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: ENST00000308018
Querying Taster for transcript #2: ENST00000407800
Querying Taster for transcript #3: ENST00000402029
MT speed 0.34 s - this script 2.757666 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
ENST00000407800	MRPS12	Benign	13\|87	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000402029	MRPS12	Benign	13\|87	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000308018(MANE Select)	MRPS12	Benign	16\|84	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected

MutationT@ster 2025

Variant:

19:38932422C>T_2_ENST00000407800

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Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 13|87 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr19:38932422C>T (GRCh38)

Gene symbol

MRPS12

Gene constraints

LOEUF: 1.57, LOF (oe): 0.91, misssense (oe): 1.01, synonymous (oe): 0.98 ? (gnomAD)

Ensembl transcript ID

ENST00000407800.2

Genbank transcript ID

NM_021107 (by similarity)

UniProt / AlphaMissense peptide

RT12_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.139C>T
g.1479C>T

AA changes

AAE:	R47W	?
Score:	101

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs772487012
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	0	168	168

Protein conservation

Species	Match	AA	Alignment
Human		47	M	H	R	L	G	P	P	K	R	P	P	R	K	L	G	P	T	E	G	R	P	Q	L	K
mutated	not conserved	47	M	H	R	L	G	P	P	K	R	P	P	W	K	L	G	P	T	E	G	R	P	Q	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
30	138	CHAIN		lost
36	56	REGION		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-1.857	0
	-0.475	0
(flanking)	-0.629	0

?

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

19

Strand

1

Original gDNA sequence snippet

GGCCCCCCAAGCGGCCGCCTCGGAAGCTGGGCCCCACGGAA

Altered gDNA sequence snippet

GGCCCCCCAAGCGGCCGCCTTGGAAGCTGGGCCCCACGGAA

Original cDNA sequence snippet

GGCCCCCCAAGCGGCCGCCTCGGAAGCTGGGCCCCACGGAA

Altered cDNA sequence snippet

GGCCCCCCAAGCGGCCGCCTTGGAAGCTGGGCCCCACGGAA

Wildtype AA sequence

MSWSGLLHGL NTSLTCGPAL VPRLWATCSM ATLNQMHRLG PPKRPPRKLG PTEGRPQLKG
VVLCTFTRKP KKPNSANRKC CRVRLSTGRE AVCFIPGEGH TLQEHQIVLV EGGRTQDLPG
VKLTVVRGKY DCGHVQKK*

Mutated AA sequence

MSWSGLLHGL NTSLTCGPAL VPRLWATCSM ATLNQMHRLG PPKRPPWKLG PTEGRPQLKG
VVLCTFTRKP KKPNSANRKC CRVRLSTGRE AVCFIPGEGH TLQEHQIVLV EGGRTQDLPG
VKLTVVRGKY DCGHVQKK*

Position of stopcodon in wt / mu CDS

417 / 417

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

139 / 139

Position of stopcodon in wt / mu cDNA

758 / 758

Position of start ATG in wt / mu cDNA

342 / 342

Last intron/exon boundary

390

Theoretical NMD boundary in CDS

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

Length of CDS

417

Coding sequence (CDS) position

139

cDNA position

480

gDNA position

1479

Chromosomal position

38932422

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:

19:38932422C>T_3_ENST00000402029

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Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 13|87 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr19:38932422C>T (GRCh38)

Gene symbol

MRPS12

Gene constraints

LOEUF: 1.57, LOF (oe): 0.91, misssense (oe): 1.01, synonymous (oe): 0.98 ? (gnomAD)

Ensembl transcript ID

ENST00000402029.3

Genbank transcript ID

NM_033363 (by similarity)

UniProt / AlphaMissense peptide

RT12_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.139C>T
g.1479C>T

AA changes

AAE:	R47W	?
Score:	101

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs772487012
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	0	168	168

Protein conservation

Species	Match	AA	Alignment
Human		47	M	H	R	L	G	P	P	K	R	P	P	R	K	L	G	P	T	E	G	R	P	Q	L	K
mutated	not conserved	47	M	H	R	L	G	P	P	K	R	P	P	W	K	L	G	P	T	E	G	R	P	Q	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
30	138	CHAIN		lost
36	56	REGION		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-1.857	0
	-0.475	0
(flanking)	-0.629	0

?

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

19

Strand

1

Original gDNA sequence snippet

GGCCCCCCAAGCGGCCGCCTCGGAAGCTGGGCCCCACGGAA

Altered gDNA sequence snippet

GGCCCCCCAAGCGGCCGCCTTGGAAGCTGGGCCCCACGGAA

Original cDNA sequence snippet

GGCCCCCCAAGCGGCCGCCTCGGAAGCTGGGCCCCACGGAA

Altered cDNA sequence snippet

GGCCCCCCAAGCGGCCGCCTTGGAAGCTGGGCCCCACGGAA

Wildtype AA sequence

MSWSGLLHGL NTSLTCGPAL VPRLWATCSM ATLNQMHRLG PPKRPPRKLG PTEGRPQLKG
VVLCTFTRKP KKPNSANRKC CRVRLSTGRE AVCFIPGEGH TLQEHQIVLV EGGRTQDLPG
VKLTVVRGKY DCGHVQKK*

