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: ENST00000281043
Querying Taster for transcript #2: ENST00000638417
MT speed 0.18 s - this script 2.653449 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
ENST00000281043(MANE Select)	MYCN	Deleterious	10\|0	complex_aae		No	Yes		Q25Afs*11	Insertion		NMD	Amino acid sequence changed Frameshift Known disease mutation: ClinVar ID 433150 (pathogenic) NMD Protein features (might be) affected
ENST00000638417	MYCN	Deleterious	167\|33	without_aae		No	Yes			Insertion		N/A	Known disease mutation: ClinVar ID 433150 (pathogenic)

MutationT@ster 2025

Variant:

2:15942129A>ACTCG_1_ENST00000281043

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Frameshift
Known disease mutation: ClinVar ID 433150 (pathogenic)
NMD
Protein features (might be) affected

Model: complex_aae
Tree vote: 10|0 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr2:15942129_15942130insCTCG (GRCh38)

Gene symbol

MYCN

Gene constraints

LOEUF: 0.31, LOF (oe): 0.12, misssense (oe): 0.99, synonymous (oe): 1.25 ? (gnomAD)

Ensembl transcript ID

ENST00000281043.4

Genbank transcript ID

NM_005378 (exact from MANE), NM_001293228 (by similarity)

UniProt / AlphaMissense peptide

MYCN_HUMAN | AlphaMissense: transcript, gene

Variant type

Insertion

Gene region

CDS

DNA changes

c.65_66insCTCG
g.1580_1581insCTCG

AA changes

Q25Afs*11

Frameshift

Yes

Length of protein

NMD

Pathogenic variant (ClinVar)

