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
MT speed 0.07 s - this script 2.525325 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
ENST00000407008(MANE Select)	NLK	Deleterious	94\|6	simple_aae		No				Single base exchange		Normal	Amino acid sequence changed Protein features (might be) affected

MutationT@ster 2025

Variant:

17:28163584A>G_1_ENST00000407008

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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

Chr17:28163584A>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.793A>G
g.121848A>G

AA changes

AAE:	I265V	?
Score:	29

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs147671384
gnomAD	homozygous (G/G)	heterozygous	allele carriers
	0	265	265

Protein conservation

Species	Match	AA	Alignment
Human		265	Y	L	H	S	A	G	I	L	H	R	D	I	K	P	G	N	L	L	V	N	S	N	C	V
mutated	all conserved	265	Y	L	H	S	A	G	I	L	H	R	D	V	K	P	G	N	L	L	V	N	S	N	C
Ptroglodytes	all identical	265	Y	L	H	S	A	G	I	L	H	R	D	I	K	P	G	N	L	L	V	N	S	N	C
Mmulatta	all identical	265	Y	L	H	S	A	G	I	L	H	R	D	I	K	P	G	N	L	L	V	N	S	N	C
Fcatus	all identical	265	Y	L	H	S	A	G	I	L	H	R	D	I	K	P	G	N	L	L	V	N	S	N	C
Mmusculus	all identical	265	Y	L	H	S	A	G	I	L	H	R	D	I	K	P	G	N	L	L	V	N	S	N	C
Ggallus	all identical	266	Y	L	H	S	A	G	I	L	H	R	D	I	K	P	G	N	L	L	V	N	S	N	C
Trubripes	all identical	179	Y	L	H	S	A	G	I	L	H	R	D	I	K	P	G	N	L	L	V	N	S	N	C
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	all identical	272	Y	L	H	S	A	G	I	L	H	R	D	I	K	P	G	N	L	L	V	N	S	N	C

Protein features

Start (aa)	End (aa)	Feature	Details
1	304	REGION	Required	lost
1	527	CHAIN		lost
124	416	REGION		lost
138	427	DOMAIN	Protein kinase	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	4.692	1
	8.863	1
(flanking)	7.67	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

CTGGCATTTTACATCGAGACATTAAGCCAGGGAATCTCCTT

Altered gDNA sequence snippet

CTGGCATTTTACATCGAGACGTTAAGCCAGGGAATCTCCTT

Original cDNA sequence snippet

CTGGCATTTTACATCGAGACATTAAGCCAGGGAATCTCCTT

Altered cDNA sequence snippet

CTGGCATTTTACATCGAGACGTTAAGCCAGGGAATCTCCTT

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

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 LHRDVKPGNL 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

793

cDNA position

990

gDNA position

121848

Chromosomal position

28163584

Speed

0.07 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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