MutationT@ster 2025

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Input seems to be ok - now mapping the variant to the different transcripts...
Querying Taster for transcript #1: ENST00000366577
Querying Taster for transcript #2: ENST00000674797
Querying Taster for transcript #3: ENST00000535889
Querying Taster for transcript #4: ENST00000681102
Querying Taster for transcript #5: ENST00000679842
Querying Taster for transcript #6: ENST00000681177
MT speed 0.55 s - this script 3.062419 s

Transcript summary:

Permalink

Transcript	Gene symbol	Prediction	Tree vote	Model	Splice site change	Variant type	Protein length	Features at a glance
ENST00000366577(MANE Select)	MTR	Benign	93\|7	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Homozygous in gnomAD Protein features (might be) affected
ENST00000679842	MTR	Benign	95\|5	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Homozygous in gnomAD
ENST00000674797	MTR	Benign	96\|4	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Homozygous in gnomAD
ENST00000681102	MTR	Benign	96\|4	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Homozygous in gnomAD
ENST00000681177	MTR	Benign	96\|4	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Homozygous in gnomAD
ENST00000535889	MTR	Benign	97\|3	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Homozygous in gnomAD Protein features (might be) affected

MutationT@ster 2025

Variant:

1:236885200A>G_1_ENST00000366577

Back to summary table

Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Homozygous in gnomAD
Protein features (might be) affected

Model: simple_aae
Tree vote: 93|7 (del | benign) ?
Automatic classification due to gnomAD,
tree vote conflicts with the automatic classification ?

Analysed issue

Analysis result

Variant

Chr1:236885200A>G (GRCh38)

Gene symbol

MTR

Gene constraints

LOEUF: 0.62, LOF (oe): 0.52, misssense (oe): 0.77, synonymous (oe): 0.97 ? (gnomAD)

Ensembl transcript ID

ENST00000366577.10

Genbank transcript ID

NM_000254 (exact from MANE)

UniProt / AlphaMissense peptide

METH_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.2756A>G
g.89941A>G

AA changes

AAE:	D919G	?
Score:	94

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs1805087
gnomAD	homozygous (G/G)	heterozygous	allele carriers
	>32000	>32000	>32000

Protein conservation

Species	Match	AA	Alignment
Human		919	E	I	M	E	E	Y	E	D	I	R	Q	D	H	Y	E	S	L	K	E	R	R	Y	L	P
mutated	not conserved	919	E	I	M	E	E	Y	E	D	I	R	Q	G	H	Y	E	S	L	K	E	R	R	Y	L
Ptroglodytes	all identical	921	E	I	M	E	E	Y	E	D	I	R	Q	D	H	Y	E	S	L	K	E	R	R	Y	L
Mmulatta	all identical	919	E	I	M	E	E	Y	E	D	I	R	Q	D	H	Y	E	S	L	K	E	R	R	Y	L
Fcatus	all identical	868	E	I	L	E	E	Y	E	E	I	R	Q	D	H	Y	E	S	L	R	E	R	R	Y	L
Mmusculus	all identical	907						Y	E	D	I	R	Q	D	H	Y	E	S	L	K	E	R	K	Y	V
Ggallus	all conserved	921	E	I	L	E	E	Y	E	E	I	R	Q	E	H	Y	E	S	L	K	E	R	R	Y	L
Trubripes	all conserved	933											Q	E	H	Y	D	S	L	K	A	R	H	Y	L
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	all conserved	909						Y	E	D	V	R	Q	E	H	Y	A	S	L	K	D	R	R	F	T
Xtropicalis	all identical	919	E	I	T	E	E	Y	E	D	I	R	Q	D	H	Y	E	S	L	R	E	R	R	Y	L

Protein features

Start (aa)	End (aa)	Feature	Details
1	1265	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	9.16	1
	8.536	1
(flanking)	-0.422	0.378

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

20

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

1

Strand

1

Original gDNA sequence snippet

ATATGAAGATATTAGACAGGACCATTATGAGTCTCTCAAGG

Altered gDNA sequence snippet

ATATGAAGATATTAGACAGGGCCATTATGAGTCTCTCAAGG

Original cDNA sequence snippet

ATATGAAGATATTAGACAGGACCATTATGAGTCTCTCAAGG

Altered cDNA sequence snippet

ATATGAAGATATTAGACAGGGCCATTATGAGTCTCTCAAGG

Wildtype AA sequence

MSPALQDLSQ PEGLKKTLRD EINAILQKRI MVLDGGMGTM IQREKLNEEH FRGQEFKDHA
RPLKGNNDIL SITQPDVIYQ IHKEYLLAGA DIIETNTFSS TSIAQADYGL EHLAYRMNMC
SAGVARKAAE EVTLQTGIKR FVAGALGPTN KTLSVSPSVE RPDYRNITFD ELVEAYQEQA
KGLLDGGVDI LLIETIFDTA NAKAALFALQ NLFEEKYAPR PIFISGTIVD KSGRTLSGQT
GEGFVISVSH GEPLCIGLNC ALGAAEMRPF IEIIGKCTTA YVLCYPNAGL PNTFGDYDET
PSMMAKHLKD FAMDGLVNIV GGCCGSTPDH IREIAEAVKN CKPRVPPATA FEGHMLLSGL
EPFRIGPYTN FVNIGERCNV AGSRKFAKLI MAGNYEEALC VAKVQVEMGA QVLDVNMDDG
MLDGPSAMTR FCNLIASEPD IAKVPLCIDS SNFAVIEAGL KCCQGKCIVN SISLKEGEDD
FLEKARKIKK YGAAMVVMAF DEEGQATETD TKIRVCTRAY HLLVKKLGFN PNDIIFDPNI
LTIGTGMEEH NLYAINFIHA TKVIKETLPG ARISGGLSNL SFSFRGMEAI REAMHGVFLY
HAIKSGMDMG IVNAGNLPVY DDIHKELLQL CEDLIWNKDP EATEKLLRYA QTQGTGGKKV
IQTDEWRNGP VEERLEYALV KGIEKHIIED TEEARLNQKK YPRPLNIIEG PLMNGMKIVG
DLFGAGKMFL PQVIKSARVM KKAVGHLIPF MEKEREETRV LNGTVEEEDP YQGTIVLATV
KGDVHDIGKN IVGVVLGCNN FRVIDLGVMT PCDKILKAAL DHKADIIGLS GLITPSLDEM
IFVAKEMERL AIRIPLLIGG ATTSKTHTAV KIAPRYSAPV IHVLDASKSV VVCSQLLDEN
LKDEYFEEIM EEYEDIRQDH YESLKERRYL PLSQARKSGF QMDWLSEPHP VKPTFIGTQV
FEDYDLQKLV DYIDWKPFFD VWQLRGKYPN RGFPKIFNDK TVGGEARKVY DDAHNMLNTL
ISQKKLRARG VVGFWPAQSI QDDIHLYAEA AVPQAAEPIA TFYGLRQQAE KDSASTEPYY
CLSDFIAPLH SGIRDYLGLF AVACFGVEEL SKAYEDDGDD YSSIMVKALG DRLAEAFAEE
LHERVRRELW AYCGSEQLDV ADLRRLRYKG IRPAPGYPSQ PDHTEKLTMW RLADIEQSTG
IRLTESLAMA PASAVSGLYF SNLKSKYFAV GKISKDQVED YALRKNISVA EVEKWLGPIL
GYDTD*

