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: ENST00000647318
Querying Taster for transcript #2: ENST00000300589
MT speed 0.1 s - this script 2.528843 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
ENST00000300589	NOD2	Deleterious	89\|11	simple_aae		No				Single base exchange		Normal	Amino acid sequence changed Heterozygous in gnomAD Protein features (might be) affected
ENST00000647318(MANE Select)	NOD2	Deleterious	90\|10	simple_aae		No				Single base exchange		Normal	Amino acid sequence changed Heterozygous in gnomAD Protein features (might be) affected

MutationT@ster 2025

Variant:

16:50711232G>A_2_ENST00000300589

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Prediction:

DeleteriousPermalink

Summary:

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

Model: simple_aae
Tree vote: 89|11 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr16:50711232G>A (GRCh38)

Gene symbol

NOD2

Gene constraints

LOEUF: 1.05, LOF (oe): 0.87, misssense (oe): 0.94, synonymous (oe): 0.99 ? (gnomAD)

Ensembl transcript ID

ENST00000300589.6

Genbank transcript ID

NM_022162 (by similarity)

UniProt / AlphaMissense peptide

NOD2_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1321G>A
g.17645G>A

AA changes

AAE:	E441K	?
Score:	56

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs104895432
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	513	513

Protein conservation

Species	Match	AA	Alignment
Human		441	V	S	A	F	L	R	K	Y	I	R	T	E	F	N	L	K	G	F	S	E	Q	G	I	E
mutated	all conserved	441	V	S	A	F	L	R	K	Y	I	R	T	K	F	N	L	K	G	F	S	E	Q	G	I
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	1040	CHAIN		lost
293	618	DOMAIN	NACHT	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.441	0
	3.384	1
(flanking)	8.97	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

16

Strand

1

Original gDNA sequence snippet

TCAGGAAGTACATCCGCACCGAGTTCAACCTCAAGGGCTTC

Altered gDNA sequence snippet

TCAGGAAGTACATCCGCACCAAGTTCAACCTCAAGGGCTTC

Original cDNA sequence snippet

TCAGGAAGTACATCCGCACCGAGTTCAACCTCAAGGGCTTC

Altered cDNA sequence snippet

TCAGGAAGTACATCCGCACCAAGTTCAACCTCAAGGGCTTC

Wildtype AA sequence

MGEEGGSASH DEEERASVLL GHSPGCEMCS QEAFQAQRSQ LVELLVSGSL EGFESVLDWL
LSWEVLSWED YEGFHLLGQP LSHLARRLLD TVWNKGTWAC QKLIAAAQEA QADSQSPKLH
GCWDPHSLHP ARDLQSHRPA IVRRLHSHVE NMLDLAWERG FVSQYECDEI RLPIFTPSQR
ARRLLDLATV KANGLAAFLL QHVQELPVPL ALPLEAATCK KYMAKLRTTV SAQSRFLSTY
DGAETLCLED IYTENVLEVW ADVGMAGPPQ KSPATLGLEE LFSTPGHLND DADTVLVVGE
AGSGKSTLLQ RLHLLWAAGQ DFQEFLFVFP FSCRQLQCMA KPLSVRTLLF EHCCWPDVGQ
EDIFQLLLDH PDRVLLTFDG FDEFKFRFTD RERHCSPTDP TSVQTLLFNL LQGNLLKNAR
KVVTSRPAAV SAFLRKYIRT EFNLKGFSEQ GIELYLRKRH HEPGVADRLI RLLQETSALH
GLCHLPVFSW MVSKCHQELL LQEGGSPKTT TDMYLLILQH FLLHATPPDS ASQGLGPSLL
RGRLPTLLHL GRLALWGLGM CCYVFSAQQL QAAQVSPDDI SLGFLVRAKG VVPGSTAPLE
FLHITFQCFF AAFYLALSAD VPPALLRHLF NCGRPGNSPM ARLLPTMCIQ ASEGKDSSVA
ALLQKAEPHN LQITAAFLAG LLSREHWGLL AECQTSEKAL LRRQACARWC LARSLRKHFH
SIPPAAPGEA KSVHAMPGFI WLIRSLYEMQ EERLARKAAR GLNVGHLKLT FCSVGPTECA
ALAFVLQHLR RPVALQLDYN SVGDIGVEQL LPCLGVCKAL YLRDNNISDR GICKLIECAL
HCEQLQKLAL FNNKLTDGCA HSMAKLLACR QNFLALRLGN NYITAAGAQV LAEGLRGNTS
LQFLGFWGNR VGDEGAQALA EALGDHQSLR WLSLVGNNIG SVGAQALALM LAKNVMLEEL
CLEENHLQDE GVCSLAEGLK KNSSLKILKL SNNCITYLGA EALLQALERN DTILEVWLRG
NTFSLEEVDK LGCRDTRLLL *

