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: ENST00000456935
Querying Taster for transcript #2: ENST00000221363
MT speed 0.65 s - this script 3.08253 s

Transcript summary:

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Transcript	Gene symbol	Prediction	Tree vote	Model	Prediction problem	Splice site change	Known ClinVar disease mutation	Potential ClinVar disease mutation	Amino acid changes	Variant type	dbSNP ID	Protein length	Features at a glance
ENST00000456935(MANE Select)	MAN2B1	Deleterious	73\|27	simple_aae		No				Single base exchange		Normal	Amino acid sequence changed Heterozygous in gnomAD Protein features (might be) affected
ENST00000221363	MAN2B1	Deleterious	85\|15	simple_aae		No				Single base exchange		Normal	Amino acid sequence changed Heterozygous in gnomAD Protein features (might be) affected

MutationT@ster 2025

Variant:

19:12663382G>A_1_ENST00000456935

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Prediction:

DeleteriousPermalink

Summary:

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

Model: simple_aae
Tree vote: 73|27 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr19:12663382G>A (GRCh38)

Gene symbol

MAN2B1

Gene constraints

LOEUF: 0.90, LOF (oe): 0.76, misssense (oe): 0.93, synonymous (oe): 1.00 ? (gnomAD)

Ensembl transcript ID

ENST00000456935.7

Genbank transcript ID

NM_000528 (exact from MANE)

UniProt / AlphaMissense peptide

MA2B1_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.844C>T
g.3361C>T

AA changes

AAE:	P282S	?
Score:	74

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs45576136
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	16	5855	5871

Protein conservation

Species	Match	AA	Alignment
Human		282	V	L	C	V	D	Q	P	L	V	E	D	P	R	S	P	E	Y	N	A	K	E	L	V	D
mutated	not conserved	282	V	L	C	V	D	Q	P	L	V	E	D	S	R	S	P	E	Y	N	A	K	E	L	V
Ptroglodytes	all identical	282	V	L	C	V	D	Q	P	V	V	E	D	P	R	S	P	E	Y	N	A	K	E	L	V
Mmulatta	all identical	283	V	L	C	V	D	Q	P	V	V	E	D	P	R	S	P	E	Y	N	A	K	E	L	V
Fcatus	not conserved	283	T	L	C	A	D	K	P	F	V	E	D	R	R	S	P	E	Y	N	A	E	E	L	V
Mmusculus	all identical	282	V	L	C	T	D	P	P	V	V	D	N	P	R	S	P	E	F	N	A	K	T	L	V
Ggallus	no homologue
Trubripes	all identical	274	Q	S	C	S	D	P	P	I	R	D	D	P	D	L	E	D	Y	N	V	D	E	V	V
Drerio	no homologue
Dmelanogaster	not conserved	266	I	L	C	N	D	A	P	I	I	D	G	K	H	S	P	D	N	N	V	K
Celegans	not conserved	254	S	L	C	G	D	D	P	I	M	D	N	L	N	I	E	G	Y	N	V	K	E	K	V
Xtropicalis	all identical	258					D	T	P	I	I	D	D	P	S	V	E	D	Y	N	A	D	V	I	V

Protein features

Start (aa)	End (aa)	Feature	Details
50	345	CHAIN		lost
50	1011	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	3.468	1
	3.446	1
(flanking)	0.903	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