Mutated AA sequence

MSPALQDLSQ PEGLKKTLRD EINAILQKRI MVLDGGMGTM IQREKLNEEH FRGQEFKDHA
RPLKGNNDIL SITQPDVIYQ IHKEYLLAGA DIIETNTFSS TSIAQADYGL EHLAYRMNMC
SAGVARKAAE EVTLQTGIKR FVAGALGPTN KTLSVSPSVE RPDYRNITFD ELVEAYQEQA
KGLLDGGVDI LLIETIFDTA NAKAALFALQ NLFEEKYAPR PIFISGTIVD KSGRTLSGQT
GEGFVISVSH GEPLCIGLNC ALGAAEMRPF IEIIGKCTTA YVLCYPNAGL PNTFGDYDET
PSMMAKHLKD FAMDGLVNIV GGCCGSTPDH IREIAEAVKN CKPRVPPATA FEGHMLLSGL
EPFRIGPYTN FVNIGERCNV AGSRKFAKLI MAGNYEEALC VAKVQVEMGA QVLDVNMDDG
MLDGPSAMTR FCNLIASEPD IAKVPLCIDS SNFAVIEAGL KCCQGKCIVN SISLKEGEDD
FLEKARKIKK YGAAMVVMAF DEEGQATETD TKIRVCTRAY HLLVKKLGFN PNDIIFDPNI
LTIGTGMEEH NLYAINFIHA TKVIKETLPG ARISGGLSNL SFSFRGMEAI REAMHGVFLY
HAIKSGMDMG IVNAGNLPVY DDIHKELLQL CEDLIWNKDP EATEKLLRYA QTQGTGGKKV
IQTDEWRNGP VEERLEYALV KGIEKHIIED TEEARLNQKK YPRPLNIIEG PLMNGMKIVG
DLFGAGKMFL PQVIKSARVM KKAVGHLIPF MEKEREETRV LNGTVEEEDP YQGTIVLATV
KGDVHDIGKN IVGVVLGCNN FRVIDLGVMT PCDKILKAAL DHKADIIGLS GLITPSLDEM
IFVAKEMERL AIRIPLLIGG ATTSKTHTAV KIAPRYSAPV IHVLDASKSV VVCSQLLDEN
LKDEYFEEIM EEYEDIRQGH YESLKERRYL PLSQARKSGF QMDWLSEPHP VKPTFIGTQV
FEDYDLQKLV DYIDWKPFFD VWQLRGKYPN RGFPKIFNDK TVGGEARKVY DDAHNMLNTL
ISQKKLRARG VVGFWPAQSI QDDIHLYAEA AVPQAAEPIA TFYGLRQQAE KDSASTEPYY
CLSDFIAPLH SGIRDYLGLF AVACFGVEEL SKAYEDDGDD YSSIMVKALG DRLAEAFAEE
LHERVRRELW AYCGSEQLDV ADLRRLRYKG IRPAPGYPSQ PDHTEKLTMW RLADIEQSTG
IRLTESLAMA PASAVSGLYF SNLKSKYFAV GKISKDQVED YALRKNISVA EVEKWLGPIL
GYDTD*

Position of stopcodon in wt / mu CDS

3798 / 3798

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

1266 / 1266

Position of stopcodon in wt / mu cDNA

4210 / 4210

Position of start ATG in wt / mu cDNA

413 / 413

Last intron/exon boundary

4123

Theoretical NMD boundary in CDS

3660

Length of CDS

3798

Coding sequence (CDS) position

2756

cDNA position

3168

gDNA position

89941

Chromosomal position

236885200

Speed

0.06 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

MutationT@ster 2025

Variant:

1:236885200A>G_5_ENST00000679842

Back to summary table

Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Homozygous in gnomAD

Model: simple_aae
Tree vote: 95|5 (del | benign) ?
Automatic classification due to gnomAD,
tree vote conflicts with the automatic classification ?

Analysed issue

Analysis result

Variant

Chr1:236885200A>G (GRCh38)

Gene symbol

MTR

Gene constraints

LOEUF: 0.61, LOF (oe): 0.50, misssense (oe): 0.77, synonymous (oe): 0.97 ? (gnomAD)

Ensembl transcript ID

ENST00000679842.1

Genbank transcript ID

NM_001410942 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.2567A>G
g.89941A>G

AA changes

AAE:	D856G	?
Score:	94

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs1805087
gnomAD	homozygous (G/G)	heterozygous	allele carriers
	>32000	>32000	>32000

Protein conservation

Species	Match	AA	Alignment
Human		856	E	I	M	E	E	Y	E	D	I	R	Q	D	H	Y	E	S	L	K	E	R	R	Y	L	P
mutated	not conserved	856	E	I	M	E	E	Y	E	D	I	R	Q	G	H	Y	E	S	L	K	E	R	R	Y	L
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	9.16	1
	8.536	1
(flanking)	-0.422	0.378

