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: ENST00000528057
Querying Taster for transcript #2: ENST00000334205
MT speed 0.7 s - this script 3.13915 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
ENST00000528057	RPS6KA4	Deleterious	90\|10	simple_aae		No				Single base exchange		Normal	Amino acid sequence changed
ENST00000334205(MANE Select)	RPS6KA4	Deleterious	93\|7	simple_aae		No				Single base exchange		Normal	Amino acid sequence changed Protein features (might be) affected

MutationT@ster 2025

Variant:

11:64361871C>T_1_ENST00000528057

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed

Model: simple_aae
Tree vote: 90|10 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr11:64361871C>T (GRCh38)

Gene symbol

RPS6KA4

Gene constraints

LOEUF: 0.65, LOF (oe): 0.50, misssense (oe): 0.84, synonymous (oe): 1.08 ? (gnomAD)

Ensembl transcript ID

ENST00000528057.5

Genbank transcript ID

NM_001006944 (by similarity), NM_001300802 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.775C>T
g.2724C>T

AA changes

AAE:	P259S	?
Score:	74

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

	Not in dbSNP
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	0	6	6

Protein conservation

Species	Match	AA	Alignment
Human		259	A	E	V	S	R	R	I	L	K	C	S	P	P	F	P	P	R	I	G	P	V	A	Q	D
mutated	not conserved	259	A	E	V	S	R	R	I	L	K	C	S	S	P	F	P	P	R	I	G	P	V	A	Q
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)	0.083	0.035
	4.487	0.997
(flanking)	4.497	0.998

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

20

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

11

Strand

1

Original gDNA sequence snippet

GACGGATCCTGAAGTGCTCCCCTCCCTTCCCCCCTCGGATC

Altered gDNA sequence snippet

GACGGATCCTGAAGTGCTCCTCTCCCTTCCCCCCTCGGATC

Original cDNA sequence snippet

GACGGATCCTGAAGTGCTCCCCTCCCTTCCCCCCTCGGATC

Altered cDNA sequence snippet

GACGGATCCTGAAGTGCTCCTCTCCCTTCCCCCCTCGGATC

Wildtype AA sequence

MGDEDDDESC AVELRITEAN LTGHEEKVSV ENFELLKVLG TGAYGKVFLV RKAGGHDAGK
LYAMKVLRKA ALVQRAKTQE HTRTERSVLE LVRQAPFLVT LHYAFQTDAK LHLILDYVSG
GEMFTHLYQR QYFKEAEVRV YGGEIVLALE HLHKLGIIYR DLKLENVLLD SEGHIVLTDF
GLSKEFLTEE KERTFSFCGT IEYMAPEIIR SKTGHGKAVD WWSLGILLFE LLTGASPFTL
EGERNTQAEV SRRILKCSPP FPPRIGPVAQ DLLQRLLCKD PKKRLGAGPQ GAQEVRNHPF
FQGLDWVALA ARKIPAPFRP QIRSELDVGN FAEEFTRLEP VYSPPGSPPP GDPRIFQGYS
FVAPSILFDH NNAVMTDGLE APGAGDRPGR AAVARSAMMQ YELDLREPAL GQGSFSVCRR
CRQRQSGQEF AVKILSRRLE ANTQREVAAL RLCQSHPNVV NLHEVHHDQL HTYLVLELLR
GGELLEHIRK KRHFSESEAS QILRSLVSAV SFMHEEAGVV HRDLKPENIL YADDTPGAPV
KIIDFGFARL RPQSPGVPMQ TPCFTLQYAA PELLAQQGYD ESCDLWSLGV ILYMMLSGQV
PFQGASGQGG QSQAAEIMCK IREGRFSLDG EAWQGVSEEA KELVRGLLTV DPAKRLKLEG
LRGSSWLQDG SARSSPPLRT PDVLESSGPA VRSGLNATFM AFNRGKREGF FLKSVENAPL
AKRRKQKLRS ATASRRGSPA PANPGRAPVA SKGAPRRANG PLPPS*