Mutated AA sequence

MGEEGGSASH DEEERASVLL GHSPGCEMCS QEAFQAQRSQ LVELLVSGSL EGFESVLDWL
LSWEVLSWED YEGFHLLGQP LSHLARRLLD TVWNKGTWAC QKLIAAAQEA QADSQSPKLH
GCWDPHSLHP ARDLQSHRPA IVRRLHSHVE NMLDLAWERG FVSQYECDEI RLPIFTPSQR
ARRLLDLATV KANGLAAFLL QHVQELPVPL ALPLEAATCK KYMAKLRTTV SAQSRFLSTY
DGAETLCLED IYTENVLEVW ADVGMAGPPQ KSPATLGLEE LFSTPGHLND DADTVLVVGE
AGSGKSTLLQ RLHLLWAAGQ DFQEFLFVFP FSCRQLQCMA KPLSVRTLLF EHCCWPDVGQ
EDIFQLLLDH PDRVLLTFDG FDEFKFRFTD RERHCSPTDP TSVQTLLFNL LQGNLLKNAR
KVVTSRPAAV SAFLRKYIRT KFNLKGFSEQ GIELYLRKRH HEPGVADRLI RLLQETSALH
GLCHLPVFSW MVSKCHQELL LQEGGSPKTT TDMYLLILQH FLLHATPPDS ASQGLGPSLL
RGRLPTLLHL GRLALWGLGM CCYVFSAQQL QAAQVSPDDI SLGFLVRAKG VVPGSTAPLE
FLHITFQCFF AAFYLALSAD VPPALLRHLF NCGRPGNSPM ARLLPTMCIQ ASEGKDSSVA
ALLQKAEPHN LQITAAFLAG LLSREHWGLL AECQTSEKAL LRRQACARWC LARSLRKHFH
SIPPAAPGEA KSVHAMPGFI WLIRSLYEMQ EERLARKAAR GLNVGHLKLT FCSVGPTECA
ALAFVLQHLR RPVALQLDYN SVGDIGVEQL LPCLGVCKAL YLRDNNISDR GICKLIECAL
HCEQLQKLAL FNNKLTDGCA HSMAKLLACR QNFLALRLGN NYITAAGAQV LAEGLRGNTS
LQFLGFWGNR VGDEGAQALA EALGDHQSLR WLSLVGNNIG SVGAQALALM LAKNVMLEEL
CLEENHLQDE GVCSLAEGLK KNSSLKILKL SNNCITYLGA EALLQALERN DTILEVWLRG
NTFSLEEVDK LGCRDTRLLL *

Position of stopcodon in wt / mu CDS

3123 / 3123

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

1041 / 1041

Position of stopcodon in wt / mu cDNA

3228 / 3228

Position of start ATG in wt / mu cDNA

106 / 106

Last intron/exon boundary

3155

Theoretical NMD boundary in CDS

2999

Length of CDS

3123

Coding sequence (CDS) position

1321

cDNA position

1426

gDNA position

17645

Chromosomal position

50711232

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:

