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: ENST00000601492
Querying Taster for transcript #2: ENST00000600467
Querying Taster for transcript #3: ENST00000598742
Querying Taster for transcript #4: ENST00000221975
Querying Taster for transcript #5: ENST00000593863
MT speed 0.32 s - this script 2.743316 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
ENST00000598742(MANE Select)	RPS19	Deleterious	96\|4	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000600467	RPS19	Deleterious	99\|1	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000593863	RPS19	Deleterious	99\|1	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000221975	RPS19	Deleterious	197\|3	without_aae	No	Single base exchange	N/A	Splice site lost

Some transcripts had annotation problems and are not shown

MutationT@ster 2025

Variant:

19:41860784G>T_3_ENST00000598742

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 96|4 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr19:41860784G>T (GRCh38)

Gene symbol

RPS19

Gene constraints

LOEUF: 0.24, LOF (oe): 0.05, misssense (oe): 0.55, synonymous (oe): 1.10 ? (gnomAD)

Ensembl transcript ID

ENST00000598742.6

Genbank transcript ID

NM_001022 (exact from MANE), NM_001321484 (by similarity), NM_001321485 (by similarity)

UniProt / AlphaMissense peptide

RS19_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.10G>T
g.530G>T

AA changes

AAE:	V4F	?
Score:	50

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs782693679
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	0	13	13

Protein conservation

Species	Match	AA
Human		4	M	P	G	V	T	V	K	D	V	N	Q	Q	E	F	V	R
mutated	not conserved	4	M	P	G	F	T	V	K	D	V	N	Q	Q	E	F	V	R	A	L	A	A	F	L
Ptroglodytes	all identical	4	M	P	G	V	T	V	K	D	V	N	Q	Q	E	F	V	R	A	L	A	A	F	L
Mmulatta	all identical	182	M	P	G	V	T	V	K	D	V	N	Q	Q	E	F	V	R	A	L	A	A	F	L
Fcatus	no homologue
Mmusculus	all identical	4	M	P	G	V	T	V	K	D	V	N	Q	Q	E	F	V	R	A	L	A	A	F	L
Ggallus	no homologue
Trubripes	all identical	46	M	P	G	V	T	V	K	D	V	N	Q	Q	E	F	V	R	A	L	A	A	F	L
Drerio	no homologue
Dmelanogaster	all identical	4	M	P	G	V	T	V	K	E	I	D	Q	H	V	L	T	K	N	M	A	A	F	L
Celegans	no homologue
Xtropicalis	all identical	4	M	P	G	V	T	V	K	D	V	N	Q	Q	E	F	V	R	A	L	A	A	F	L

Protein features

Start (aa)	End (aa)	Feature	Details
2	145	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.632	1
	7.028	1
(flanking)	5.381	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

10

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

19

Strand

1

Original gDNA sequence snippet

TTCTCCCTCAGATGCCTGGAGTTACTGTAAAAGACGTGAAC

Altered gDNA sequence snippet

TTCTCCCTCAGATGCCTGGATTTACTGTAAAAGACGTGAAC

Original cDNA sequence snippet

GAGGCCGCACGATGCCTGGAGTTACTGTAAAAGACGTGAAC

Altered cDNA sequence snippet

GAGGCCGCACGATGCCTGGATTTACTGTAAAAGACGTGAAC

Wildtype AA sequence

MPGVTVKDVN QQEFVRALAA FLKKSGKLKV PEWVDTVKLA KHKELAPYDE NWFYTRAAST
ARHLYLRGGA GVGSMTKIYG GRQRNGVMPS HFSRGSKSVA RRVLQALEGL KMVEKDQDGG
RKLTPQGQRD LDRIAGQVAA ANKKH*

Mutated AA sequence

MPGFTVKDVN QQEFVRALAA FLKKSGKLKV PEWVDTVKLA KHKELAPYDE NWFYTRAAST
ARHLYLRGGA GVGSMTKIYG GRQRNGVMPS HFSRGSKSVA RRVLQALEGL KMVEKDQDGG
RKLTPQGQRD LDRIAGQVAA ANKKH*