19

Strand

-1

Original gDNA sequence snippet

ATCAGCCGCTGGTGGAGGACCCTCGCAGCCCCGAGTACAAC

Altered gDNA sequence snippet

ATCAGCCGCTGGTGGAGGACTCTCGCAGCCCCGAGTACAAC

Original cDNA sequence snippet

ATCAGCCGCTGGTGGAGGACCCTCGCAGCCCCGAGTACAAC

Altered cDNA sequence snippet

ATCAGCCGCTGGTGGAGGACTCTCGCAGCCCCGAGTACAAC

Wildtype AA sequence

MGAYARASGV CARGCLDSAG PWTMSRALRP PLPPLCFFLL LLAAAGARAG GYETCPTVQP
NMLNVHLLPH THDDVGWLKT VDQYFYGIKN DIQHAGVQYI LDSVISALLA DPTRRFIYVE
IAFFSRWWHQ QTNATQEVVR DLVRQGRLEF ANGGWVMNDE AATHYGAIVD QMTLGLRFLE
DTFGNDGRPR VAWHIDPFGH SREQASLFAQ MGFDGFFFGR LDYQDKWVRM QKLEMEQVWR
ASTSLKPPTA DLFTGVLPNG YNPPRNLCWD VLCVDQPLVE DPRSPEYNAK ELVDYFLNVA
TAQGRYYRTN HTVMTMGSDF QYENANMWFK NLDKLIRLVN AQQAKGSSVH VLYSTPACYL
WELNKANLTW SVKHDDFFPY ADGPHQFWTG YFSSRPALKR YERLSYNFLQ VCNQLEALVG
LAANVGPYGS GDSAPLNEAM AVLQHHDAVS GTSRQHVAND YARQLAAGWG PCEVLLSNAL
ARLRGFKDHF TFCQQLNISI CPLSQTAARF QVIVYNPLGR KVNWMVRLPV SEGVFVVKDP
NGRTVPSDVV IFPSSDSQAH PPELLFSASL PALGFSTYSV AQVPRWKPQA RAPQPIPRRS
WSPALTIENE HIRATFDPDT GLLMEIMNMN QQLLLPVRQT FFWYNASIGD NESDQASGAY
IFRPNQQKPL PVSRWAQIHL VKTPLVQEVH QNFSAWCSQV VRLYPGQRHL ELEWSVGPIP
VGDTWGKEVI SRFDTPLETK GRFYTDSNGR EILERRRDYR PTWKLNQTEP VAGNYYPVNT
RIYITDGNMQ LTVLTDRSQG GSSLRDGSLE LMVHRRLLKD DGRGVSEPLM ENGSGAWVRG
RHLVLLDTAQ AAAAGHRLLA EQEVLAPQVV LAPGGGAAYN LGAPPRTQFS GLRRDLPPSV
HLLTLASWGP EMVLLRLEHQ FAVGEDSGRN LSAPVTLNLR DLFSTFTITR LQETTLVANQ
LREAASRLKW TTNTGPTPHQ TPYQLDPANI TLEPMEIRTF LASVQWKEVD G*

Mutated AA sequence

MGAYARASGV CARGCLDSAG PWTMSRALRP PLPPLCFFLL LLAAAGARAG GYETCPTVQP
NMLNVHLLPH THDDVGWLKT VDQYFYGIKN DIQHAGVQYI LDSVISALLA DPTRRFIYVE
IAFFSRWWHQ QTNATQEVVR DLVRQGRLEF ANGGWVMNDE AATHYGAIVD QMTLGLRFLE
DTFGNDGRPR VAWHIDPFGH SREQASLFAQ MGFDGFFFGR LDYQDKWVRM QKLEMEQVWR
ASTSLKPPTA DLFTGVLPNG YNPPRNLCWD VLCVDQPLVE DSRSPEYNAK ELVDYFLNVA
TAQGRYYRTN HTVMTMGSDF QYENANMWFK NLDKLIRLVN AQQAKGSSVH VLYSTPACYL
WELNKANLTW SVKHDDFFPY ADGPHQFWTG YFSSRPALKR YERLSYNFLQ VCNQLEALVG
LAANVGPYGS GDSAPLNEAM AVLQHHDAVS GTSRQHVAND YARQLAAGWG PCEVLLSNAL
ARLRGFKDHF TFCQQLNISI CPLSQTAARF QVIVYNPLGR KVNWMVRLPV SEGVFVVKDP
NGRTVPSDVV IFPSSDSQAH PPELLFSASL PALGFSTYSV AQVPRWKPQA RAPQPIPRRS
WSPALTIENE HIRATFDPDT GLLMEIMNMN QQLLLPVRQT FFWYNASIGD NESDQASGAY
IFRPNQQKPL PVSRWAQIHL VKTPLVQEVH QNFSAWCSQV VRLYPGQRHL ELEWSVGPIP
VGDTWGKEVI SRFDTPLETK GRFYTDSNGR EILERRRDYR PTWKLNQTEP VAGNYYPVNT
RIYITDGNMQ LTVLTDRSQG GSSLRDGSLE LMVHRRLLKD DGRGVSEPLM ENGSGAWVRG
RHLVLLDTAQ AAAAGHRLLA EQEVLAPQVV LAPGGGAAYN LGAPPRTQFS GLRRDLPPSV
HLLTLASWGP EMVLLRLEHQ FAVGEDSGRN LSAPVTLNLR DLFSTFTITR LQETTLVANQ
LREAASRLKW TTNTGPTPHQ TPYQLDPANI TLEPMEIRTF LASVQWKEVD G*