16:50711232G>A_1_ENST00000647318

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

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

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

Analysed issue

Analysis result

Variant

Chr16:50711232G>A (GRCh38)

Gene symbol

NOD2

Gene constraints

LOEUF: 1.03, LOF (oe): 0.85, misssense (oe): 0.93, synonymous (oe): 0.99 ? (gnomAD)

Ensembl transcript ID

ENST00000647318.2

Genbank transcript ID

NM_001370466 (exact from MANE), NM_001293557 (by similarity)

UniProt / AlphaMissense peptide

NOD2_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1240G>A
g.17645G>A

AA changes

AAE:	E414K	?
Score:	56

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs104895432
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	513	513

Protein conservation

Species	Match	AA	Alignment
Human		414	V	S	A	F	L	R	K	Y	I	R	T	E	F	N	L	K	G	F	S	E	Q	G	I	E
mutated	all conserved	414	V	S	A	F	L	R	K	Y	I	R	T	K	F	N	L	K	G	F
Ptroglodytes	all identical	441	V	S	A	F	L	R	K	Y	I	R	T	E	F	N	L	K	G	F
Mmulatta	all identical	445	V	S	A	F	L	R	K	Y	I	R	T	E	F	N	L	K	G	F
Fcatus	all identical	414	V	S	A	L	L	R	K	Y	L	R	V	E	L	N	L	K	G
Mmusculus	all identical	436	V	S	A	L	L	R	K	F	V	R	T	E	L	Q	L	K	G	F	S	E	E	G	I
Ggallus	no homologue
Trubripes	all identical	440								N	L	C	K	E	V	L	L	K	G	F	S	P	S	G	I
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

Start (aa)	End (aa)	Feature	Details
1	1040	CHAIN		lost
293	618	DOMAIN	NACHT	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.441	0
	3.384	1
(flanking)	8.97	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

16

Strand

1

Original gDNA sequence snippet

TCAGGAAGTACATCCGCACCGAGTTCAACCTCAAGGGCTTC

Altered gDNA sequence snippet

TCAGGAAGTACATCCGCACCAAGTTCAACCTCAAGGGCTTC

Original cDNA sequence snippet

TCAGGAAGTACATCCGCACCGAGTTCAACCTCAAGGGCTTC

Altered cDNA sequence snippet

TCAGGAAGTACATCCGCACCAAGTTCAACCTCAAGGGCTTC

Wildtype AA sequence

MCSQEAFQAQ RSQLVELLVS GSLEGFESVL DWLLSWEVLS WEDYEGFHLL GQPLSHLARR
LLDTVWNKGT WACQKLIAAA QEAQADSQSP KLHGCWDPHS LHPARDLQSH RPAIVRRLHS
HVENMLDLAW ERGFVSQYEC DEIRLPIFTP SQRARRLLDL ATVKANGLAA FLLQHVQELP
VPLALPLEAA TCKKYMAKLR TTVSAQSRFL STYDGAETLC LEDIYTENVL EVWADVGMAG
PPQKSPATLG LEELFSTPGH LNDDADTVLV VGEAGSGKST LLQRLHLLWA AGQDFQEFLF
VFPFSCRQLQ CMAKPLSVRT LLFEHCCWPD VGQEDIFQLL LDHPDRVLLT FDGFDEFKFR
FTDRERHCSP TDPTSVQTLL FNLLQGNLLK NARKVVTSRP AAVSAFLRKY IRTEFNLKGF
SEQGIELYLR KRHHEPGVAD RLIRLLQETS ALHGLCHLPV FSWMVSKCHQ ELLLQEGGSP
KTTTDMYLLI LQHFLLHATP PDSASQGLGP SLLRGRLPTL LHLGRLALWG LGMCCYVFSA
QQLQAAQVSP DDISLGFLVR AKGVVPGSTA PLEFLHITFQ CFFAAFYLAL SADVPPALLR
HLFNCGRPGN SPMARLLPTM CIQASEGKDS SVAALLQKAE PHNLQITAAF LAGLLSREHW
GLLAECQTSE KALLRRQACA RWCLARSLRK HFHSIPPAAP GEAKSVHAMP GFIWLIRSLY
EMQEERLARK AARGLNVGHL KLTFCSVGPT ECAALAFVLQ HLRRPVALQL DYNSVGDIGV
EQLLPCLGVC KALYLRDNNI SDRGICKLIE CALHCEQLQK LALFNNKLTD GCAHSMAKLL
ACRQNFLALR LGNNYITAAG AQVLAEGLRG NTSLQFLGFW GNRVGDEGAQ ALAEALGDHQ
SLRWLSLVGN NIGSVGAQAL ALMLAKNVML EELCLEENHL QDEGVCSLAE GLKKNSSLKI
LKLSNNCITY LGAEALLQAL ERNDTILEVW LRGNTFSLEE VDKLGCRDTR LLL*

