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: ENST00000579755
Querying Taster for transcript #2: ENST00000530628
Querying Taster for transcript #3: ENST00000498628
Querying Taster for transcript #4: ENST00000494262
MT speed 0.15 s - this script 2.534703 s

Transcript summary:

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Transcript	Gene symbol	Prediction	Tree vote	Model	Splice site change	Variant type	Protein length	Features at a glance
ENST00000579755(MANE Select)	CDKN2A	Deleterious	76\|24	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000530628	CDKN2A	Deleterious	76\|24	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000498628	CDKN2A	Benign	32\|168	without_aae	No	Single base exchange	N/A
ENST00000494262	CDKN2A	Benign	32\|168	without_aae	No	Single base exchange	N/A

MutationT@ster 2025

Variant:

9:21994325G>A_1_ENST00000579755

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 76|24 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr9:21994325G>A (GRCh38)

Gene symbol

CDKN2A

Gene constraints

LOEUF: 1.50, LOF (oe): 0.81, misssense (oe): 1.16, synonymous (oe): 1.11 ? (gnomAD)

Ensembl transcript ID

ENST00000579755.2

Genbank transcript ID

NM_058195 (exact from MANE)

UniProt / AlphaMissense peptide

ARF_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.7C>T
g.977C>T

AA changes

AAE:	R3C	?
Score:	180

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs1554659249
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	3	3

Protein conservation

Species	Match	AA
Human		3	M	V	R	R	F	L	V	T	L	R	I	R	R	A	C
mutated	not conserved	3	M	V	C	R	F	L	V	T	L	R	I	R	R	A	C	G	P	P	R	V	R	V
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	64	REGION	Interaction with CDK5RAP3 and MDM2	lost
1	132	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.615	0.997
	1.481	0.993
(flanking)	-0.479	0.914

?

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

9

Strand

-1

Original gDNA sequence snippet

GAGGCGGCGAGAACATGGTGCGCAGGTTCTTGGTGACCCTC

Altered gDNA sequence snippet

GAGGCGGCGAGAACATGGTGTGCAGGTTCTTGGTGACCCTC

Original cDNA sequence snippet

GAGGCGGCGAGAACATGGTGCGCAGGTTCTTGGTGACCCTC

Altered cDNA sequence snippet

GAGGCGGCGAGAACATGGTGTGCAGGTTCTTGGTGACCCTC

Wildtype AA sequence

MVRRFLVTLR IRRACGPPRV RVFVVHIPRL TGEWAAPGAP AAVALVLMLL RSQRLGQQPL
PRRPGHDDGQ RPSGGAAAAP RRGAQLRRPR HSHPTRARRC PGGLPGHAGG AAPGRGAAGR
ARCLGPSARG PG*

Mutated AA sequence

MVCRFLVTLR IRRACGPPRV RVFVVHIPRL TGEWAAPGAP AAVALVLMLL RSQRLGQQPL
PRRPGHDDGQ RPSGGAAAAP RRGAQLRRPR HSHPTRARRC PGGLPGHAGG AAPGRGAAGR
ARCLGPSARG PG*

Position of stopcodon in wt / mu CDS

399 / 399

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

133 / 133

Position of stopcodon in wt / mu cDNA

460 / 460

Position of start ATG in wt / mu cDNA

62 / 62

Last intron/exon boundary

561

Theoretical NMD boundary in CDS

449

Length of CDS

399

Coding sequence (CDS) position

7

cDNA position

68

gDNA position

977

Chromosomal position

21994325

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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MutationT@ster 2025

Variant:

9:21994325G>A_2_ENST00000530628

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 76|24 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr9:21994325G>A (GRCh38)

Gene symbol

CDKN2A

Gene constraints

LOEUF: 1.38, LOF (oe): 0.70, misssense (oe): 1.16, synonymous (oe): 1.11 ? (gnomAD)

Ensembl transcript ID

ENST00000530628.2

Genbank transcript ID

UniProt / AlphaMissense peptide

ARF_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.7C>T
g.977C>T

AA changes

AAE:	R3C	?
Score:	180

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs1554659249
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	3	3

Protein conservation

Species	Match	AA
Human		3	M	V	R	R	F	L	V	T	L	R	I	R	R	A	C
mutated	not conserved	3	M	V	C	R	F	L	V	T	L	R	I	R	R	A	C	G	P	P	R	V	R	V
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	64	REGION	Interaction with CDK5RAP3 and MDM2	lost
1	132	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.615	0.997
	1.481	0.993
(flanking)	-0.479	0.914

?