Position of stopcodon in wt / mu CDS

3036 / 3036

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

1012 / 1012

Position of stopcodon in wt / mu cDNA

3077 / 3077

Position of start ATG in wt / mu cDNA

42 / 42

Last intron/exon boundary

2964

Theoretical NMD boundary in CDS

2872

Length of CDS

3036

Coding sequence (CDS) position

844

cDNA position

885

gDNA position

3361

Chromosomal position

12663382

Speed

0.32 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:

19:12663382G>A_2_ENST00000221363

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

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

Model: simple_aae
Tree vote: 85|15 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr19:12663382G>A (GRCh38)

Gene symbol

MAN2B1

Gene constraints

LOEUF: 0.88, LOF (oe): 0.74, misssense (oe): 0.93, synonymous (oe): 1.00 ? (gnomAD)

Ensembl transcript ID

ENST00000221363.8

Genbank transcript ID

NM_001173498 (by similarity)

UniProt / AlphaMissense peptide

MA2B1_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.844C>T
g.3361C>T

AA changes

AAE:	P282S	?
Score:	74

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs45576136
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	16	5855	5871

Protein conservation

Species	Match	AA	Alignment
Human		282	V	L	C	V	D	Q	P	L	V	E	D	P	R	S	P	E	Y	N	A	K	E	L	V	D
mutated	not conserved	282	V	L	C	V	D	Q	P	L	V	E	D	S	R	S	P	E	Y	N	A	K	E	L	V
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
50	345	CHAIN		lost
50	1011	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	3.468	1
	3.446	1
(flanking)	0.903	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

19

Strand

-1

Original gDNA sequence snippet

ATCAGCCGCTGGTGGAGGACCCTCGCAGCCCCGAGTACAAC

Altered gDNA sequence snippet

ATCAGCCGCTGGTGGAGGACTCTCGCAGCCCCGAGTACAAC

Original cDNA sequence snippet

ATCAGCCGCTGGTGGAGGACCCTCGCAGCCCCGAGTACAAC

Altered cDNA sequence snippet

ATCAGCCGCTGGTGGAGGACTCTCGCAGCCCCGAGTACAAC

Wildtype AA sequence

MGAYARASGV CARGCLDSAG PWTMSRALRP PLPPLCFFLL LLAAAGARAG GYETCPTVQP
NMLNVHLLPH THDDVGWLKT VDQYFYGIKN DIQHAGVQYI LDSVISALLA DPTRRFIYVE
IAFFSRWWHQ QTNATQEVVR DLVRQGRLEF ANGGWVMNDE AATHYGAIVD QMTLGLRFLE
DTFGNDGRPR VAWHIDPFGH SREQASLFAQ MGFDGFFFGR LDYQDKWVRM QKLEMEQVWR
ASTSLKPPTA DLFTGVLPNG YNPPRNLCWD VLCVDQPLVE DPRSPEYNAK ELVDYFLNVA
TAQGRYYRTN HTVMTMGSDF QYENANMWFK NLDKLIRLVN AQAKGSSVHV LYSTPACYLW
ELNKANLTWS VKHDDFFPYA DGPHQFWTGY FSSRPALKRY ERLSYNFLQV CNQLEALVGL
AANVGPYGSG DSAPLNEAMA VLQHHDAVSG TSRQHVANDY ARQLAAGWGP CEVLLSNALA
RLRGFKDHFT FCQQLNISIC PLSQTAARFQ VIVYNPLGRK VNWMVRLPVS EGVFVVKDPN
GRTVPSDVVI FPSSDSQAHP PELLFSASLP ALGFSTYSVA QVPRWKPQAR APQPIPRRSW
SPALTIENEH IRATFDPDTG LLMEIMNMNQ QLLLPVRQTF FWYNASIGDN ESDQASGAYI
FRPNQQKPLP VSRWAQIHLV KTPLVQEVHQ NFSAWCSQVV RLYPGQRHLE LEWSVGPIPV
GDTWGKEVIS RFDTPLETKG RFYTDSNGRE ILERRRDYRP TWKLNQTEPV AGNYYPVNTR
IYITDGNMQL TVLTDRSQGG SSLRDGSLEL MVHRRLLKDD GRGVSEPLME NGSGAWVRGR
HLVLLDTAQA AAAGHRLLAE QEVLAPQVVL APGGGAAYNL GAPPRTQFSG LRRDLPPSVH
LLTLASWGPE MVLLRLEHQF AVGEDSGRNL SAPVTLNLRD LFSTFTITRL QETTLVANQL
REAASRLKWT TNTGPTPHQT PYQLDPANIT LEPMEIRTFL ASVQWKEVDG *

