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: ENST00000257904
Querying Taster for transcript #2: ENST00000312990
Querying Taster for transcript #3: ENST00000549606
Querying Taster for transcript #4: ENST00000257910
Querying Taster for transcript #5: ENST00000547992
MT speed 0.22 s - this script 2.578691 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
ENST00000257910(MANE Select)	TSPAN31	Deleterious	76\|24	3utr	No	Single base exchange	N/A
ENST00000312990	CDK4	Deleterious	81\|19	3utr	No	Single base exchange	N/A
ENST00000547992	TSPAN31	Deleterious	94\|6	3utr	No	Single base exchange	N/A
ENST00000257904(MANE Select)	CDK4	Deleterious	95\|5	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000549606	CDK4	Deleterious	98\|2	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed

MutationT@ster 2025

Variant:

12:57748571G>A_4_ENST00000257910

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Prediction:

DeleteriousPermalink

Summary:

Model: 3utr
Tree vote: 76|24 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr12:57748571G>A (GRCh38)

Gene symbol

TSPAN31

Gene constraints

LOEUF: 0.92, LOF (oe): 0.61, misssense (oe): 0.80, synonymous (oe): 0.93 ? (gnomAD)

Ensembl transcript ID

ENST00000257910.8

Genbank transcript ID

NM_005981 (exact from MANE), NM_001330169 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

3'UTR

DNA changes

cDNA.2030G>A
g.10559G>A

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

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

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.841	1
	8.207	1
(flanking)	6.52	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

polyA signal ok

AA sequence altered

N/A

Chromosome

12

Strand

1

Original gDNA sequence snippet

GTAGATAAGAGTGCTGCAGAGCTCGAAAGGCAGAGATTCGC

Altered gDNA sequence snippet

GTAGATAAGAGTGCTGCAGAACTCGAAAGGCAGAGATTCGC

Original cDNA sequence snippet

GTAGATAAGAGTGCTGCAGAGCTCGAAAGGCAGAGATTCGC

Altered cDNA sequence snippet

GTAGATAAGAGTGCTGCAGAACTCGAAAGGCAGAGATTCGC

Wildtype AA sequence

MVCGGFACSK NALCALNVVY MLVSLLLIGV AAWGKGLGLV SSIHIIGGVI AVGVFLLLIA
VAGLVGAVNH HQVLLFFYMI ILGLVFIFQF VISCSCLAIN RSKQTDVINA SWWVMSNKTR
DELERSFDCC GLFNLTTLYQ QDYDFCTAIC KSQSPTCQMC GEKFLKHSDE ALKILGGVGL
FFSFTEILGV WLAMRFRNQK DPRANPSAFL *

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

117 / 117

Last intron/exon boundary

674

Theoretical NMD boundary in CDS

507

Length of CDS

633

Coding sequence (CDS) position

N/A

cDNA position

2030

gDNA position

10559

Chromosomal position

57748571

Speed

0.03 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:

12:57748571G>A_2_ENST00000312990

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Prediction:

DeleteriousPermalink

Summary:

Model: 3utr
Tree vote: 81|19 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr12:57748571G>A (GRCh38)

Gene symbol

CDK4

Gene constraints

LOEUF: 0.92, LOF (oe): 0.51, misssense (oe): 0.72, synonymous (oe): 0.80 ? (gnomAD)

Ensembl transcript ID

ENST00000312990.10

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

3'UTR

DNA changes

cDNA.806C>T
g.7443C>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

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

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.841	1
	8.207	1
(flanking)	6.52	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

polyA signal ok

AA sequence altered

N/A

Chromosome

12

Strand

-1

Original gDNA sequence snippet

GCGAATCTCTGCCTTTCGAGCTCTGCAGCACTCTTATCTAC

Altered gDNA sequence snippet

GCGAATCTCTGCCTTTCGAGTTCTGCAGCACTCTTATCTAC

Original cDNA sequence snippet

GCGAATCTCTGCCTTTCGAGCTCTGCAGCACTCTTATCTAC

Altered cDNA sequence snippet

GCGAATCTCTGCCTTTCGAGTTCTGCAGCACTCTTATCTAC

Wildtype AA sequence

MATSRYEPVA EIGVGAYGTV YKARDPHSGH FVALKSVRVP NGGGGGGGLP ISTVREVALL
RRLEAFEHPN VVRLMDVCAT SRTDREIKRC FVESLSSVET LKPTSWAKSL T*