Mutated AA sequence

MGDEDDDESC AVELRITEAN LTGHEEKVSV ENFELLKVLG TGAYGKVFLV RKAGGHDAGK
LYAMKVLRKA ALVQRAKTQE HTRTERSVLE LVRQAPFLVT LHYAFQTDAK LHLILDYVSG
GEMFTHLYQR QYFKEAEVRV YGGEIVLALE HLHKLGIIYR DLKLENVLLD SEGHIVLTDF
GLSKEFLTEE KERTFSFCGT IEYMAPEIIR SKTGHGKAVD WWSLGILLFE LLTGASPFTL
EGERNTQAEV SRRILKCSSP FPPRIGPVAQ DLLQRLLCKD PKKRLGAGPQ GAQEVRNHPF
FQGLDWVALA ARKIPAPFRP QIRSELDVGN FAEEFTRLEP VYSPPGSPPP GDPRIFQGYS
FVAPSILFDH NNAVMTDGLE APGAGDRPGR AAVARSAMMQ YELDLREPAL GQGSFSVCRR
CRQRQSGQEF AVKILSRRLE ANTQREVAAL RLCQSHPNVV NLHEVHHDQL HTYLVLELLR
GGELLEHIRK KRHFSESEAS QILRSLVSAV SFMHEEAGVV HRDLKPENIL YADDTPGAPV
KIIDFGFARL RPQSPGVPMQ TPCFTLQYAA PELLAQQGYD ESCDLWSLGV ILYMMLSGQV
PFQGASGQGG QSQAAEIMCK IREGRFSLDG EAWQGVSEEA KELVRGLLTV DPAKRLKLEG
LRGSSWLQDG SARSSPPLRT PDVLESSGPA VRSGLNATFM AFNRGKREGF FLKSVENAPL
AKRRKQKLRS ATASRRGSPA PANPGRAPVA SKGAPRRANG PLPPS*

Position of stopcodon in wt / mu CDS

2298 / 2298

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

766 / 766

Position of stopcodon in wt / mu cDNA

2386 / 2386

Position of start ATG in wt / mu cDNA

89 / 89

Last intron/exon boundary

2188

Theoretical NMD boundary in CDS

2049

Length of CDS

2298

Coding sequence (CDS) position

775

cDNA position

863

gDNA position

2724

Chromosomal position

64361871

Speed

0.35 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:

11:64361871C>T_2_ENST00000334205

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 93|7 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr11:64361871C>T (GRCh38)

Gene symbol

RPS6KA4

Gene constraints

LOEUF: 0.63, LOF (oe): 0.48, misssense (oe): 0.84, synonymous (oe): 1.08 ? (gnomAD)

Ensembl transcript ID

ENST00000334205.9

Genbank transcript ID

NM_003942 (exact from MANE), NM_001318361 (by similarity)

UniProt / AlphaMissense peptide

KS6A4_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.775C>T
g.2724C>T

AA changes

AAE:	P259S	?
Score:	74

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

	Not in dbSNP
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	0	6	6

Protein conservation

Species	Match	AA	Alignment
Human		259	A	E	V	S	R	R	I	L	K	C	S	P	P	F	P	P	R	I	G	P	V	A	Q	D
mutated	not conserved	259	A	E	V	S	R	R	I	L	K	C	S	S	P	F	P	P	R	I	G	P	V	A	Q
Ptroglodytes	all identical	259	A	E	V	S	R	R	I	L	K	C	S	P	P	F	P	P	R	I	G	P	V	A	Q
Mmulatta	all identical	259	A	E	V	S	R	R	I	L	K	C	S	P	P	F	P	P	R	I	G	P	V	A	Q
Fcatus	all identical	259	A	E	V	S	R	R	I	L	K	C	S	P	P	F	P	P	R	I	G	P	V	A	Q
Mmusculus	all identical	259	A	E	V	S	R	R	I	L	K	C	S	P	P	F	P	L	R	I	G	P	V	A	Q
Ggallus	no homologue
Trubripes	all identical	287	S	E	V	S	K	R	I	L	R	C	D	P	P	F	P	S	M	I	G	H	T	A	Q
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	not conserved	273	A	D	K	D	K	S	I	L	K	G	K	V	R	L	P	P
Xtropicalis	no homologue

Protein features

Start (aa)	End (aa)	Feature	Details
1	772	CHAIN		lost
33	301	DOMAIN	Protein kinase	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.083	0.035
	4.487	0.997
(flanking)	4.497	0.998