Feingold syndrome type 1

pathogenic

ClinVar OMIM

Variant DBs

	Not in dbSNP
	Allele 'CTCG' was not found in gnomAD

Protein conservation

Species	Match	AA	Alignment
Human		25	C	K	N	P	D	L	E	F	D	S	L	Q	P	C	F	Y	P	D	E	D	D	F	Y	F	G	G	P	D	S	T	P	P	G	E	D	I	W	K	K	F	E	L	L	P	T	P	P	L	S	P	S	R	G	F	A	E	H	S	S	E	P	P	S	W	V	T	E	M	L	L	E	N	E	L	W	G	S	P	A	E	E	D	A	F	G	L	G	G	L	G	G	L	T	P	N	P	V	I	L	Q	D	C	M	W	S	G	F	S	A	R	E	K	L	E	R	A	V	S	E	K	L	Q	H	G	R	G	P
mutated	no alignment	n/a
Ptroglodytes	all identical	25	C	K	N	P	D	L	E	F	D	S	L	Q	P	C	F	Y	P	D	E	D	D	F	Y	F	G	G	P	D	S	T	P	P	G	E	D	I	W	K	K	F	E	L	L	P	T	P	P	L	S	P	S	R	G	F	A	E	H	S	S	E	P	P	S	W	V	T	E	M	L	L	E	N	E	L	W	G	S	P	A	E	E	D	A	F	G	L	G	G	L	G	G	L	T	P	N	P	V	I	L	Q	D	C	M	W	S	G	F
Mmulatta	all identical	116	C	K	N	P	D	L	E	F	D	S	L	Q	P	C	F	Y	P	D	E	D	D	F	Y	F	G	G	P	D	S	T	P	P	G	E	D	I	W	K	K	F	E	L	L	P	T	P	P	L	S	P	S	R	G	F	A	E	H	S	S	E	P	P	S	W	V	T	E	M	L	L	E	N	E	L	W	G	S	P	A	E	E	D	A	F	G	L	G	G	L	G	G	L	T	P	N	P	V	I	L	Q	D	C	M	W	S	G	F
Fcatus	partly conserved	25	C	K	N	P	D	L	E	F	D	S	L	Q	P	C	F	Y	P	D	E	D	D	F	Y	F	G	G	P	D	S	T	P	P	G	E	D	I	W	K	K	F	E	L	L	P	T	P	P	L	S	P	S	R	A	F	P	E	H	S	P	E	P	P	N	W	A	T	E	M	L	L	P	E	A	D	L	W	G	N	P	A	E	E	D	A	F	G	L	G	G	L	S	G	L	T	P	N	P	V	I	L	Q	D	C	M	W	S	G
Mmusculus	partly conserved	25	C	K	N	P	D	L	E	F	D	S	L	Q	P	C	F	Y	P	D	E	D	D	F	Y	F	G	G	P	D	S	T	P	P	G	E	D	I	W	K	K	F	E	L	L	P	T	P	P	L	S	P	S	R	A	F	P	E	H	S	P	E	P	S	N	W	A	T	E	M	L	L	P	E	A	D	L	W	G	N	P	A	E	E	D	A	F	G	L	G	G	L	G	G	L	T	P	N	P	V	I	L	Q	D	C	M	W	S	G
Ggallus	partly conserved	17	S	K	N	P	D	L	E	F	D	S	L	Q	P	C	F	Y	P	D	E	D	D	F	Y	L	C	G	P	D	S	A	P	P	G	E	D	I	W	K	K	F	E	L	L	P	T	P	P	L	S	P	S	RA	G	L	Q	E	H	P	P	G	G	A	P	L	P	W	G	G	A	A	L	G	S	C	R	P	A	D	P	L	D	W	A	S	E	L	L	L	L	P	P	E	A	E	L	W	G	S	T	D	G	A	D	F	F	E	T	G	L	G	A	S	N	N
Trubripes	partly conserved	17	S	K	N	S	D	L	E	F	D	S	L	Q	P	C	F	Y	P	D	E	D	D	F	Y	F	C	G	P	D	S	A	P	P	G	E	D	I	W	K	K	F	E	L	L	P	T	P	P	L	S	P	S	R	A	A	L	P	G	E	P	A	T	A	S	P	E	A	D	P	L	D	F	G	L	G	D	P	L	D	W	A	S	E	L	T	F	L	P	E	D	D	I	W	G	A	S	D	D	G	D	L	F	G	S	G	L	-	-	D	T	N	P	N	S	I	I
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	partly conserved	17	S	R	N	L	D	L	E	F	D	S	L	Q	P	C	F	Y	P	D	E	D	D	F	Y	L	C	G	P	D	S	A	P	P	G	E	D	I	W	K	K	F	E	L	L	P	T	P	P	L	S	P	S	RSGL	H	G	D	P	L	S	P	G	L	P	G	D	Y	G	D	S	L	D	W	A	S	E	L	L	L	-	-	-	-	-	-	L	P	P	E	T	D	L	L	G	G	S	G	W	G	E	L	G	L	S	P	C	N	V	K	S	I	I	I	Q

Protein features

Start (aa)	End (aa)	Feature	Details
1	464	CHAIN		lost
19	47	REGION	Interaction with AURKA	lost
58	58	MOD_RES	Phosphothreonine	lost
61	89	REGION	Interaction with AURKA and FBXW7	lost
69	71	HELIX		lost
76	84	MOTIF	9aaTAD	lost
76	88	HELIX		lost
129	172	REGION		lost
196	294	REGION		lost
259	278	COMPBIAS	Acidic residues	lost
261	261	MOD_RES	Phosphoserine	lost
263	263	MOD_RES	Phosphoserine	lost
334	392	REGION		lost
372	392	COMPBIAS	Basic and acidic residues	lost
381	433	DOMAIN	bHLH	lost
433	454	REGION	Leucine-zipper	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	9.069	1
(flanking)	2.633	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