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

293 / 293

Last intron/exon boundary

759

Theoretical NMD boundary in CDS

416

Length of CDS

336

Coding sequence (CDS) position

N/A

cDNA position

806

gDNA position

7443

Chromosomal position

57748571

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:

12:57748571G>A_5_ENST00000547992

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Prediction:

DeleteriousPermalink

Summary:

Model: 3utr
Tree vote: 94|6 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr12:57748571G>A (GRCh38)

Gene symbol

TSPAN31

Gene constraints

LOEUF: 1.35, LOF (oe): 0.83, misssense (oe): 0.85, synonymous (oe): 0.88 ? (gnomAD)

Ensembl transcript ID

ENST00000547992.5

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

3'UTR

DNA changes

cDNA.1794G>A
g.10559G>A

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

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

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.841	1
	8.207	1
(flanking)	6.52	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

polyA signal ok

AA sequence altered

N/A

Chromosome

12

Strand

1

Original gDNA sequence snippet

GTAGATAAGAGTGCTGCAGAGCTCGAAAGGCAGAGATTCGC

Altered gDNA sequence snippet

GTAGATAAGAGTGCTGCAGAACTCGAAAGGCAGAGATTCGC

Original cDNA sequence snippet

GTAGATAAGAGTGCTGCAGAGCTCGAAAGGCAGAGATTCGC

Altered cDNA sequence snippet

GTAGATAAGAGTGCTGCAGAACTCGAAAGGCAGAGATTCGC

Wildtype AA sequence

MVCGGFACSK NALCALNVVY MLVSLLLIGV AAWGKGLGLV SSIHIIGGVI AVGVFLLLIA
VAGLICKSQS PTCQMCGEKF LKHSDEALKI LGGVGLFFSF TEILGVWLAM RFRNQKDPRA
NPSAFL*

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

133 / 133

Last intron/exon boundary

438

Theoretical NMD boundary in CDS

255

Length of CDS

381

Coding sequence (CDS) position

N/A

cDNA position

1794

gDNA position

10559

Chromosomal position

57748571

Speed

0.04 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:

12:57748571G>A_1_ENST00000257904

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 95|5 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr12:57748571G>A (GRCh38)

Gene symbol

CDK4

Gene constraints

LOEUF: 0.61, LOF (oe): 0.38, misssense (oe): 0.69, synonymous (oe): 1.01 ? (gnomAD)

Ensembl transcript ID

ENST00000257904.11

Genbank transcript ID

NM_000075 (exact from MANE)

UniProt / AlphaMissense peptide

CDK4_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.866C>T
g.7443C>T

AA changes

AAE:	A289V	?
Score:	64

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

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

Protein conservation

Species	Match	AA	Alignment
Human		289	F	N	P	H	K	R	I	S	A	F	R	A	L	Q	H	S	Y	L	H	K	D	E	G	N
mutated	not conserved	289	F	N	P	H	K	R	I	S	A	F	R	V	L	Q	H	S	Y	L	H	K	D	E	G
Ptroglodytes	all identical	289	F	N	P	H	K	R	I	S	A	F	R	A	L	Q	H	S	Y	L	H	K	D	E	G
Mmulatta	all identical	289	F	N	P	H	K	R	I	S	A	F	R	A	L	Q	H	S	Y	L	H	K	D	E	G
Fcatus	no alignment	n/a
Mmusculus	all identical	289	F	N	P	H	K	R	I	S	A	F	R	A	L	Q	H	S	Y	L	H	K	E	E	S
Ggallus	no homologue
Trubripes	all identical	291	F	D	P	T	K	R	I	S	A	L	K	A	L	E	H	P	Y
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	all identical	289	F	S	P	Q	K	R	I	S	A	S	D	A	L	L	H	P	F	F	A	E	D

Protein features

Start (aa)	End (aa)	Feature	Details
2	303	CHAIN		lost
6	295	DOMAIN	Protein kinase	lost
286	290	HELIX		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.841	1
	8.207	1
(flanking)	6.52	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