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

20

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

1

Strand

1

Original gDNA sequence snippet

ATATGAAGATATTAGACAGGACCATTATGAGTCTCTCAAGG

Altered gDNA sequence snippet

ATATGAAGATATTAGACAGGGCCATTATGAGTCTCTCAAGG

Original cDNA sequence snippet

ATATGAAGATATTAGACAGGACCATTATGAGTCTCTCAAGG

Altered cDNA sequence snippet

ATATGAAGATATTAGACAGGGCCATTATGAGTCTCTCAAGG

Wildtype AA sequence

MSPALQDLSQ PEGLKKTLRD EINAILQKRI MVLDGGMGTM IQREKLNEEH FRGQEFKDHA
RPLKGNNDIL SITQPDVIYQ IHKEYLLAGA DIIETNTFSS TSIAQADYGL EHLAYRMNMC
SAGVARKAAE EVTLQTGIKR FVAGALGPTN KTLSVSPSVE RPDYRNITFD ELVEAYQEQA
KGLLDGGVDI LLIETIFDTA NAKAALFALQ NLFEEKYAPR PIFISGTIVD KSGRTLSGQT
GEGFVISVSH GEPLCIGLNC ALGAAEMRPF IEIIGKCTTA YVLCYPNAGL PNTFGDYDET
PSMMAKHLKD FAMDGLVNIV GGCCGSTPDH IREIAEAVKN CKPRVPPATA FEGHMLLSGL
EPFRIGPYTN FVNIGERCNV AGSRKFAKLI MAGNYEEALC VAKVQVEMGA QVLDVNMDDG
MLDGPSAMTR FCNLIASEPD IAKVPLCIDS SNFAVIEAGL KCCQGKCIVN SISLKEGEDD
FLEKARKIKK YGAAMVVMAF DEEGQATETD TKIRVCTRAY HLLVKKLGFN PNDIIFDPNI
LTIGTGMEEH NLYAINFIHA TKVIKETLPG ARISGGLSNL SFSFRGMEAI REAMHGVFLY
HAIKSGMDMG IVNAGNLPVY DDIHKELLQL CEDLIWNKDP EATEKLLRYA QTQGTGGKKV
IQTDEWRNGP VEERLEYALV KGIEKHIIED TEEARLNQKK YPRPLNIIEG PLMNGMKIVG
DLFGAGKMFL PQVIKSARVM KKAVGHLIPF MEKEREETRV LNGTVEEEDP YQGTIVLATV
KGDVHDIGKN IVGVVLGCNN FRTHTAVKIA PRYSAPVIHV LDASKSVVVC SQLLDENLKD
EYFEEIMEEY EDIRQDHYES LKERRYLPLS QARKSGFQMD WLSEPHPVKP TFIGTQVFED
YDLQKLVDYI DWKPFFDVWQ LRGKYPNRGF PKIFNDKTVG GEARKVYDDA HNMLNTLISQ
KKLRARGVVG FWPAQSIQDD IHLYAEAAVP QAAEPIATFY GLRQQAEKDS ASTEPYYCLS
DFIAPLHSGI RDYLGLFAVA CFGVEELSKA YEDDGDDYSS IMVKALGDRL AEAFAEELHE
RVRRELWAYC GSEQLDVADL RRLRYKGIRP APGYPSQPDH TEKLTMWRLA DIEQSTGIRL
TESLAMAPAS AVSGLYFSNL KSKYFAVGKI SKDQVEDYAL RKNISVAEVE KWLGPILGYD
TD*

Mutated AA sequence

MSPALQDLSQ PEGLKKTLRD EINAILQKRI MVLDGGMGTM IQREKLNEEH FRGQEFKDHA
RPLKGNNDIL SITQPDVIYQ IHKEYLLAGA DIIETNTFSS TSIAQADYGL EHLAYRMNMC
SAGVARKAAE EVTLQTGIKR FVAGALGPTN KTLSVSPSVE RPDYRNITFD ELVEAYQEQA
KGLLDGGVDI LLIETIFDTA NAKAALFALQ NLFEEKYAPR PIFISGTIVD KSGRTLSGQT
GEGFVISVSH GEPLCIGLNC ALGAAEMRPF IEIIGKCTTA YVLCYPNAGL PNTFGDYDET
PSMMAKHLKD FAMDGLVNIV GGCCGSTPDH IREIAEAVKN CKPRVPPATA FEGHMLLSGL
EPFRIGPYTN FVNIGERCNV AGSRKFAKLI MAGNYEEALC VAKVQVEMGA QVLDVNMDDG
MLDGPSAMTR FCNLIASEPD IAKVPLCIDS SNFAVIEAGL KCCQGKCIVN SISLKEGEDD
FLEKARKIKK YGAAMVVMAF DEEGQATETD TKIRVCTRAY HLLVKKLGFN PNDIIFDPNI
LTIGTGMEEH NLYAINFIHA TKVIKETLPG ARISGGLSNL SFSFRGMEAI REAMHGVFLY
HAIKSGMDMG IVNAGNLPVY DDIHKELLQL CEDLIWNKDP EATEKLLRYA QTQGTGGKKV
IQTDEWRNGP VEERLEYALV KGIEKHIIED TEEARLNQKK YPRPLNIIEG PLMNGMKIVG
DLFGAGKMFL PQVIKSARVM KKAVGHLIPF MEKEREETRV LNGTVEEEDP YQGTIVLATV
KGDVHDIGKN IVGVVLGCNN FRTHTAVKIA PRYSAPVIHV LDASKSVVVC SQLLDENLKD
EYFEEIMEEY EDIRQGHYES LKERRYLPLS QARKSGFQMD WLSEPHPVKP TFIGTQVFED
YDLQKLVDYI DWKPFFDVWQ LRGKYPNRGF PKIFNDKTVG GEARKVYDDA HNMLNTLISQ
KKLRARGVVG FWPAQSIQDD IHLYAEAAVP QAAEPIATFY GLRQQAEKDS ASTEPYYCLS
DFIAPLHSGI RDYLGLFAVA CFGVEELSKA YEDDGDDYSS IMVKALGDRL AEAFAEELHE
RVRRELWAYC GSEQLDVADL RRLRYKGIRP APGYPSQPDH TEKLTMWRLA DIEQSTGIRL
TESLAMAPAS AVSGLYFSNL KSKYFAVGKI SKDQVEDYAL RKNISVAEVE KWLGPILGYD
TD*

Position of stopcodon in wt / mu CDS

3609 / 3609

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

1203 / 1203

Position of stopcodon in wt / mu cDNA

3609 / 3609

Position of start ATG in wt / mu cDNA

1 / 1

Last intron/exon boundary

3522

Theoretical NMD boundary in CDS

3471

Length of CDS

3609

Coding sequence (CDS) position

2567

cDNA position

2567

gDNA position

89941

Chromosomal position

236885200

Speed

0.06 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

MutationT@ster 2025

Variant:

1:236885200A>G_2_ENST00000674797

Back to summary table

Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Homozygous in gnomAD

Model: simple_aae
Tree vote: 96|4 (del | benign) ?
Automatic classification due to gnomAD,
tree vote conflicts with the automatic classification ?