2

Strand

1

Original gDNA sequence snippet

AACCCAGACCTCGAGTTTGACTCGCTACAGCCCTGCTTCT

Altered gDNA sequence snippet

AACCCAGACCTCGAGTTTGACTCGCTCGCTACAGCCCTGCTTCT

Original cDNA sequence snippet

AACCCAGACCTCGAGTTTGACTCGCTACAGCCCTGCTTCT

Altered cDNA sequence snippet

AACCCAGACCTCGAGTTTGACTCGCTCGCTACAGCCCTGCTTCT

Wildtype AA sequence

MPSCSTSTMP GMICKNPDLE FDSLQPCFYP DEDDFYFGGP DSTPPGEDIW KKFELLPTPP
LSPSRGFAEH SSEPPSWVTE MLLENELWGS PAEEDAFGLG GLGGLTPNPV ILQDCMWSGF
SAREKLERAV SEKLQHGRGP PTAGSTAQSP GAGAASPAGR GHGGAAGAGR AGAALPAELA
HPAAECVDPA VVFPFPVNKR EPAPVPAAPA SAPAAGPAVA SGAGIAAPAG APGVAPPRPG
GRQTSGGDHK ALSTSGEDTL SDSDDEDDEE EDEEEEIDVV TVEKRRSSSN TKAVTTFTIT
VRPKNAALGP GRAQSSELIL KRCLPIHQQH NYAAPSPYVE SEDAPPQKKI KSEASPRPLK
SVIPPKAKSL SPRNSDSEDS ERRRNHNILE RQRRNDLRSS FLTLRDHVPE LVKNEKAAKV
VILKKATEYV HSLQAEEHQL LLEKEKLQAR QQQLLKKIEH ARTC*

Mutated AA sequence

MPSCSTSTMP GMICKNPDLE FDSLATALLL PGRR*

Position of stopcodon in wt / mu CDS

1395 / 105

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

465 / 35

Position of stopcodon in wt / mu cDNA

1706 / 416

Position of start ATG in wt / mu cDNA

312 / 312

Last intron/exon boundary

1101

Theoretical NMD boundary in CDS

739

Length of CDS

1395

Coding sequence (CDS) position

65 / 66

cDNA position

376 / 377

gDNA position

1580 / 1581

Chromosomal position

15942129 / 15942130

Speed

0.16 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:

2:15942129A>ACTCG_2_ENST00000638417

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Known disease mutation: ClinVar ID 433150 (pathogenic)

Model: without_aae
Tree vote: 167|33 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr2:15942129_15942130insCTCG (GRCh38)

Gene symbol

MYCN

Gene constraints

LOEUF: 0.32, LOF (oe): 0.07, misssense (oe): 0.75, synonymous (oe): 1.02 ? (gnomAD)

Ensembl transcript ID

ENST00000638417.1

Genbank transcript ID

NM_001293233 (by similarity), NM_001293231 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Insertion

Gene region

intron

DNA changes

c.157+1386_157+1387insCTCG
g.1580_1581insCTCG

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Feingold syndrome type 1

pathogenic

ClinVar OMIM

Variant DBs

	Not in dbSNP
	Allele 'CTCG' was not found in gnomAD

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	9.069	1
(flanking)	2.633	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

2

Strand

1

Original gDNA sequence snippet

AACCCAGACCTCGAGTTTGACTCGCTACAGCCCTGCTTCT

Altered gDNA sequence snippet

AACCCAGACCTCGAGTTTGACTCGCTCGCTACAGCCCTGCTTCT

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MRGAPGNCVG AEQALARRKR AQTVAIRGHP RPPGPPGDTR AESPPDPLQS AGDDEDDEEE
DEEEEIDVVT VEKRRSSSNT KAVTTFTITV RPKNAALGPG RAQSSELILK RCLPIHQQHN
YAAPSPYVES EDAPPQKKIK SEASPRPLKS VIPPKAKSLS PRNSDSEDSE RRRNHNILER
QRRNDLRSSF LTLRDHVPEL VKNEKAAKVV ILKKATEYVH SLQAEEHQLL LEKEKLQARQ
QQLLKKIEHA RTC*

Mutated AA sequence

Position of stopcodon in wt / mu CDS

N/A

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

N/A

Position of stopcodon in wt / mu cDNA

N/A

Position of start ATG in wt / mu cDNA

22 / 22

Last intron/exon boundary

178

Theoretical NMD boundary in CDS

106

Length of CDS

762

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

1580 / 1581

Chromosomal position

15942129 / 15942130

Speed

0.02 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