Position of stopcodon in wt / mu CDS

438 / 438

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

146 / 146

Position of stopcodon in wt / mu cDNA

473 / 473

Position of start ATG in wt / mu cDNA

36 / 36

Last intron/exon boundary

446

Theoretical NMD boundary in CDS

360

Length of CDS

438

Coding sequence (CDS) position

10

cDNA position

45

gDNA position

530

Chromosomal position

41860784

Speed

0.09 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:

19:41860784G>T_2_ENST00000600467

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 99|1 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr19:41860784G>T (GRCh38)

Gene symbol

RPS19

Gene constraints

LOEUF: 0.24, LOF (oe): 0.05, misssense (oe): 0.55, synonymous (oe): 1.10 ? (gnomAD)

Ensembl transcript ID

ENST00000600467.6

Genbank transcript ID

UniProt / AlphaMissense peptide

RS19_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.10G>T
g.530G>T

AA changes

AAE:	V4F	?
Score:	50

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs782693679
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	0	13	13

Protein conservation

Species	Match	AA
Human		4	M	P	G	V	T	V	K	D	V	N	Q	Q	E	F	V	R
mutated	not conserved	4	M	P	G	F	T	V	K	D	V	N	Q	Q	E	F	V	R	A	L	A	A	F	L
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
2	145	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.632	1
	7.028	1
(flanking)	5.381	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

10

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

19

Strand

1

Original gDNA sequence snippet

TTCTCCCTCAGATGCCTGGAGTTACTGTAAAAGACGTGAAC

Altered gDNA sequence snippet

TTCTCCCTCAGATGCCTGGATTTACTGTAAAAGACGTGAAC

Original cDNA sequence snippet

GGACATGCCCGATGCCTGGAGTTACTGTAAAAGACGTGAAC

Altered cDNA sequence snippet

GGACATGCCCGATGCCTGGATTTACTGTAAAAGACGTGAAC

Wildtype AA sequence

MPGVTVKDVN QQEFVRALAA FLKKSGKLKV PEWVDTVKLA KHKELAPYDE NWFYTRAAST
ARHLYLRGGA GVGSMTKIYG GRQRNGVMPS HFSRGSKSVA RRVLQALEGL KMVEKDQDGG
RKLTPQGQRD LDRIAGQVAA ANKKH*

Mutated AA sequence

MPGFTVKDVN QQEFVRALAA FLKKSGKLKV PEWVDTVKLA KHKELAPYDE NWFYTRAAST
ARHLYLRGGA GVGSMTKIYG GRQRNGVMPS HFSRGSKSVA RRVLQALEGL KMVEKDQDGG
RKLTPQGQRD LDRIAGQVAA ANKKH*

Position of stopcodon in wt / mu CDS

438 / 438

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

146 / 146

Position of stopcodon in wt / mu cDNA

629 / 629

Position of start ATG in wt / mu cDNA

192 / 192

Last intron/exon boundary

602

Theoretical NMD boundary in CDS

360

Length of CDS

438

Coding sequence (CDS) position

10

cDNA position

201

gDNA position

530

Chromosomal position

41860784

Speed

0.11 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:

19:41860784G>T_5_ENST00000593863

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 99|1 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr19:41860784G>T (GRCh38)

Gene symbol

RPS19

Gene constraints

LOEUF: 0.24, LOF (oe): 0.05, misssense (oe): 0.55, synonymous (oe): 1.10 ? (gnomAD)

Ensembl transcript ID

ENST00000593863.5

Genbank transcript ID

NM_001321483 (by similarity)

UniProt / AlphaMissense peptide

RS19_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.10G>T
g.530G>T

AA changes

AAE:	V4F	?
Score:	50

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs782693679
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	0	13	13

