AA changes

AAE:	H665Q	?
Score:	24

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs1553368723
	Allele 'A' was not found in gnomAD

Protein conservation

Species	Match	AA	Alignment
Human		665	D	V	Y	F	E	K	D	K	Q	M	F	H	I	I	T	G	P	N	M	G	G	K	S	T
mutated	not conserved	665								K	Q	M	F	Q	I	I	T	G	P	N	M	G	G	K	S
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	8.655	1
	0.866	1
(flanking)	8.655	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

11

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

2

Strand

1

Original gDNA sequence snippet

AAAGATAAACAGATGTTCCACATCATTACTGGTAAAAAACC

Altered gDNA sequence snippet

AAAGATAAACAGATGTTCCAAATCATTACTGGTAAAAAACC

Original cDNA sequence snippet

AAAGATAAACAGATGTTCCACATCATTACTGGCCCCAATAT

Altered cDNA sequence snippet

AAAGATAAACAGATGTTCCAAATCATTACTGGCCCCAATAT

Wildtype AA sequence

MAVQPKETLQ LESAAEVGFV RFFQGMPEKP TTTVRLFDRG DFYTAHGEDA LLAAREVFKT
QGVIKYMGPA GAKNLQSVVL SKMNFESFVK DLLLVRQYRV EVYKNRAGNK ASKENDWYLA
YKASPGNLSQ FEDILFGNND MSASIGVVGV KMSAVDGQRQ VGVGYVDSIQ RKLGLCEFPD
NDQFSNLEAL LIQIGPKECV LPGGETAGDM GKLRQIIQRG GILITERKKA DFSTKDIYQD
LNRLLKGKKG EQMNSAVLPE MENQVAVSSL SAVIKFLELL SDDSNFGQFE LTTFDFSQYM
KLDIAAVRAL NLFQGSVEDT TGSQSLAALL NKCKTPQGQR LVNQWIKQPL MDKNRIEERL
NLVEAFVEDA ELRQTLQEDL LRRFPDLNRL AKKFQRQAAN LQDCYRLYQG INQLPNVIQA
LEKHEGKHQK LLLAVFVTPL TDLRSDFSKF QEMIETTLDM DQVENHEFLV KPSFDPNLSE
LREIMNDLEK KMQSTLISAA RDLGLDPGKQ IKLDSSAQFG YYFRVTCKEE KVLRNNKNFS
TVDIQKNGVK FTNSKLTSLN EEYTKNKTEY EEAQDAIVKE IVNISSGYVE PMQTLNDVLA
QLDAVVSFAH VSNGAPVPYV RPAILEKGQG RIILKASRHA CVEVQDEIAF IPNDVYFEKD
KQMFHIITGP NMGGKSTYIR QTGVIVLMAQ IGCFVPCESA EVSIVDCILA RVGAGDSQLK
GVSTFMAEML ETASILRSAT KDSLIIIDEL GRGTSTYDGF GLAWAISEYI ATKIGAFCMF
ATHFHELTAL ANQIPTVNNL HVTALTTEET LTMLYQVKKG VCDQSFGIHV AELANFPKHV
IECAKQKALE LEEFQYIGES QGYDIMEPAA KKCYLERENL RVTEPKDQCL ILLTWKRKLR
GGKRSACSRP ERQNQGSATP SASA*

Mutated AA sequence

MAVQPKETLQ LESAAEVGFV RFFQGMPEKP TTTVRLFDRG DFYTAHGEDA LLAAREVFKT
QGVIKYMGPA GAKNLQSVVL SKMNFESFVK DLLLVRQYRV EVYKNRAGNK ASKENDWYLA
YKASPGNLSQ FEDILFGNND MSASIGVVGV KMSAVDGQRQ VGVGYVDSIQ RKLGLCEFPD
NDQFSNLEAL LIQIGPKECV LPGGETAGDM GKLRQIIQRG GILITERKKA DFSTKDIYQD
LNRLLKGKKG EQMNSAVLPE MENQVAVSSL SAVIKFLELL SDDSNFGQFE LTTFDFSQYM
KLDIAAVRAL NLFQGSVEDT TGSQSLAALL NKCKTPQGQR LVNQWIKQPL MDKNRIEERL
NLVEAFVEDA ELRQTLQEDL LRRFPDLNRL AKKFQRQAAN LQDCYRLYQG INQLPNVIQA
LEKHEGKHQK LLLAVFVTPL TDLRSDFSKF QEMIETTLDM DQVENHEFLV KPSFDPNLSE
LREIMNDLEK KMQSTLISAA RDLGLDPGKQ IKLDSSAQFG YYFRVTCKEE KVLRNNKNFS
TVDIQKNGVK FTNSKLTSLN EEYTKNKTEY EEAQDAIVKE IVNISSGYVE PMQTLNDVLA
QLDAVVSFAH VSNGAPVPYV RPAILEKGQG RIILKASRHA CVEVQDEIAF IPNDVYFEKD
KQMFQIITGP NMGGKSTYIR QTGVIVLMAQ IGCFVPCESA EVSIVDCILA RVGAGDSQLK
GVSTFMAEML ETASILRSAT KDSLIIIDEL GRGTSTYDGF GLAWAISEYI ATKIGAFCMF
ATHFHELTAL ANQIPTVNNL HVTALTTEET LTMLYQVKKG VCDQSFGIHV AELANFPKHV
IECAKQKALE LEEFQYIGES QGYDIMEPAA KKCYLERENL RVTEPKDQCL ILLTWKRKLR
GGKRSACSRP ERQNQGSATP SASA*