Analysed issue

Analysis result

Variant

Chr1:236885200A>G (GRCh38)

Gene symbol

MTR

Gene constraints

LOEUF: 0.64, LOF (oe): 0.52, misssense (oe): 0.76, synonymous (oe): 0.97 ? (gnomAD)

Ensembl transcript ID

ENST00000674797.2

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.2408A>G
g.89941A>G

AA changes

AAE:	D803G	?
Score:	94

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs1805087
gnomAD	homozygous (G/G)	heterozygous	allele carriers
	>32000	>32000	>32000

Protein conservation

Species	Match	AA	Alignment
Human		803	E	I	M	E	E	Y	E	D	I	R	Q	D	H	Y	E	S	L	K	E	R	R	Y	L	P
mutated	not conserved	803	E	I	M	E	E	Y	E	D	I	R	Q	G	H	Y	E	S	L	K	E	R	R	Y	L
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	9.16	1
	8.536	1
(flanking)	-0.422	0.378

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

20

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

1

Strand

1

Original gDNA sequence snippet

ATATGAAGATATTAGACAGGACCATTATGAGTCTCTCAAGG

Altered gDNA sequence snippet

ATATGAAGATATTAGACAGGGCCATTATGAGTCTCTCAAGG

Original cDNA sequence snippet

ATATGAAGATATTAGACAGGACCATTATGAGTCTCTCAAGG

Altered cDNA sequence snippet

ATATGAAGATATTAGACAGGGCCATTATGAGTCTCTCAAGG

Wildtype AA sequence

MNMCSAGVAR KAAEEVTLQT GIKRFVAGAL GPTNKTLSVS PSVERPDYRN ITFDELVEAY
QEQAKGLLDG GVDILLIETI FDTANAKAAL FALQNLFEEK YAPRPIFISG TIVDKSGRTL
SGQTGEGFVI SVSHGEPLCI GLNCALGAAE MRPFIEIIGK CTTAYVLCYP NAGLPNTFGD
YDETPSMMAK HLKDFAMDGL VNIVGGCCGS TPDHIREIAE AVKNCKPRVP PATAFEGHML
LSGLEPFRIG PYTNFVNIGE RCNVAGSRKF AKLIMAGNYE EALCVAKVQV EMGAQVLDVN
MDDGMLDGPS AMTRFCNLIA SEPDIAKVPL CIDSSNFAVI EAGLKCCQGK CIVNSISLKE
GEDDFLEKAR KIKKYGAAMV VMAFDEEGQA TETDTKIRVC TRAYHLLVKK LGFNPNDIIF
DPNILTIGTG MEEHNLYAIN FIHATKVIKE TLPGARISGG LSNLSFSFRG MEAIREAMHG
VFLYHAIKSG MDMGIVNAGN LPVYDDIHKE LLQLCEDLIW NKDPEATEKL LRYAQTQGTG
GKKVIQTDEW RNGPVEERLE YALVKGIEKH IIEDTEEARL NQKKYPRPLN IIEGPLMNGM
KIVGDLFGAG KMFLPQVIKS ARVMKKAVGH LIPFMEKERE ETRVLNGTVE EEDPYQGTIV
LATVKGDVHD IGKNIVGVVL GCNNFRVIDL GVMTPCDKIL KAALDHKADI IGLSGLITPS
LDEMIFVAKE MERLAIRIPL LIGGATTSKT HTAVKIAPRY SAPVIHVLDA SKSVVVCSQL
LDENLKDEYF EEIMEEYEDI RQDHYESLKE RRYLPLSQAR KSGFQMDWLS EPHPVKPTFI
GTQVFEDYDL QKLVDYIDWK PFFDVWQLRG KYPNRGFPKI FNDKTVGGEA RKVYDDAHNM
LNTLISQKKL RARGVVGFWP AQSIQDDIHL YAEAAVPQAA EPIATFYGLR QQAEKDSAST
EPYYCLSDFI APLHSGIRDY LGLFAVACFG VEELSKAYED DGDDYSSIMV KALGDRLAEA
FAEELHERVR RELWAYCGSE QLDVADLRRL RYKGIRPAPG YPSQPDHTEK LTMWRLADIE
QSTGIRLTES LAMAPASAVS GLYFSNLKSK YFAVGKISKD QVEDYALRKN ISVAEVEKWL
GPILGYDTD*

Mutated AA sequence

MNMCSAGVAR KAAEEVTLQT GIKRFVAGAL GPTNKTLSVS PSVERPDYRN ITFDELVEAY
QEQAKGLLDG GVDILLIETI FDTANAKAAL FALQNLFEEK YAPRPIFISG TIVDKSGRTL
SGQTGEGFVI SVSHGEPLCI GLNCALGAAE MRPFIEIIGK CTTAYVLCYP NAGLPNTFGD
YDETPSMMAK HLKDFAMDGL VNIVGGCCGS TPDHIREIAE AVKNCKPRVP PATAFEGHML
LSGLEPFRIG PYTNFVNIGE RCNVAGSRKF AKLIMAGNYE EALCVAKVQV EMGAQVLDVN
MDDGMLDGPS AMTRFCNLIA SEPDIAKVPL CIDSSNFAVI EAGLKCCQGK CIVNSISLKE
GEDDFLEKAR KIKKYGAAMV VMAFDEEGQA TETDTKIRVC TRAYHLLVKK LGFNPNDIIF
DPNILTIGTG MEEHNLYAIN FIHATKVIKE TLPGARISGG LSNLSFSFRG MEAIREAMHG
VFLYHAIKSG MDMGIVNAGN LPVYDDIHKE LLQLCEDLIW NKDPEATEKL LRYAQTQGTG
GKKVIQTDEW RNGPVEERLE YALVKGIEKH IIEDTEEARL NQKKYPRPLN IIEGPLMNGM
KIVGDLFGAG KMFLPQVIKS ARVMKKAVGH LIPFMEKERE ETRVLNGTVE EEDPYQGTIV
LATVKGDVHD IGKNIVGVVL GCNNFRVIDL GVMTPCDKIL KAALDHKADI IGLSGLITPS
LDEMIFVAKE MERLAIRIPL LIGGATTSKT HTAVKIAPRY SAPVIHVLDA SKSVVVCSQL
LDENLKDEYF EEIMEEYEDI RQGHYESLKE RRYLPLSQAR KSGFQMDWLS EPHPVKPTFI
GTQVFEDYDL QKLVDYIDWK PFFDVWQLRG KYPNRGFPKI FNDKTVGGEA RKVYDDAHNM
LNTLISQKKL RARGVVGFWP AQSIQDDIHL YAEAAVPQAA EPIATFYGLR QQAEKDSAST
EPYYCLSDFI APLHSGIRDY LGLFAVACFG VEELSKAYED DGDDYSSIMV KALGDRLAEA
FAEELHERVR RELWAYCGSE QLDVADLRRL RYKGIRPAPG YPSQPDHTEK LTMWRLADIE
QSTGIRLTES LAMAPASAVS GLYFSNLKSK YFAVGKISKD QVEDYALRKN ISVAEVEKWL
GPILGYDTD*

