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: ENST00000407008
Querying Taster for transcript #2: ENST00000582037
MT speed 0.18 s - this script 2.616007 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
ENST00000582037	NLK	Deleterious	78\|22	simple_aae		No				Single base exchange		Normal	Amino acid sequence changed
ENST00000407008(MANE Select)	NLK	Deleterious	82\|18	simple_aae		No				Single base exchange		Normal	Amino acid sequence changed Protein features (might be) affected

MutationT@ster 2025

Variant:

17:28042880C>G_2_ENST00000582037

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed

Model: simple_aae
Tree vote: 78|22 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr17:28042880C>G (GRCh38)

Gene symbol

NLK

Gene constraints

LOEUF: 0.48, LOF (oe): 0.10, misssense (oe): 0.87, synonymous (oe): 1.08 ? (gnomAD)

Ensembl transcript ID

ENST00000582037.2

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.7C>G
g.1144C>G

AA changes

AAE:	L3V	?
Score:	32

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs1210231697
gnomAD	homozygous (G/G)	heterozygous	allele carriers
	0	86	86

Protein conservation

Species	Match	AA
Human		3	M	S	L	C	G	A	R	A	N	A	K	M	M	A	A
mutated	all conserved	3	M	S	V	C	G	A	R	A	N	A	K	M	M	A	A	Y	N	G	G	T	S	A
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)	5.346	1
	6.957	1
(flanking)	7.053	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

17

Strand

1

Original gDNA sequence snippet

GGCATTTATTTTGAATGTCTCTTTGTGGCGCAAGAGCCAAC

Altered gDNA sequence snippet

GGCATTTATTTTGAATGTCTGTTTGTGGCGCAAGAGCCAAC

Original cDNA sequence snippet

GGCATTTATTTTGAATGTCTCTTTGTGGCGCAAGAGCCAAC

Altered cDNA sequence snippet

GGCATTTATTTTGAATGTCTGTTTGTGGCGCAAGAGCCAAC

Wildtype AA sequence

MSLCGARANA KMMAAYNGGT SAAAAGHHHH HHHHLPHLPP PHLHHHHHPQ HHLHPGSAAA
VHPVQQHTSS AAAAAAAAAA AAAMLNPGQQ QPYFPSPAPG QAPGPAAAAP AQVQAAAAAT
VKAHHHQHSH HPQQQLDIEP DRPIGYGAFG VVWLRICSTE KFLHYQPRLT ATAGFFGGSA
L*

Mutated AA sequence

MSVCGARANA KMMAAYNGGT SAAAAGHHHH HHHHLPHLPP PHLHHHHHPQ HHLHPGSAAA
VHPVQQHTSS AAAAAAAAAA AAAMLNPGQQ QPYFPSPAPG QAPGPAAAAP AQVQAAAAAT
VKAHHHQHSH HPQQQLDIEP DRPIGYGAFG VVWLRICSTE KFLHYQPRLT ATAGFFGGSA
L*

Position of stopcodon in wt / mu CDS

546 / 546

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

182 / 182

Position of stopcodon in wt / mu cDNA

581 / 581

Position of start ATG in wt / mu cDNA

36 / 36

Last intron/exon boundary

493

Theoretical NMD boundary in CDS

407

Length of CDS

546

Coding sequence (CDS) position

7

cDNA position

42

gDNA position

1144

Chromosomal position

28042880

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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MutationT@ster 2025

Variant:

17:28042880C>G_1_ENST00000407008

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 82|18 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr17:28042880C>G (GRCh38)

Gene symbol

NLK

Gene constraints

LOEUF: 0.31, LOF (oe): 0.15, misssense (oe): 0.67, synonymous (oe): 0.93 ? (gnomAD)

Ensembl transcript ID

ENST00000407008.8

Genbank transcript ID

NM_016231 (exact from MANE)

UniProt / AlphaMissense peptide

NLK_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.7C>G
g.1144C>G

AA changes

AAE:	L3V	?
Score:	32

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs1210231697
gnomAD	homozygous (G/G)	heterozygous	allele carriers
	0	86	86