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

20

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

11

Strand

1

Original gDNA sequence snippet

GACGGATCCTGAAGTGCTCCCCTCCCTTCCCCCCTCGGATC

Altered gDNA sequence snippet

GACGGATCCTGAAGTGCTCCTCTCCCTTCCCCCCTCGGATC

Original cDNA sequence snippet

GACGGATCCTGAAGTGCTCCCCTCCCTTCCCCCCTCGGATC

Altered cDNA sequence snippet

GACGGATCCTGAAGTGCTCCTCTCCCTTCCCCCCTCGGATC

Wildtype AA sequence

MGDEDDDESC AVELRITEAN LTGHEEKVSV ENFELLKVLG TGAYGKVFLV RKAGGHDAGK
LYAMKVLRKA ALVQRAKTQE HTRTERSVLE LVRQAPFLVT LHYAFQTDAK LHLILDYVSG
GEMFTHLYQR QYFKEAEVRV YGGEIVLALE HLHKLGIIYR DLKLENVLLD SEGHIVLTDF
GLSKEFLTEE KERTFSFCGT IEYMAPEIIR SKTGHGKAVD WWSLGILLFE LLTGASPFTL
EGERNTQAEV SRRILKCSPP FPPRIGPVAQ DLLQRLLCKD PKKRLGAGPQ GAQEVRNHPF
FQGLDWVALA ARKIPAPFRP QIRSELDVGN FAEEFTRLEP VYSPPGSPPP GDPRIFQGYS
FVAPSILFDH NNAVMTDGLE APGAGDRPGR AAVARSAMMQ DSPFFQQYEL DLREPALGQG
SFSVCRRCRQ RQSGQEFAVK ILSRRLEANT QREVAALRLC QSHPNVVNLH EVHHDQLHTY
LVLELLRGGE LLEHIRKKRH FSESEASQIL RSLVSAVSFM HEEAGVVHRD LKPENILYAD
DTPGAPVKII DFGFARLRPQ SPGVPMQTPC FTLQYAAPEL LAQQGYDESC DLWSLGVILY
MMLSGQVPFQ GASGQGGQSQ AAEIMCKIRE GRFSLDGEAW QGVSEEAKEL VRGLLTVDPA
KRLKLEGLRG SSWLQDGSAR SSPPLRTPDV LESSGPAVRS GLNATFMAFN RGKREGFFLK
SVENAPLAKR RKQKLRSATA SRRGSPAPAN PGRAPVASKG APRRANGPLP PS*

Mutated AA sequence

MGDEDDDESC AVELRITEAN LTGHEEKVSV ENFELLKVLG TGAYGKVFLV RKAGGHDAGK
LYAMKVLRKA ALVQRAKTQE HTRTERSVLE LVRQAPFLVT LHYAFQTDAK LHLILDYVSG
GEMFTHLYQR QYFKEAEVRV YGGEIVLALE HLHKLGIIYR DLKLENVLLD SEGHIVLTDF
GLSKEFLTEE KERTFSFCGT IEYMAPEIIR SKTGHGKAVD WWSLGILLFE LLTGASPFTL
EGERNTQAEV SRRILKCSSP FPPRIGPVAQ DLLQRLLCKD PKKRLGAGPQ GAQEVRNHPF
FQGLDWVALA ARKIPAPFRP QIRSELDVGN FAEEFTRLEP VYSPPGSPPP GDPRIFQGYS
FVAPSILFDH NNAVMTDGLE APGAGDRPGR AAVARSAMMQ DSPFFQQYEL DLREPALGQG
SFSVCRRCRQ RQSGQEFAVK ILSRRLEANT QREVAALRLC QSHPNVVNLH EVHHDQLHTY
LVLELLRGGE LLEHIRKKRH FSESEASQIL RSLVSAVSFM HEEAGVVHRD LKPENILYAD
DTPGAPVKII DFGFARLRPQ SPGVPMQTPC FTLQYAAPEL LAQQGYDESC DLWSLGVILY
MMLSGQVPFQ GASGQGGQSQ AAEIMCKIRE GRFSLDGEAW QGVSEEAKEL VRGLLTVDPA
KRLKLEGLRG SSWLQDGSAR SSPPLRTPDV LESSGPAVRS GLNATFMAFN RGKREGFFLK
SVENAPLAKR RKQKLRSATA SRRGSPAPAN PGRAPVASKG APRRANGPLP PS*

Position of stopcodon in wt / mu CDS

2319 / 2319

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

773 / 773

Position of stopcodon in wt / mu cDNA

2393 / 2393

Position of start ATG in wt / mu cDNA

75 / 75

Last intron/exon boundary

2195

Theoretical NMD boundary in CDS

2070

Length of CDS

2319

Coding sequence (CDS) position

775

cDNA position

849

gDNA position

2724

Chromosomal position

64361871

Speed

0.35 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