Protein conservation

Species	Match	AA
Human		4	M	P	G	V	T	V	K	D	V	N	Q	Q	E	F	V	R
mutated	not conserved	4	M	P	G	F	T	V	K	D	V	N	Q	Q	E	F	V	R	A	L	A	A	F	L
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
2	145	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.632	1
	7.028	1
(flanking)	5.381	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

10

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

19

Strand

1

Original gDNA sequence snippet

TTCTCCCTCAGATGCCTGGAGTTACTGTAAAAGACGTGAAC

Altered gDNA sequence snippet

TTCTCCCTCAGATGCCTGGATTTACTGTAAAAGACGTGAAC

Original cDNA sequence snippet

GCAGCGGCGGGATGCCTGGAGTTACTGTAAAAGACGTGAAC

Altered cDNA sequence snippet

GCAGCGGCGGGATGCCTGGATTTACTGTAAAAGACGTGAAC

Wildtype AA sequence

MPGVTVKDVN QQEFVRALAA FLKKSGKLKV PEWVDTVKLA KHKELAPYDE NWFYTRAAST
ARHLYLRGGA GVGSMTKIYG GRQRNGVMPS HFSRGSKSVA RRVLQALEGL KMVEKDQDGG
RKLTPQGQRD LDRIAGQVAA ANKKH*

Mutated AA sequence

MPGFTVKDVN QQEFVRALAA FLKKSGKLKV PEWVDTVKLA KHKELAPYDE NWFYTRAAST
ARHLYLRGGA GVGSMTKIYG GRQRNGVMPS HFSRGSKSVA RRVLQALEGL KMVEKDQDGG
RKLTPQGQRD LDRIAGQVAA ANKKH*

Position of stopcodon in wt / mu CDS

438 / 438

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

146 / 146

Position of stopcodon in wt / mu cDNA

487 / 487

Position of start ATG in wt / mu cDNA

50 / 50

Last intron/exon boundary

460

Theoretical NMD boundary in CDS

360

Length of CDS

438

Coding sequence (CDS) position

10

cDNA position

59

gDNA position

530

Chromosomal position

41860784

Speed

0.11 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:

19:41860784G>T_4_ENST00000221975

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Prediction:

DeleteriousPermalink

Summary:

Splice site lost

Model: without_aae
Tree vote: 197|3 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr19:41860784G>T (GRCh38)

Gene symbol

RPS19

Gene constraints

LOEUF: 0.29, LOF (oe): 0.00, misssense (oe): 0.53, synonymous (oe): 0.87 ? (gnomAD)

Ensembl transcript ID

ENST00000221975.6

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.-212-1G>T
g.530G>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	rs782693679
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	0	13	13

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.632	1
	7.028	1
(flanking)	5.381	1

?

Splice sites

alteration within used splice site, likely to disturb normal splicing

MaxEntScan:

effect	gDNA position	score	sequence	exon-intron border
Acceptor lost	530	wt: 0.00 / mu: 0.00	-	wt: atgcctggag\|TTACTGTAAA mu: atgcctggat\|TTACTGTAAA

Distance from splice site

1

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

19

Strand

1

Original gDNA sequence snippet

TTCTCCCTCAGATGCCTGGAGTTACTGTAAAAGACGTGAAC

Altered gDNA sequence snippet

TTCTCCCTCAGATGCCTGGATTTACTGTAAAAGACGTGAAC

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MTKIYGGRQR NGVMPSHFSR GSKSVARRVL QALEGLKMVE KDQDGGRKLT PQGQRDLDRI
AGQVAAANKK H*

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

246 / 246

Last intron/exon boundary

434

Theoretical NMD boundary in CDS

138

Length of CDS

216

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

530

Chromosomal position

41860784

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

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Problem:

1

MutationT@ster 2025

annotation problem

The chosen transcript ENST00000601492 on chromosome 19 has no correct in-frame stop codon (TGA, TAA or TAG) annotated
This is likely to cause a false prediction. You should choose another transcript.

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