Mutated AA sequence

MCSQEAFQAQ RSQLVELLVS GSLEGFESVL DWLLSWEVLS WEDYEGFHLL GQPLSHLARR
LLDTVWNKGT WACQKLIAAA QEAQADSQSP KLHGCWDPHS LHPARDLQSH RPAIVRRLHS
HVENMLDLAW ERGFVSQYEC DEIRLPIFTP SQRARRLLDL ATVKANGLAA FLLQHVQELP
VPLALPLEAA TCKKYMAKLR TTVSAQSRFL STYDGAETLC LEDIYTENVL EVWADVGMAG
PPQKSPATLG LEELFSTPGH LNDDADTVLV VGEAGSGKST LLQRLHLLWA AGQDFQEFLF
VFPFSCRQLQ CMAKPLSVRT LLFEHCCWPD VGQEDIFQLL LDHPDRVLLT FDGFDEFKFR
FTDRERHCSP TDPTSVQTLL FNLLQGNLLK NARKVVTSRP AAVSAFLRKY IRTKFNLKGF
SEQGIELYLR KRHHEPGVAD RLIRLLQETS ALHGLCHLPV FSWMVSKCHQ ELLLQEGGSP
KTTTDMYLLI LQHFLLHATP PDSASQGLGP SLLRGRLPTL LHLGRLALWG LGMCCYVFSA
QQLQAAQVSP DDISLGFLVR AKGVVPGSTA PLEFLHITFQ CFFAAFYLAL SADVPPALLR
HLFNCGRPGN SPMARLLPTM CIQASEGKDS SVAALLQKAE PHNLQITAAF LAGLLSREHW
GLLAECQTSE KALLRRQACA RWCLARSLRK HFHSIPPAAP GEAKSVHAMP GFIWLIRSLY
EMQEERLARK AARGLNVGHL KLTFCSVGPT ECAALAFVLQ HLRRPVALQL DYNSVGDIGV
EQLLPCLGVC KALYLRDNNI SDRGICKLIE CALHCEQLQK LALFNNKLTD GCAHSMAKLL
ACRQNFLALR LGNNYITAAG AQVLAEGLRG NTSLQFLGFW GNRVGDEGAQ ALAEALGDHQ
SLRWLSLVGN NIGSVGAQAL ALMLAKNVML EELCLEENHL QDEGVCSLAE GLKKNSSLKI
LKLSNNCITY LGAEALLQAL ERNDTILEVW LRGNTFSLEE VDKLGCRDTR LLL*

Position of stopcodon in wt / mu CDS

3042 / 3042

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

1014 / 1014

Position of stopcodon in wt / mu cDNA

3107 / 3107

Position of start ATG in wt / mu cDNA

66 / 66

Last intron/exon boundary

3034

Theoretical NMD boundary in CDS

2918

Length of CDS

3042

Coding sequence (CDS) position

1240

cDNA position

1305

gDNA position

17645

Chromosomal position

50711232

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