Position of stopcodon in wt / mu CDS

2775 / 2775

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

925 / 925

Position of stopcodon in wt / mu cDNA

2848 / 2848

Position of start ATG in wt / mu cDNA

74 / 74

Last intron/exon boundary

2825

Theoretical NMD boundary in CDS

2701

Length of CDS

2775

Coding sequence (CDS) position

1995

cDNA position

2068

gDNA position

72194

Chromosomal position

47475260

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:

2:47475260C>A_2_ENST00000713919

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed

Model: simple_aae
Tree vote: 100|0 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr2:47475260C>A (GRCh38)

Gene symbol

MSH2

Gene constraints

no data

Ensembl transcript ID

ENST00000713919.1

Genbank transcript ID

NM_001406660 (by similarity), NM_001406661 (by similarity), NM_001406662 (by similarity), NM_001406659 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1716C>A
g.72194C>A

AA changes

AAE:	H572Q	?
Score:	24

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs1553368723
	Allele 'A' was not found in gnomAD

Protein conservation

Species	Match	AA	Alignment
Human		572	D	V	Y	F	E	K	D	K	Q	M	F	H	I	I	T	G	P	N	M	G	G	K	S	T
mutated	not conserved	572	D	V	Y	F	E	K	D	K	Q	M	F	Q	I	I	T	G	P	N	M	G	G	K	S
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	8.655	1
	0.866	1
(flanking)	8.655	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

11

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

2

Strand

1

Original gDNA sequence snippet

AAAGATAAACAGATGTTCCACATCATTACTGGTAAAAAACC

Altered gDNA sequence snippet

AAAGATAAACAGATGTTCCAAATCATTACTGGTAAAAAACC

Original cDNA sequence snippet

AAAGATAAACAGATGTTCCACATCATTACTGGCCCCAATAT

Altered cDNA sequence snippet

AAAGATAAACAGATGTTCCAAATCATTACTGGCCCCAATAT

Wildtype AA sequence

MAVQPKETLQ LESAAEVGFV RFFQGMPEKP TTTVRLFDRG DFYTAHGEDA LLAAREVFKT
QGVIKYMGPA GAKNLQSVVL SKMNFESFVK DLLLVRQYRV EVYKNRAGNK ASKENDWYLA
YKIIQRGGIL ITERKKADFS TKDIYQDLNR LLKGKKGEQM NSAVLPEMEN QVAVSSLSAV
IKFLELLSDD SNFGQFELTT FDFSQYMKLD IAAVRALNLF QGSVEDTTGS QSLAALLNKC
KTPQGQRLVN QWIKQPLMDK NRIEERLNLV EAFVEDAELR QTLQEDLLRR FPDLNRLAKK
FQRQAANLQD CYRLYQGINQ LPNVIQALEK HEGKHQKLLL AVFVTPLTDL RSDFSKFQEM
IETTLDMDQV ENHEFLVKPS FDPNLSELRE IMNDLEKKMQ STLISAARDL GLDPGKQIKL
DSSAQFGYYF RVTCKEEKVL RNNKNFSTVD IQKNGVKFTN SKLTSLNEEY TKNKTEYEEA
QDAIVKEIVN ISSGYVEPMQ TLNDVLAQLD AVVSFAHVSN GAPVPYVRPA ILEKGQGRII
LKASRHACVE VQDEIAFIPN DVYFEKDKQM FHIITGPNMG GKSTYIRQTG VIVLMAQIGC
FVPCESAEVS IVDCILARVG AGDSQLKGVS TFMAEMLETA SILRSATKDS LIIIDELGRG
TSTYDGFGLA WAISEYIATK IGAFCMFATH FHELTALANQ IPTVNNLHVT ALTTEETLTM
LYQVKKGVCD QSFGIHVAEL ANFPKHVIEC AKQKALELEE FQYIGESQGY DIMEPAAKKC
YLEREQGEKI IQEFLSKVKQ MPFTEMSEEN ITIKLKQLKA EVIAKNNSFV NEIISRIKVT
T*