Position of stopcodon in wt / mu CDS

3450 / 3450

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

1150 / 1150

Position of stopcodon in wt / mu cDNA

3995 / 3995

Position of start ATG in wt / mu cDNA

546 / 546

Last intron/exon boundary

3908

Theoretical NMD boundary in CDS

3312

Length of CDS

3450

Coding sequence (CDS) position

2408

cDNA position

2953

gDNA position

89941

Chromosomal position

236885200

Speed

0.06 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

MutationT@ster 2025

Variant:

1:236885200A>G_4_ENST00000681102

Back to summary table

Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Homozygous in gnomAD

Model: simple_aae
Tree vote: 96|4 (del | benign) ?
Automatic classification due to gnomAD,
tree vote conflicts with the automatic classification ?

Analysed issue

Analysis result

Variant

Chr1:236885200A>G (GRCh38)

Gene symbol

MTR

Gene constraints

LOEUF: 0.63, LOF (oe): 0.52, misssense (oe): 0.77, synonymous (oe): 0.97 ? (gnomAD)

Ensembl transcript ID

ENST00000681102.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.2576A>G
g.89941A>G

AA changes

AAE:	D859G	?
Score:	94

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs1805087
gnomAD	homozygous (G/G)	heterozygous	allele carriers
	>32000	>32000	>32000

Protein conservation

Species	Match	AA	Alignment
Human		859	E	I	M	E	E	Y	E	D	I	R	Q	D	H	Y	E	S	L	K	E	R	R	Y	L	P
mutated	not conserved	859	E	I	M	E	E	Y	E	D	I	R	Q	G	H	Y	E	S	L	K	E	R	R	Y	L
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	9.16	1
	8.536	1
(flanking)	-0.422	0.378

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

20

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

1

Strand

1

Original gDNA sequence snippet

ATATGAAGATATTAGACAGGACCATTATGAGTCTCTCAAGG

Altered gDNA sequence snippet

ATATGAAGATATTAGACAGGGCCATTATGAGTCTCTCAAGG

Original cDNA sequence snippet

ATATGAAGATATTAGACAGGACCATTATGAGTCTCTCAAGG

Altered cDNA sequence snippet

ATATGAAGATATTAGACAGGGCCATTATGAGTCTCTCAAGG

Wildtype AA sequence

MSPALQDLSQ PEGLKKTLRD EINAILQKRI MVLDGGMGTM IQREKLNEEH FRGQEFKDHA
RPLKGNNDIL SITQPDVIYQ IHKEYLLAGA DIIETNTFSS TSIAQADYGL EHLAYRMNMC
SAGVARKAAE EVTLQTGIKR FVAGALGPTN KTLSVSPSVE RPDYRNITFD ELVEAYQEQA
KGLLDGGVDI LLIETIFDTA NAKAALFALQ NLFEEKYAPR PIFISGTIVD KSGRTLSGQT
GEGFVISVSH GEPLCIGLNC ALGAAEMRPF IEIIGKCTTA YVLCYPNAGL PNTFGDYDET
PSMMAKHLKD FAMDGLVNIV GGCCGSTPDH IREIAEAVKN CKPRVPPATA FEGHMLLSGL
EPFRIGPYTN FVNIGERCNV AGSRKFAKLI MAGNYEEALC VAKVQVEMGA QVLDVNMDDG
MLDGPSAMTR FCNLIASEPD IAKVPLCIDS SNFAVIEAGL KCCQGKCIVN SISLKEGEDD
FLEKARKIKK YGAAMVVMAF DEEGQETLPG ARISGGLSNL SFSFRGMEAI REAMHGVFLY
HAIKSGMDMG IVNAGNLPVY DDIHKELLQL CEDLIWNKDP EATEKLLRYA QTQGTGGKKV
IQTDEWRNGP VEERLEYALV KGIEKHIIED TEEARLNQKK YPRPLNIIEG PLMNGMKIVG
DLFGAGKMFL PQVIKSARVM KKAVGHLIPF MEKEREETRV LNGTVEEEDP YQGTIVLATV
KGDVHDIGKN IVGVVLGCNN FRVIDLGVMT PCDKILKAAL DHKADIIGLS GLITPSLDEM
IFVAKEMERL AIRIPLLIGG ATTSKTHTAV KIAPRYSAPV IHVLDASKSV VVCSQLLDEN
LKDEYFEEIM EEYEDIRQDH YESLKERRYL PLSQARKSGF QMDWLSEPHP VKPTFIGTQV
FEDYDLQKLV DYIDWKPFFD VWQLRGKYPN RGFPKIFNDK TVGGEARKVY DDAHNMLNTL
ISQKKLRARG VVGFWPAQSI QDDIHLYAEA AVPQAAEPIA TFYGLRQQAE KDSASTEPYY
CLSDFIAPLH SGIRDYLGLF AVACFGVEEL SKAYEDDGDD YSSIMVKALG DRLAEAFAEE
LHERVRRELW AYCGSEQLDV ADLRRLRYKG IRPAPGYPSQ PDHTEKLTMW RLADIEQSTG
IRLTESLAMA PASAVSGLYF SNLKSKYFAV GKISKDQVED YALRKNISVA EVEKWLGPIL
GYDTD*