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

9

Strand

-1

Original gDNA sequence snippet

GAGGCGGCGAGAACATGGTGCGCAGGTTCTTGGTGACCCTC

Altered gDNA sequence snippet

GAGGCGGCGAGAACATGGTGTGCAGGTTCTTGGTGACCCTC

Original cDNA sequence snippet

GAGGCGGCGAGAACATGGTGCGCAGGTTCTTGGTGACCCTC

Altered cDNA sequence snippet

GAGGCGGCGAGAACATGGTGTGCAGGTTCTTGGTGACCCTC

Wildtype AA sequence

MVRRFLVTLR IRRACGPPRV RVFVVHIPRL TGEWAAPGAP AAVALVLMLL RSQRLGQQPL
PRRPGHDDGQ RPSGGAAAAP RRGAQLRRPR HSHPTRARRC PGGLPGHAGG AAPGRGAAGR
ARCLGPSARG PG*

Mutated AA sequence

MVCRFLVTLR IRRACGPPRV RVFVVHIPRL TGEWAAPGAP AAVALVLMLL RSQRLGQQPL
PRRPGHDDGQ RPSGGAAAAP RRGAQLRRPR HSHPTRARRC PGGLPGHAGG AAPGRGAAGR
ARCLGPSARG PG*

Position of stopcodon in wt / mu CDS

399 / 399

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

133 / 133

Position of stopcodon in wt / mu cDNA

479 / 479

Position of start ATG in wt / mu cDNA

81 / 81

Last intron/exon boundary

506

Theoretical NMD boundary in CDS

375

Length of CDS

399

Coding sequence (CDS) position

7

cDNA position

87

gDNA position

977

Chromosomal position

21994325

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

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MutationT@ster 2025

Variant:

9:21994325G>A_3_ENST00000498628

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Prediction:

BenignPermalink

Summary:

Model: without_aae
Tree vote: 32|168 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr9:21994325G>A (GRCh38)

Gene symbol

CDKN2A

Gene constraints

LOEUF: 1.30, LOF (oe): 0.42, misssense (oe): 1.24, synonymous (oe): 1.27 ? (gnomAD)

Ensembl transcript ID

ENST00000498628.6

Genbank transcript ID

NM_001363763 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.-4+496C>T
g.977C>T

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	rs1554659249
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	3	3

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.615	0.997
	1.481	0.993
(flanking)	-0.479	0.914

?

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

9

Strand

-1

Original gDNA sequence snippet

GAGGCGGCGAGAACATGGTGCGCAGGTTCTTGGTGACCCTC

Altered gDNA sequence snippet

GAGGCGGCGAGAACATGGTGTGCAGGTTCTTGGTGACCCTC

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MMMGSARVAE LLLLHGAEPN CADPATLTRP VHDAAREGFL DTLVVLHRAG ARLDVRDAWG
RLPVDLAEEL GHRDVARYLR AAAGGTRGSN HARIDAAEGP SDIPD*

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

485 / 485

Last intron/exon boundary

788

Theoretical NMD boundary in CDS

253

Length of CDS

318

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

977

Chromosomal position

21994325

Speed

0.01 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:

9:21994325G>A_4_ENST00000494262

Back to summary table

Prediction:

BenignPermalink

Summary:

Model: without_aae
Tree vote: 32|168 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr9:21994325G>A (GRCh38)

Gene symbol

CDKN2A

Gene constraints

LOEUF: 1.30, LOF (oe): 0.42, misssense (oe): 1.24, synonymous (oe): 1.27 ? (gnomAD)

Ensembl transcript ID

ENST00000494262.5

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.-175-272C>T
g.977C>T

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	rs1554659249
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	3	3

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.615	0.997
	1.481	0.993
(flanking)	-0.479	0.914

?

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

9

Strand

-1

Original gDNA sequence snippet

GAGGCGGCGAGAACATGGTGCGCAGGTTCTTGGTGACCCTC

Altered gDNA sequence snippet

GAGGCGGCGAGAACATGGTGTGCAGGTTCTTGGTGACCCTC

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MMMGSARVAE LLLLHGAEPN CADPATLTRP VHDAAREGFL DTLVVLHRAG ARLDVRDAWG
RLPVDLAEEL GHRDVARYLR AAAGGTRGSN HARIDAAEGP SDIPD*

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

625 / 625

Last intron/exon boundary

928

Theoretical NMD boundary in CDS

253

Length of CDS

318

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

977

Chromosomal position

21994325

Speed

0.01 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