Mutated AA sequence

MAVQPKETLQ LESAAEVGFV RFFQGMPEKP TTTVRLFDRG DFYTAHGEDA LLAAREVFKT
QGVIKYMGPA GAKNLQSVVL SKMNFESFVK DLLLVRQYRV EVYKNRAGNK ASKENDWYLA
YKIIQRGGIL ITERKKADFS TKDIYQDLNR LLKGKKGEQM NSAVLPEMEN QVAVSSLSAV
IKFLELLSDD SNFGQFELTT FDFSQYMKLD IAAVRALNLF QGSVEDTTGS QSLAALLNKC
KTPQGQRLVN QWIKQPLMDK NRIEERLNLV EAFVEDAELR QTLQEDLLRR FPDLNRLAKK
FQRQAANLQD CYRLYQGINQ LPNVIQALEK HEGKHQKLLL AVFVTPLTDL RSDFSKFQEM
IETTLDMDQV ENHEFLVKPS FDPNLSELRE IMNDLEKKMQ STLISAARDL GLDPGKQIKL
DSSAQFGYYF RVTCKEEKVL RNNKNFSTVD IQKNGVKFTN SKLTSLNEEY TKNKTEYEEA
QDAIVKEIVN ISSGYVEPMQ TLNDVLAQLD AVVSFAHVSN GAPVPYVRPA ILEKGQGRII
LKASRHACVE VQDEIAFIPN DVYFEKDKQM FQIITGPNMG GKSTYIRQTG VIVLMAQIGC
FVPCESAEVS IVDCILARVG AGDSQLKGVS TFMAEMLETA SILRSATKDS LIIIDELGRG
TSTYDGFGLA WAISEYIATK IGAFCMFATH FHELTALANQ IPTVNNLHVT ALTTEETLTM
LYQVKKGVCD QSFGIHVAEL ANFPKHVIEC AKQKALELEE FQYIGESQGY DIMEPAAKKC
YLEREQGEKI IQEFLSKVKQ MPFTEMSEEN ITIKLKQLKA EVIAKNNSFV NEIISRIKVT
T*

Position of stopcodon in wt / mu CDS

2526 / 2526

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

842 / 842

Position of stopcodon in wt / mu cDNA

2551 / 2551

Position of start ATG in wt / mu cDNA

26 / 26

Last intron/exon boundary

2380

Theoretical NMD boundary in CDS

2304

Length of CDS

2526

Coding sequence (CDS) position

1716

cDNA position

1741

gDNA position

72194

Chromosomal position

47475260

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:

2:47475260C>A_4_ENST00000713854

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed

Model: simple_aae
Tree vote: 100|0 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr2:47475260C>A (GRCh38)

Gene symbol

MSH2

Gene constraints

no data

Ensembl transcript ID

ENST00000713854.1

Genbank transcript ID

NM_001406649 (by similarity), NM_001406658 (by similarity), NM_001406650 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1845C>A
g.72194C>A

AA changes

AAE:	H615Q	?
Score:	24

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs1553368723
	Allele 'A' was not found in gnomAD

Protein conservation

Species	Match	AA	Alignment
Human		615	D	V	Y	F	E	K	D	K	Q	M	F	H	I	I	T	G	P	N	M	G	G	K	S	T
mutated	not conserved	615	D	V	Y	F	E	K	D	K	Q	M	F	Q	I	I	T	G	P	N	M	G	G	K	S
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	8.655	1
	0.866	1
(flanking)	8.655	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