Mutated AA sequence

MSPALQDLSQ PEGLKKTLRD EINAILQKRI MVLDGGMGTM IQREKLNEEH FRGQEFKDHA
RPLKGNNDIL SITQPDVIYQ IHKEYLLAGA DIIETNTFSS TSIAQADYGL EHLAYRMNMC
SAGVARKAAE EVTLQTGIKR FVAGALGPTN KTLSVSPSVE RPDYRNITFD ELVEAYQEQA
KGLLDGGVDI LLIETIFDTA NAKAALFALQ NLFEEKYAPR PIFISGTIVD KSGRTLSGQT
GEGFVISVSH GEPLCIGLNC ALGAAEMRPF IEIIGKCTTA YVLCYPNAGL PNTFGDYDET
PSMMAKHLKD FAMDGLVNIV GGCCGSTPDH IREIAEAVKN CKPRVPPATA FEGHMLLSGL
EPFRIGPYTN FVNIGERCNV AGSRKFAKLI MAGNYEEALC VAKVQVEMGA QVLDVNMDDG
MLDGPSAMTR FCNLIASEPD IAKVPLCIDS SNFAVIEAGL KCCQGKCIVN SISLKEGEDD
FLEKARKIKK YGAAMVVMAF DEEGQETLPG ARISGGLSNL SFSFRGMEAI REAMHGVFLY
HAIKSGMDMG IVNAGNLPVY DDIHKELLQL CEDLIWNKDP EATEKLLRYA QTQGTGGKKV
IQTDEWRNGP VEERLEYALV KGIEKHIIED TEEARLNQKK YPRPLNIIEG PLMNGMKIVG
DLFGAGKMFL PQVIKSARVM KKAVGHLIPF MEKEREETRV LNGTVEEEDP YQGTIVLATV
KGDVHDIGKN IVGVVLGCNN FRVIDLGVMT PCDKILKAAL DHKADIIGLS GLITPSLDEM
IFVAKEMERL AIRIPLLIGG ATTSKTHTAV KIAPRYSAPV IHVLDASKSV VVCSQLLDEN
LKDEYFEEIM EEYEDIRQGH YESLKERRYL PLSQARKSGF QMDWLSEPHP VKPTFIGTQV
FEDYDLQKLV DYIDWKPFFD VWQLRGKYPN RGFPKIFNDK TVGGEARKVY DDAHNMLNTL
ISQKKLRARG VVGFWPAQSI QDDIHLYAEA AVPQAAEPIA TFYGLRQQAE KDSASTEPYY
CLSDFIAPLH SGIRDYLGLF AVACFGVEEL SKAYEDDGDD YSSIMVKALG DRLAEAFAEE
LHERVRRELW AYCGSEQLDV ADLRRLRYKG IRPAPGYPSQ PDHTEKLTMW RLADIEQSTG
IRLTESLAMA PASAVSGLYF SNLKSKYFAV GKISKDQVED YALRKNISVA EVEKWLGPIL
GYDTD*

Position of stopcodon in wt / mu CDS

3618 / 3618

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

1206 / 1206

Position of stopcodon in wt / mu cDNA

3618 / 3618

Position of start ATG in wt / mu cDNA

1 / 1

Last intron/exon boundary

3531

Theoretical NMD boundary in CDS

3480

Length of CDS

3618

Coding sequence (CDS) position

2576

cDNA position

2576

gDNA position

89941

Chromosomal position

236885200

Speed

0.12 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

MutationT@ster 2025

Variant:

1:236885200A>G_6_ENST00000681177

Back to summary table

Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Homozygous in gnomAD

Model: simple_aae
Tree vote: 96|4 (del | benign) ?
Automatic classification due to gnomAD,
tree vote conflicts with the automatic classification ?

Analysed issue

Analysis result

Variant

Chr1:236885200A>G (GRCh38)

Gene symbol

MTR

Gene constraints

LOEUF: 0.65, LOF (oe): 0.53, misssense (oe): 0.78, synonymous (oe): 0.96 ? (gnomAD)

Ensembl transcript ID

ENST00000681177.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.2318A>G
g.89941A>G

AA changes

AAE:	D773G	?
Score:	94

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs1805087
gnomAD	homozygous (G/G)	heterozygous	allele carriers
	>32000	>32000	>32000

Protein conservation

Species	Match	AA	Alignment
Human		773	E	I	M	E	E	Y	E	D	I	R	Q	D	H	Y	E	S	L	K	E	R	R	Y	L	P
mutated	not conserved	773	E	I	M	E	E	Y	E	D	I	R	Q	G	H	Y	E	S	L	K	E
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)	9.16	1
	8.536	1
(flanking)	-0.422	0.378

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

20

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

1

Strand

1

Original gDNA sequence snippet

ATATGAAGATATTAGACAGGACCATTATGAGTCTCTCAAGG

Altered gDNA sequence snippet

ATATGAAGATATTAGACAGGGCCATTATGAGTCTCTCAAGG

Original cDNA sequence snippet

ATATGAAGATATTAGACAGGACCATTATGAGTCTCTCAAGG

Altered cDNA sequence snippet

ATATGAAGATATTAGACAGGGCCATTATGAGTCTCTCAAGG

Wildtype AA sequence

MSPALQDLSQ PEGLKKTLRD EINAILQKRI MVLDGGMGTM IQREKLNEEH FRGQEFKDHA
RPLKGNNDIL SITQPDVIYQ IHKEYLLAGA DIIETNTFSS TSIAQADYGL EHLAYRMNMC
SAGVARKAAE EVTLQTGIKR FVAGALGPTN KTLSVSPSVE RPDYRNITFD ELVEAYQEQA
KGLLDGGVDI LLIETIFDTA NAKAALFALQ NLFEEKYAPR PIFISGTIVD KSGRTLSGQT
GEGFVISVSH GEPLCIGLNC ALGAAEMRPF IEIIGKCTTA YVLCYPNAGL PNTFGDYDET
PSMMAKHLKD FAMDGLVNIV GGCCGSTPDH IREIAEAVKN CKPRVPPATA FEGHMLLSGL
EPFRIGPYTN FVNIGERCNV AGSRKFAKLI MAGNYEEALC VAKVQVEMGA QVLDVNMDDG
MLDGPSAMTR FCNLIASEPD IAKVPLCIDS SNFAVIEAGL KCCQGKCIVN SISLKEGEDD
FLEKARKIKK YGAAMVVMAF DEEGQTQGTG GKKVIQTDEW RNGPVEERLE YALVKGIEKH
IIEDTEEARL NQKKYPRPLN IIEGPLMNGM KIVGDLFGAG KMFLPQVIKS ARVMKKAVGH
LIPFMEKERE ETRVLNGTVE EEDPYQGTIV LATVKGDVHD IGKNIVGVVL GCNNFRVIDL
GVMTPCDKIL KAALDHKADI IGLSGLITPS LDEMIFVAKE MERLAIRIPL LIGGATTSKT
HTAVKIAPRY SAPVIHVLDA SKSVVVCSQL LDENLKDEYF EEIMEEYEDI RQDHYESLKE
RRYLPLSQAR KSGFQMDWLS EPHPVKPTFI GTQVFEDYDL QKLVDYIDWK PFFDVWQLRG
KYPNRGFPKI FNDKTVGGEA RKVYDDAHNM LNTLISQKKL RARGVVGFWP AQSIQDDIHL
YAEAAVPQAA EPIATFYGLR QQAEKDSAST EPYYCLSDFI APLHSGIRDY LGLFAVACFG
VEELSKAYED DGDDYSSIMV KALGDRLAEA FAEELHERVR RELWAYCGSE QLDVADLRRL
RYKGIRPAPG YPSQPDHTEK LTMWRLADIE QSTGIRLTES LAMAPASAVS GLYFSNLKSK
YFAVGKISKD QVEDYALRKN ISVAEVEKWL GPILGYDTD*