Mutated AA sequence

MGAYARASGV CARGCLDSAG PWTMSRALRP PLPPLCFFLL LLAAAGARAG GYETCPTVQP
NMLNVHLLPH THDDVGWLKT VDQYFYGIKN DIQHAGVQYI LDSVISALLA DPTRRFIYVE
IAFFSRWWHQ QTNATQEVVR DLVRQGRLEF ANGGWVMNDE AATHYGAIVD QMTLGLRFLE
DTFGNDGRPR VAWHIDPFGH SREQASLFAQ MGFDGFFFGR LDYQDKWVRM QKLEMEQVWR
ASTSLKPPTA DLFTGVLPNG YNPPRNLCWD VLCVDQPLVE DSRSPEYNAK ELVDYFLNVA
TAQGRYYRTN HTVMTMGSDF QYENANMWFK NLDKLIRLVN AQAKGSSVHV LYSTPACYLW
ELNKANLTWS VKHDDFFPYA DGPHQFWTGY FSSRPALKRY ERLSYNFLQV CNQLEALVGL
AANVGPYGSG DSAPLNEAMA VLQHHDAVSG TSRQHVANDY ARQLAAGWGP CEVLLSNALA
RLRGFKDHFT FCQQLNISIC PLSQTAARFQ VIVYNPLGRK VNWMVRLPVS EGVFVVKDPN
GRTVPSDVVI FPSSDSQAHP PELLFSASLP ALGFSTYSVA QVPRWKPQAR APQPIPRRSW
SPALTIENEH IRATFDPDTG LLMEIMNMNQ QLLLPVRQTF FWYNASIGDN ESDQASGAYI
FRPNQQKPLP VSRWAQIHLV KTPLVQEVHQ NFSAWCSQVV RLYPGQRHLE LEWSVGPIPV
GDTWGKEVIS RFDTPLETKG RFYTDSNGRE ILERRRDYRP TWKLNQTEPV AGNYYPVNTR
IYITDGNMQL TVLTDRSQGG SSLRDGSLEL MVHRRLLKDD GRGVSEPLME NGSGAWVRGR
HLVLLDTAQA AAAGHRLLAE QEVLAPQVVL APGGGAAYNL GAPPRTQFSG LRRDLPPSVH
LLTLASWGPE MVLLRLEHQF AVGEDSGRNL SAPVTLNLRD LFSTFTITRL QETTLVANQL
REAASRLKWT TNTGPTPHQT PYQLDPANIT LEPMEIRTFL ASVQWKEVDG *

Position of stopcodon in wt / mu CDS

3033 / 3033

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

1011 / 1011

Position of stopcodon in wt / mu cDNA

3066 / 3066

Position of start ATG in wt / mu cDNA

34 / 34

Last intron/exon boundary

2953

Theoretical NMD boundary in CDS

2869

Length of CDS

3033

Coding sequence (CDS) position

844

cDNA position

877

gDNA position

3361

Chromosomal position

12663382

Speed

0.33 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