11

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

2

Strand

1

Original gDNA sequence snippet

AAAGATAAACAGATGTTCCACATCATTACTGGTAAAAAACC

Altered gDNA sequence snippet

AAAGATAAACAGATGTTCCAAATCATTACTGGTAAAAAACC

Original cDNA sequence snippet

AAAGATAAACAGATGTTCCACATCATTACTGGCCCCAATAT

Altered cDNA sequence snippet

AAAGATAAACAGATGTTCCAAATCATTACTGGCCCCAATAT

Wildtype AA sequence

MAVQPKETLQ LESAAEVGFV RFFQGMPEKP TTTVRLFDRG DFYTAHGEDA LLAAREVFKT
QGVIKYMGPA GAKNLQSVVL SKMNFESFVK DLLLVRQYRV EVYKNRAGNK ASKENDWYLA
YKASPGNLSQ FEDILFGNND MSASIGVVGV KMSAVDGQRQ VGVGYVDSIQ RKLGLCEFPD
NDQFSNLEAL LIQIGPKECV LPGGETAGDM GKLRQIIQRG GILITERKKA DFSTKDIYQD
LNRLLKGKKG EQMNSAVLPE MENQGSVEDT TGSQSLAALL NKCKTPQGQR LVNQWIKQPL
MDKNRIEERL NLVEAFVEDA ELRQTLQEDL LRRFPDLNRL AKKFQRQAAN LQDCYRLYQG
INQLPNVIQA LEKHEGKHQK LLLAVFVTPL TDLRSDFSKF QEMIETTLDM DQVENHEFLV
KPSFDPNLSE LREIMNDLEK KMQSTLISAA RDLGLDPGKQ IKLDSSAQFG YYFRVTCKEE
KVLRNNKNFS TVDIQKNGVK FTNSKLTSLN EEYTKNKTEY EEAQDAIVKE IVNISSGYVE
PMQTLNDVLA QLDAVVSFAH VSNGAPVPYV RPAILEKGQG RIILKASRHA CVEVQDEIAF
IPNDVYFEKD KQMFHIITGP NMGGKSTYIR QTGVIVLMAQ IGCFVPCESA EVSIVDCILA
RVGAGDSQLK GVSTFMAEML ETASILRSAT KDSLIIIDEL GRGTSTYDGF GLAWAISEYI
ATKIGAFCMF ATHFHELTAL ANQIPTVNNL HVTALTTEET LTMLYQVKKG VCDQSFGIHV
AELANFPKHV IECAKQKALE LEEFQYIGES QGYDIMEPAA KKCYLEREQG EKIIQEFLSK
VKQMPFTEMS EENITIKLKQ LKAEVIAKNN SFVNEIISRI KVTT*

Mutated AA sequence

MAVQPKETLQ LESAAEVGFV RFFQGMPEKP TTTVRLFDRG DFYTAHGEDA LLAAREVFKT
QGVIKYMGPA GAKNLQSVVL SKMNFESFVK DLLLVRQYRV EVYKNRAGNK ASKENDWYLA
YKASPGNLSQ FEDILFGNND MSASIGVVGV KMSAVDGQRQ VGVGYVDSIQ RKLGLCEFPD
NDQFSNLEAL LIQIGPKECV LPGGETAGDM GKLRQIIQRG GILITERKKA DFSTKDIYQD
LNRLLKGKKG EQMNSAVLPE MENQGSVEDT TGSQSLAALL NKCKTPQGQR LVNQWIKQPL
MDKNRIEERL NLVEAFVEDA ELRQTLQEDL LRRFPDLNRL AKKFQRQAAN LQDCYRLYQG
INQLPNVIQA LEKHEGKHQK LLLAVFVTPL TDLRSDFSKF QEMIETTLDM DQVENHEFLV
KPSFDPNLSE LREIMNDLEK KMQSTLISAA RDLGLDPGKQ IKLDSSAQFG YYFRVTCKEE
KVLRNNKNFS TVDIQKNGVK FTNSKLTSLN EEYTKNKTEY EEAQDAIVKE IVNISSGYVE
PMQTLNDVLA QLDAVVSFAH VSNGAPVPYV RPAILEKGQG RIILKASRHA CVEVQDEIAF
IPNDVYFEKD KQMFQIITGP NMGGKSTYIR QTGVIVLMAQ IGCFVPCESA EVSIVDCILA
RVGAGDSQLK GVSTFMAEML ETASILRSAT KDSLIIIDEL GRGTSTYDGF GLAWAISEYI
ATKIGAFCMF ATHFHELTAL ANQIPTVNNL HVTALTTEET LTMLYQVKKG VCDQSFGIHV
AELANFPKHV IECAKQKALE LEEFQYIGES QGYDIMEPAA KKCYLEREQG EKIIQEFLSK
VKQMPFTEMS EENITIKLKQ LKAEVIAKNN SFVNEIISRI KVTT*

Position of stopcodon in wt / mu CDS

2655 / 2655

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

885 / 885

Position of stopcodon in wt / mu cDNA

2717 / 2717

Position of start ATG in wt / mu cDNA

63 / 63

Last intron/exon boundary

2546

Theoretical NMD boundary in CDS

2433

Length of CDS

2655

Coding sequence (CDS) position

1845

cDNA position

1907

gDNA position

72194

Chromosomal position

47475260

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