Mutated AA sequence

MSPALQDLSQ PEGLKKTLRD EINAILQKRI MVLDGGMGTM IQREKLNEEH FRGQEFKDHA
RPLKGNNDIL SITQPDVIYQ IHKEYLLAGA DIIETNTFSS TSIAQADYGL EHLAYRMNMC
SAGVARKAAE EVTLQTGIKR FVAGALGPTN KTLSVSPSVE RPDYRNITFD ELVEAYQEQA
KGLLDGGVDI LLIETIFDTA NAKAALFALQ NLFEEKYAPR PIFISGTIVD KSGRTLSGQT
GEGFVISVSH GEPLCIGLNC ALGAAEMRPF IEIIGKCTTA YVLCYPNAGL PNTFGDYDET
PSMMAKHLKD FAMDGLVNIV GGCCGSTPDH IREIAEAVKN CKPRVPPATA FEGHMLLSGL
EPFRIGPYTN FVNIGERCNV AGSRKFAKLI MAGNYEEALC VAKVQVEMGA QVLDVNMDDG
MLDGPSAMTR FCNLIASEPD IAKVPLCIDS SNFAVIEAGL KCCQGKCIVN SISLKEGEDD
FLEKARKIKK YGAAMVVMAF DEEGQTQGTG GKKVIQTDEW RNGPVEERLE YALVKGIEKH
IIEDTEEARL NQKKYPRPLN IIEGPLMNGM KIVGDLFGAG KMFLPQVIKS ARVMKKAVGH
LIPFMEKERE ETRVLNGTVE EEDPYQGTIV LATVKGDVHD IGKNIVGVVL GCNNFRVIDL
GVMTPCDKIL KAALDHKADI IGLSGLITPS LDEMIFVAKE MERLAIRIPL LIGGATTSKT
HTAVKIAPRY SAPVIHVLDA SKSVVVCSQL LDENLKDEYF EEIMEEYEDI RQGHYESLKE
RRYLPLSQAR KSGFQMDWLS EPHPVKPTFI GTQVFEDYDL QKLVDYIDWK PFFDVWQLRG
KYPNRGFPKI FNDKTVGGEA RKVYDDAHNM LNTLISQKKL RARGVVGFWP AQSIQDDIHL
YAEAAVPQAA EPIATFYGLR QQAEKDSAST EPYYCLSDFI APLHSGIRDY LGLFAVACFG
VEELSKAYED DGDDYSSIMV KALGDRLAEA FAEELHERVR RELWAYCGSE QLDVADLRRL
RYKGIRPAPG YPSQPDHTEK LTMWRLADIE QSTGIRLTES LAMAPASAVS GLYFSNLKSK
YFAVGKISKD QVEDYALRKN ISVAEVEKWL GPILGYDTD*

Position of stopcodon in wt / mu CDS

3360 / 3360

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

1120 / 1120

Position of stopcodon in wt / mu cDNA

3360 / 3360

Position of start ATG in wt / mu cDNA

1 / 1

Last intron/exon boundary

3273

Theoretical NMD boundary in CDS

3222

Length of CDS

3360

Coding sequence (CDS) position

2318

cDNA position

2318

gDNA position

89941

Chromosomal position

236885200

Speed

0.12 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

MutationT@ster 2025

Variant:

1:236885200A>G_3_ENST00000535889

Back to summary table

Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Homozygous in gnomAD
Protein features (might be) affected

Model: simple_aae
Tree vote: 97|3 (del | benign) ?
Automatic classification due to gnomAD,
tree vote conflicts with the automatic classification ?

Analysed issue

Analysis result

Variant

Chr1:236885200A>G (GRCh38)

Gene symbol

MTR

Gene constraints

LOEUF: 0.63, LOF (oe): 0.52, misssense (oe): 0.78, synonymous (oe): 0.97 ? (gnomAD)

Ensembl transcript ID

ENST00000535889.6

Genbank transcript ID

NM_001291939 (by similarity)

UniProt / AlphaMissense peptide

METH_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.2603A>G
g.89941A>G

AA changes

AAE:	D868G	?
Score:	94

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs1805087
gnomAD	homozygous (G/G)	heterozygous	allele carriers
	>32000	>32000	>32000

Protein conservation

Species	Match	AA	Alignment
Human		868	E	I	M	E	E	Y	E	D	I	R	Q	D	H	Y	E	S	L	K	E	R	R	Y	L	P
mutated	not conserved	868	E	I	M	E	E	Y	E	D	I	R	Q	G	H	Y	E	S	L	K	E	R	R	Y	L
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

Start (aa)	End (aa)	Feature	Details
1	1265	CHAIN		lost
772	907	DOMAIN	B12-binding	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	9.16	1
	8.536	1
(flanking)	-0.422	0.378