12

Strand

-1

Original gDNA sequence snippet

GCGAATCTCTGCCTTTCGAGCTCTGCAGCACTCTTATCTAC

Altered gDNA sequence snippet

GCGAATCTCTGCCTTTCGAGTTCTGCAGCACTCTTATCTAC

Original cDNA sequence snippet

GCGAATCTCTGCCTTTCGAGCTCTGCAGCACTCTTATCTAC

Altered cDNA sequence snippet

GCGAATCTCTGCCTTTCGAGTTCTGCAGCACTCTTATCTAC

Wildtype AA sequence

MATSRYEPVA EIGVGAYGTV YKARDPHSGH FVALKSVRVP NGGGGGGGLP ISTVREVALL
RRLEAFEHPN VVRLMDVCAT SRTDREIKVT LVFEHVDQDL RTYLDKAPPP GLPAETIKDL
MRQFLRGLDF LHANCIVHRD LKPENILVTS GGTVKLADFG LARIYSYQMA LTPVVVTLWY
RAPEVLLQST YATPVDMWSV GCIFAEMFRR KPLFCGNSEA DQLGKIFDLI GLPPEDDWPR
DVSLPRGAFP PRGPRPVQSV VPEMEESGAQ LLLEMLTFNP HKRISAFRAL QHSYLHKDEG
NPE*

Mutated AA sequence

MATSRYEPVA EIGVGAYGTV YKARDPHSGH FVALKSVRVP NGGGGGGGLP ISTVREVALL
RRLEAFEHPN VVRLMDVCAT SRTDREIKVT LVFEHVDQDL RTYLDKAPPP GLPAETIKDL
MRQFLRGLDF LHANCIVHRD LKPENILVTS GGTVKLADFG LARIYSYQMA LTPVVVTLWY
RAPEVLLQST YATPVDMWSV GCIFAEMFRR KPLFCGNSEA DQLGKIFDLI GLPPEDDWPR
DVSLPRGAFP PRGPRPVQSV VPEMEESGAQ LLLEMLTFNP HKRISAFRVL QHSYLHKDEG
NPE*

Position of stopcodon in wt / mu CDS

912 / 912

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

304 / 304

Position of stopcodon in wt / mu cDNA

1067 / 1067

Position of start ATG in wt / mu cDNA

156 / 156

Last intron/exon boundary

974

Theoretical NMD boundary in CDS

768

Length of CDS

912

Coding sequence (CDS) position

866

cDNA position

1021

gDNA position

7443

Chromosomal position

57748571

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

MutationT@ster 2025

Variant:

12:57748571G>A_3_ENST00000549606

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed

Model: simple_aae
Tree vote: 98|2 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr12:57748571G>A (GRCh38)

Gene symbol

CDK4

Gene constraints

LOEUF: 1.37, LOF (oe): 0.54, misssense (oe): 0.80, synonymous (oe): 1.04 ? (gnomAD)

Ensembl transcript ID

ENST00000549606.5

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.77C>T
g.7443C>T

AA changes

AAE:	A26V	?
Score:	64

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

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

Protein conservation

Species	Match	AA	Alignment
Human		26	F	N	P	H	K	R	I	S	A	F	R	A	L	Q	H	S	Y	L	H	K	D	E	G	N
mutated	not conserved	26	F	N	P	H	K	R	I	S	A	F	R	V	L	Q	H	S	Y	L	H	K	D	E	G
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)	0.841	1
	8.207	1
(flanking)	6.52	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

12

Strand

-1

Original gDNA sequence snippet

GCGAATCTCTGCCTTTCGAGCTCTGCAGCACTCTTATCTAC

Altered gDNA sequence snippet

GCGAATCTCTGCCTTTCGAGTTCTGCAGCACTCTTATCTAC

Original cDNA sequence snippet

GCGAATCTCTGCCTTTCGAGCTCTGCAGCACTCTTATCTAC

Altered cDNA sequence snippet

GCGAATCTCTGCCTTTCGAGTTCTGCAGCACTCTTATCTAC

Wildtype AA sequence

MEESGAQLLL EMLTFNPHKR ISAFRALQHS YLHKDEGNPE *

Mutated AA sequence

MEESGAQLLL EMLTFNPHKR ISAFRVLQHS YLHKDEGNPE *

Position of stopcodon in wt / mu CDS

123 / 123

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

41 / 41

Position of stopcodon in wt / mu cDNA

459 / 459

Position of start ATG in wt / mu cDNA

337 / 337

Last intron/exon boundary

366

Theoretical NMD boundary in CDS

cannot be calculated, distance between start ATG and last intron/exon boundary is too small

Length of CDS

123

Coding sequence (CDS) position

77

cDNA position

413

gDNA position

7443

Chromosomal position

57748571

Speed

0.04 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