Protein conservation

Species	Match	AA
Human		3	M	S	L	C	G	A	R	A	N	A	K	M	M	A	A
mutated	all conserved	3	M	S	V	C	G	A	R	A	N	A	K	M	M	A	A	Y	N	G	G	T	S	A
Ptroglodytes	all identical	3	M	S	L	C	G	A	R	A	N	A	K	M	M	A	A	Y	N	G	G	T	S	A
Mmulatta	all identical	3	M	S	L	C	G	A	R	A	N	A	K	M	M	A	A	Y	N	G	G	T	S	A
Fcatus	all identical	3	M	S	L	C	G	A	R	A	N	A	K	M	M	A	A	Y	N	G	G	T	S	A
Mmusculus	all identical	3	M	S	L	C	G	T	R	A	N	A	K	M	M	A	A	Y	N	G	G	T	S	A
Ggallus	all identical	3	M	S	L	C	G	A	T	A	N	A	K	M	M	A	A	Y	N	G	G	T	S	A
Trubripes	no alignment	n/a
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	all identical	3	M	S	L	C	G	T	S	S	N	A	N	M	M	A	A	Y	N	G	G	T	S	T

Protein features

Start (aa)	End (aa)	Feature	Details
1	125	REGION		lost
1	304	REGION	Required	lost
1	527	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	5.346	1
	6.957	1
(flanking)	7.053	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

17

Strand

1

Original gDNA sequence snippet

GGCATTTATTTTGAATGTCTCTTTGTGGCGCAAGAGCCAAC

Altered gDNA sequence snippet

GGCATTTATTTTGAATGTCTGTTTGTGGCGCAAGAGCCAAC

Original cDNA sequence snippet

GGCATTTATTTTGAATGTCTCTTTGTGGCGCAAGAGCCAAC

Altered cDNA sequence snippet

GGCATTTATTTTGAATGTCTGTTTGTGGCGCAAGAGCCAAC

Wildtype AA sequence

MSLCGARANA KMMAAYNGGT SAAAAGHHHH HHHHLPHLPP PHLHHHHHPQ HHLHPGSAAA
VHPVQQHTSS AAAAAAAAAA AAAMLNPGQQ QPYFPSPAPG QAPGPAAAAP AQVQAAAAAT
VKAHHHQHSH HPQQQLDIEP DRPIGYGAFG VVWSVTDPRD GKRVALKKMP NVFQNLVSCK
RVFRELKMLC FFKHDNVLSA LDILQPPHID YFEEIYVVTE LMQSDLHKII VSPQPLSSDH
VKVFLYQILR GLKYLHSAGI LHRDIKPGNL LVNSNCVLKI CDFGLARVEE LDESRHMTQE
VVTQYYRAPE ILMGSRHYSN AIDIWSVGCI FAELLGRRIL FQAQSPIQQL DLITDLLGTP
SLEAMRTACE GAKAHILRGP HKQPSLPVLY TLSSQATHEA VHLLCRMLVF DPSKRISAKD
ALAHPYLDEG RLRYHTCMCK CCFSTSTGRV YTSDFEPVTN PKFDDTFEKN LSSVRQVKEI
IHQFILEQQK GNRVPLCINP QSAAFKSFIS STVAQPSEMP PSPLVWE*

Mutated AA sequence

MSVCGARANA KMMAAYNGGT SAAAAGHHHH HHHHLPHLPP PHLHHHHHPQ HHLHPGSAAA
VHPVQQHTSS AAAAAAAAAA AAAMLNPGQQ QPYFPSPAPG QAPGPAAAAP AQVQAAAAAT
VKAHHHQHSH HPQQQLDIEP DRPIGYGAFG VVWSVTDPRD GKRVALKKMP NVFQNLVSCK
RVFRELKMLC FFKHDNVLSA LDILQPPHID YFEEIYVVTE LMQSDLHKII VSPQPLSSDH
VKVFLYQILR GLKYLHSAGI LHRDIKPGNL LVNSNCVLKI CDFGLARVEE LDESRHMTQE
VVTQYYRAPE ILMGSRHYSN AIDIWSVGCI FAELLGRRIL FQAQSPIQQL DLITDLLGTP
SLEAMRTACE GAKAHILRGP HKQPSLPVLY TLSSQATHEA VHLLCRMLVF DPSKRISAKD
ALAHPYLDEG RLRYHTCMCK CCFSTSTGRV YTSDFEPVTN PKFDDTFEKN LSSVRQVKEI
IHQFILEQQK GNRVPLCINP QSAAFKSFIS STVAQPSEMP PSPLVWE*

Position of stopcodon in wt / mu CDS

1584 / 1584

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

528 / 528

Position of stopcodon in wt / mu cDNA

1781 / 1781

Position of start ATG in wt / mu cDNA

198 / 198

Last intron/exon boundary

1726

Theoretical NMD boundary in CDS

1478

Length of CDS

1584

Coding sequence (CDS) position

7

cDNA position

204

gDNA position

1144

Chromosomal position

28042880

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