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: ENST00000380394
Querying Taster for transcript #2: ENST00000380384
Querying Taster for transcript #3: ENST00000315377
MT speed 0.04 s - this script 2.394123 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
ENST00000380394(MANE Select)	RPS6	Benign	53\|147	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000380384	RPS6	Benign	53\|147	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000315377	RPS6	Benign	53\|147	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD

MutationT@ster 2025

Variant:

9:19376395A>G_1_ENST00000380394

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Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 53|147 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr9:19376395A>G (GRCh38)

Gene symbol

RPS6

Gene constraints

LOEUF: 0.17, LOF (oe): 0.03, misssense (oe): 0.78, synonymous (oe): 1.39 ? (gnomAD)

Ensembl transcript ID

ENST00000380394.9

Genbank transcript ID

NM_001010 (exact from MANE)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.655-7T>C
g.3842T>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	rs146329014
gnomAD	homozygous (G/G)	heterozygous	allele carriers
	54	2926	2980

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.738	0.002
	3.016	0.932
(flanking)	2.958	0.996

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

7

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

9

Strand

-1

Original gDNA sequence snippet

AACTGTTTGCTGTTTTGTTTTGTTTAGGAGGCTAAGGAGAA

Altered gDNA sequence snippet

AACTGTTTGCTGTTTTGTTTCGTTTAGGAGGCTAAGGAGAA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MKLNISFPAT GCQKLIEVDD ERKLRTFYEK RMATEVAADA LGEEWKGYVV RISGGNDKQG
FPMKQGVLTH GRVRLLLSKG HSCYRPRRTG ERKRKSVRGC IVDANLSVLN LVIVKKGEKD
IPGLTDTTVP RRLGPKRASR IRKLFNLSKE DDVRQYVVRK PLNKEGKKPR TKAPKIQRLV
TPRVLQHKRR RIALKKQRTK KNKEEAAEYA KLLAKRMKEA KEKRQEQIAK RRRLSSLRAS
TSKSESSQK*

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

42 / 42

Last intron/exon boundary

695

Theoretical NMD boundary in CDS

603

Length of CDS

750

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

3842

Chromosomal position

19376395

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:

9:19376395A>G_2_ENST00000380384

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Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 53|147 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr9:19376395A>G (GRCh38)

Gene symbol

RPS6

Gene constraints

LOEUF: 0.19, LOF (oe): 0.04, misssense (oe): 0.76, synonymous (oe): 1.40 ? (gnomAD)

Ensembl transcript ID

ENST00000380384.5

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.562-7T>C
g.3842T>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	rs146329014
gnomAD	homozygous (G/G)	heterozygous	allele carriers
	54	2926	2980

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.738	0.002
	3.016	0.932
(flanking)	2.958	0.996

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

7

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

9

Strand

-1

Original gDNA sequence snippet

AACTGTTTGCTGTTTTGTTTTGTTTAGGAGGCTAAGGAGAA

Altered gDNA sequence snippet

AACTGTTTGCTGTTTTGTTTCGTTTAGGAGGCTAAGGAGAA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MATEVAADAL GEEWKGYVVR ISGGNDKQGF PMKQGVLTHG RVRLLLSKGH SCYRPRRTGE
RKRKSVRGCI VDANLSVLNL VIVKKGEKDI PGLTDTTVPR RLGPKRASRI RKLFNLSKED
DVRQYVVRKP LNKEGKKPRT KAPKIQRLVT PRVLQHKRRR IALKKQRTKK NKEEAAEYAK
LLAKRMKEAK EKRQEQIAKR RRLSSLRAST SKSESSQK*

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

676 / 676

Last intron/exon boundary

1236

Theoretical NMD boundary in CDS

510

Length of CDS

657

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

3842

Chromosomal position

19376395

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:

9:19376395A>G_3_ENST00000315377

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 53|147 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr9:19376395A>G (GRCh38)

Gene symbol

RPS6

Gene constraints

LOEUF: 0.19, LOF (oe): 0.04, misssense (oe): 0.76, synonymous (oe): 1.40 ? (gnomAD)

Ensembl transcript ID

ENST00000315377.4

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.562-7T>C
g.3842T>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	rs146329014
gnomAD	homozygous (G/G)	heterozygous	allele carriers
	54	2926	2980

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.738	0.002
	3.016	0.932
(flanking)	2.958	0.996

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

7

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

9

Strand

-1

Original gDNA sequence snippet

AACTGTTTGCTGTTTTGTTTTGTTTAGGAGGCTAAGGAGAA

Altered gDNA sequence snippet

AACTGTTTGCTGTTTTGTTTCGTTTAGGAGGCTAAGGAGAA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MATEVAADAL GEEWKGYVVR ISGGNDKQGF PMKQGVLTHG RVRLLLSKGH SCYRPRRTGE
RKRKSVRGCI VDANLSVLNL VIVKKGEKDI PGLTDTTVPR RLGPKRASRI RKLFNLSKED
DVRQYVVRKP LNKEGKKPRT KAPKIQRLVT PRVLQHKRRR IALKKQRTKK NKEEAAEYAK
LLAKRMKEAK EKRQEQIAKR RRLSSLRAST SKSESSQK*

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

199 / 199

Last intron/exon boundary

759

Theoretical NMD boundary in CDS

510

Length of CDS

657

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

3842

Chromosomal position

19376395

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