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: ENST00000378610
Querying Taster for transcript #2: ENST00000274695
MT speed 0.04 s - this script 2.42461 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
ENST00000378610	CDKAL1	Benign	2\|198	without_aae		No				Single base exchange		N/A	Homozygous in gnomAD
ENST00000274695(MANE Select)	CDKAL1	Benign	2\|198	without_aae		No				Single base exchange		N/A	Homozygous in gnomAD

MutationT@ster 2025

Variant:

6:21118008G>C_1_ENST00000378610

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Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 2|198 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr6:21118008G>C (GRCh38)

Gene symbol

CDKAL1

Gene constraints

LOEUF: 0.64, LOF (oe): 0.39, misssense (oe): 0.88, synonymous (oe): 0.97 ? (gnomAD)

Ensembl transcript ID

ENST00000378610.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.1299+9545G>C
g.583552G>C

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs4389757
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	1017	15261	16278

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.42	0.012
	1.654	0.02
(flanking)	0.5	0.016

?

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

6

Strand

1

Original gDNA sequence snippet

TGCTGACAAAGTTTTAACCTGGGGAACTTGTTTGGAAAATT

Altered gDNA sequence snippet

TGCTGACAAAGTTTTAACCTCGGGAACTTGTTTGGAAAATT

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MPSASCDTLL DDIEDIVSQE DSKPQDRHFV RKDVVPKVRR RNTQKYLQEE ENSPPSDSTI
PGIQKIWIRT WGCSHNNSDG EYMAGQLAAY GYKITENASD ADLWLLNSCT VKNPAEDHFR
NSIKKAQEEN KKIVLAGCVP QAQPRQDYLK GLSIIGVQQI DRVVEVVEET IKGHSVRLLG
QKKDNGRRLG GARLDLPKIR KNPLIEIISI NTGCLNACTY CKTKHARGNL ASYPIDELVD
RAKQSFQEGV CEIWLTSEDT GAYGRDIGTN LPTLLWKLVE VIPEGAMLRL GMTNPPYILE
HLEEMAKILN HPRVYAFLHI PVQSASDSVL MEMKREYCVA DFKRVVDFLK EKVPGITIAT
DIICGFPGET DQDFQETVKL VEEYKFPSLF INQFYPRPGT PAAKMEQVPA QVKKQRTKDL
SRVFHSYSPY DHKIGERQQV LVTEESFDSK FYVAHNQFYE QVLVPKNPAF MGKMVEVDIY
ESGKHFMKGQ PVSDAKVYTP SISKPLAKGE VSGLTKDFRN GLGNQLSSGS HTSAASQCDS
ASSRMVLPMP RLHQDCALRM SVGLALLGLL FAFFVKVYN*

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

11 / 11

Last intron/exon boundary

1558

Theoretical NMD boundary in CDS

1497

Length of CDS

1740

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

583552

Chromosomal position

21118008

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

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MutationT@ster 2025

Variant:

6:21118008G>C_2_ENST00000274695

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 2|198 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr6:21118008G>C (GRCh38)

Gene symbol

CDKAL1

Gene constraints

LOEUF: 0.64, LOF (oe): 0.39, misssense (oe): 0.88, synonymous (oe): 0.97 ? (gnomAD)

Ensembl transcript ID

ENST00000274695.8

Genbank transcript ID

NM_017774 (exact from MANE)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.1299+9545G>C
g.583552G>C

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs4389757
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	1017	15261	16278

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.42	0.012
	1.654	0.02
(flanking)	0.5	0.016

?

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

6

Strand

1

Original gDNA sequence snippet

TGCTGACAAAGTTTTAACCTGGGGAACTTGTTTGGAAAATT

Altered gDNA sequence snippet

TGCTGACAAAGTTTTAACCTCGGGAACTTGTTTGGAAAATT

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MPSASCDTLL DDIEDIVSQE DSKPQDRHFV RKDVVPKVRR RNTQKYLQEE ENSPPSDSTI
PGIQKIWIRT WGCSHNNSDG EYMAGQLAAY GYKITENASD ADLWLLNSCT VKNPAEDHFR
NSIKKAQEEN KKIVLAGCVP QAQPRQDYLK GLSIIGVQQI DRVVEVVEET IKGHSVRLLG
QKKDNGRRLG GARLDLPKIR KNPLIEIISI NTGCLNACTY CKTKHARGNL ASYPIDELVD
RAKQSFQEGV CEIWLTSEDT GAYGRDIGTN LPTLLWKLVE VIPEGAMLRL GMTNPPYILE
HLEEMAKILN HPRVYAFLHI PVQSASDSVL MEMKREYCVA DFKRVVDFLK EKVPGITIAT
DIICGFPGET DQDFQETVKL VEEYKFPSLF INQFYPRPGT PAAKMEQVPA QVKKQRTKDL
SRVFHSYSPY DHKIGERQQV LVTEESFDSK FYVAHNQFYE QVLVPKNPAF MGKMVEVDIY
ESGKHFMKGQ PVSDAKVYTP SISKPLAKGE VSGLTKDFRN GLGNQLSSGS HTSAASQCDS
ASSRMVLPMP RLHQDCALRM SVGLALLGLL FAFFVKVYN*

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

168 / 168

Last intron/exon boundary

1715

Theoretical NMD boundary in CDS

1497

Length of CDS

1740

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

583552

Chromosomal position

21118008

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