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

20

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

1

Strand

1

Original gDNA sequence snippet

ATATGAAGATATTAGACAGGACCATTATGAGTCTCTCAAGG

Altered gDNA sequence snippet

ATATGAAGATATTAGACAGGGCCATTATGAGTCTCTCAAGG

Original cDNA sequence snippet

ATATGAAGATATTAGACAGGACCATTATGAGTCTCTCAAGG

Altered cDNA sequence snippet

ATATGAAGATATTAGACAGGGCCATTATGAGTCTCTCAAGG

Wildtype AA sequence

MSPALQDLSQ PEGLKKTLRD EINAILQKRI MVLDGGMGTM IQREKLNEEH FRGQEFKDHA
RPLKGNNDIL SITQPDVIYQ IHKEYLLAGA DIIETNTFSS TSIAQADYGL EHLAYRMNMC
SAGVARKAAE EVTLQTGIKR FVAGALGPTN KTLSVSPSVE RPDYRNITFD ELVEAYQEQA
KGLLDGGVDI LLIETIFDTA NAKAALFALQ NLFEEKYAPR PIFISGTIVD KSGRTLSGQT
GEGFVISVSH GEPLCIGLNC ALGAAEMRPF IEIIGKCTTA YVLCYPNAGL PNTFGDYDET
PSMMAKHLKD FAMDGLVNIV GGCCGSTPDH IREIAEAVKN CKPRVPPATA FEGHMLLSGL
EPFRIGPYTN FVNIGERCNV AGSRKFAKLI MAGNYEEALC VAKVQVEMGA QVLDVNMDDG
MLDGPSAMTR FCNLIASEPD IAKVPLCIDS SNFAVIEAGL KCCQGKCIVN SISLKEGEDD
FLEKARKIKK YGAAMVVMAF DEEGQATETD TKIRVCTRAY HLLVKKLGFN PNDIIFDPNI
LTIGTGMEEH NLYAINFIHA TKVIKETLPG ARISGGLSNL SFSFRGMEAI REAMHGVFLY
HAIKSGMDMG IVNAGNLPVY DDIHKELLQL CEDLIWNKDP EATEKLLRYA QTQGTGGKKV
IQTDEWRNGP VEERLEYALV KVIKSARVMK KAVGHLIPFM EKEREETRVL NGTVEEEDPY
QGTIVLATVK GDVHDIGKNI VGVVLGCNNF RVIDLGVMTP CDKILKAALD HKADIIGLSG
LITPSLDEMI FVAKEMERLA IRIPLLIGGA TTSKTHTAVK IAPRYSAPVI HVLDASKSVV
VCSQLLDENL KDEYFEEIME EYEDIRQDHY ESLKERRYLP LSQARKSGFQ MDWLSEPHPV
KPTFIGTQVF EDYDLQKLVD YIDWKPFFDV WQLRGKYPNR GFPKIFNDKT VGGEARKVYD
DAHNMLNTLI SQKKLRARGV VGFWPAQSIQ DDIHLYAEAA VPQAAEPIAT FYGLRQQAEK
DSASTEPYYC LSDFIAPLHS GIRDYLGLFA VACFGVEELS KAYEDDGDDY SSIMVKALGD
RLAEAFAEEL HERVRRELWA YCGSEQLDVA DLRRLRYKGI RPAPGYPSQP DHTEKLTMWR
LADIEQSTGI RLTESLAMAP ASAVSGLYFS NLKSKYFAVG KISKDQVEDY ALRKNISVAE
VEKWLGPILG YDTD*

Mutated AA sequence

MSPALQDLSQ PEGLKKTLRD EINAILQKRI MVLDGGMGTM IQREKLNEEH FRGQEFKDHA
RPLKGNNDIL SITQPDVIYQ IHKEYLLAGA DIIETNTFSS TSIAQADYGL EHLAYRMNMC
SAGVARKAAE EVTLQTGIKR FVAGALGPTN KTLSVSPSVE RPDYRNITFD ELVEAYQEQA
KGLLDGGVDI LLIETIFDTA NAKAALFALQ NLFEEKYAPR PIFISGTIVD KSGRTLSGQT
GEGFVISVSH GEPLCIGLNC ALGAAEMRPF IEIIGKCTTA YVLCYPNAGL PNTFGDYDET
PSMMAKHLKD FAMDGLVNIV GGCCGSTPDH IREIAEAVKN CKPRVPPATA FEGHMLLSGL
EPFRIGPYTN FVNIGERCNV AGSRKFAKLI MAGNYEEALC VAKVQVEMGA QVLDVNMDDG
MLDGPSAMTR FCNLIASEPD IAKVPLCIDS SNFAVIEAGL KCCQGKCIVN SISLKEGEDD
FLEKARKIKK YGAAMVVMAF DEEGQATETD TKIRVCTRAY HLLVKKLGFN PNDIIFDPNI
LTIGTGMEEH NLYAINFIHA TKVIKETLPG ARISGGLSNL SFSFRGMEAI REAMHGVFLY
HAIKSGMDMG IVNAGNLPVY DDIHKELLQL CEDLIWNKDP EATEKLLRYA QTQGTGGKKV
IQTDEWRNGP VEERLEYALV KVIKSARVMK KAVGHLIPFM EKEREETRVL NGTVEEEDPY
QGTIVLATVK GDVHDIGKNI VGVVLGCNNF RVIDLGVMTP CDKILKAALD HKADIIGLSG
LITPSLDEMI FVAKEMERLA IRIPLLIGGA TTSKTHTAVK IAPRYSAPVI HVLDASKSVV
VCSQLLDENL KDEYFEEIME EYEDIRQGHY ESLKERRYLP LSQARKSGFQ MDWLSEPHPV
KPTFIGTQVF EDYDLQKLVD YIDWKPFFDV WQLRGKYPNR GFPKIFNDKT VGGEARKVYD
DAHNMLNTLI SQKKLRARGV VGFWPAQSIQ DDIHLYAEAA VPQAAEPIAT FYGLRQQAEK
DSASTEPYYC LSDFIAPLHS GIRDYLGLFA VACFGVEELS KAYEDDGDDY SSIMVKALGD
RLAEAFAEEL HERVRRELWA YCGSEQLDVA DLRRLRYKGI RPAPGYPSQP DHTEKLTMWR
LADIEQSTGI RLTESLAMAP ASAVSGLYFS NLKSKYFAVG KISKDQVEDY ALRKNISVAE
VEKWLGPILG YDTD*

Position of stopcodon in wt / mu CDS

3645 / 3645

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

1215 / 1215

Position of stopcodon in wt / mu cDNA

3667 / 3667

Position of start ATG in wt / mu cDNA

23 / 23

Last intron/exon boundary

3580

Theoretical NMD boundary in CDS

3507

Length of CDS

3645

Coding sequence (CDS) position

2603

cDNA position

2625

gDNA position

89941

Chromosomal position

236885200

Speed

0.13 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

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