Mutated AA sequence

MSWSGLLHGL NTSLTCGPAL VPRLWATCSM ATLNQMHRLG PPKRPPWKLG PTEGRPQLKG
VVLCTFTRKP KKPNSANRKC CRVRLSTGRE AVCFIPGEGH TLQEHQIVLV EGGRTQDLPG
VKLTVVRGKY DCGHVQKK*

Position of stopcodon in wt / mu CDS

417 / 417

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

139 / 139

Position of stopcodon in wt / mu cDNA

609 / 609

Position of start ATG in wt / mu cDNA

193 / 193

Last intron/exon boundary

241

Theoretical NMD boundary in CDS

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

Length of CDS

417

Coding sequence (CDS) position

139

cDNA position

331

gDNA position

1479

Chromosomal position

38932422

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:

19:38932422C>T_1_ENST00000308018

Back to summary table

Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 16|84 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr19:38932422C>T (GRCh38)

Gene symbol

MRPS12

Gene constraints

LOEUF: 1.57, LOF (oe): 0.91, misssense (oe): 1.01, synonymous (oe): 0.98 ? (gnomAD)

Ensembl transcript ID

ENST00000308018.9

Genbank transcript ID

NM_033362 (exact from MANE)

UniProt / AlphaMissense peptide

RT12_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.139C>T
g.1479C>T

AA changes

AAE:	R47W	?
Score:	101

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs772487012
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	0	168	168

Protein conservation

Species	Match	AA	Alignment
Human		47	M	H	R	L	G	P	P	K	R	P	P	R	K	L	G	P	T	E	G	R	P	Q	L	K
mutated	not conserved	47	M	H	R	L	G	P	P	K	R	P	P	W	K	L	G	P	T	E	G	R	P	Q	L
Ptroglodytes	all identical	47	M	H	R	L	G	P	P	K	R	P	P	R	K	L	G	P	T	E	G	R	P	Q	L
Mmulatta	all identical	47	M	H	R	L	G	P	P	K	R	P	P	R	K	L	G	P	T	E	G	R	P	Q	L
Fcatus	not conserved	47	M	H	R	R	G	L	P	K	R	P	P	A	P	P	G	P	T	E	G	R	P	Q	L
Mmusculus	all conserved	47	M	H	R	L	G	P	R	K	E	P	P	K	R	L	G	P	T	E	G	R	P	Q	L
Ggallus	not conserved	124	M	H	R	Q	G	R	P	K	P	P	P	P	K	P	G	P	T	F	G	R	P	Q	L
Trubripes	all identical	50	M	H	R	Q	G	K	P	K	P	P	P	R	S	L	S	A	T	F	G	C	P	Q	L
Drerio	no homologue
Dmelanogaster	all identical	60	M	H	R	S	G	PHI	K	T	R	P	P	R	Q	-	-	P	L	D	G	K	P	F	A
Celegans	all identical	63		Y	R	N	G	P	P	K	R	R	A	R	S	K	D	K	SAI	S	G	Y	S	H	Y
Xtropicalis	not conserved	80	M	H	R	A	G	K	P	K	P	D	P	P	K	L	G	P	T	F	G	C	P	Q	L

Protein features

Start (aa)	End (aa)	Feature	Details
30	138	CHAIN		lost
36	56	REGION		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-1.857	0
	-0.475	0
(flanking)	-0.629	0

?

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

19

Strand

1

Original gDNA sequence snippet

GGCCCCCCAAGCGGCCGCCTCGGAAGCTGGGCCCCACGGAA

Altered gDNA sequence snippet

GGCCCCCCAAGCGGCCGCCTTGGAAGCTGGGCCCCACGGAA

Original cDNA sequence snippet

GGCCCCCCAAGCGGCCGCCTCGGAAGCTGGGCCCCACGGAA

Altered cDNA sequence snippet

GGCCCCCCAAGCGGCCGCCTTGGAAGCTGGGCCCCACGGAA

Wildtype AA sequence

MSWSGLLHGL NTSLTCGPAL VPRLWATCSM ATLNQMHRLG PPKRPPRKLG PTEGRPQLKG
VVLCTFTRKP KKPNSANRKC CRVRLSTGRE AVCFIPGEGH TLQEHQIVLV EGGRTQDLPG
VKLTVVRGKY DCGHVQKK*

Mutated AA sequence

MSWSGLLHGL NTSLTCGPAL VPRLWATCSM ATLNQMHRLG PPKRPPWKLG PTEGRPQLKG
VVLCTFTRKP KKPNSANRKC CRVRLSTGRE AVCFIPGEGH TLQEHQIVLV EGGRTQDLPG
VKLTVVRGKY DCGHVQKK*

Position of stopcodon in wt / mu CDS

417 / 417

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

139 / 139

Position of stopcodon in wt / mu cDNA

491 / 491

Position of start ATG in wt / mu cDNA

75 / 75

Last intron/exon boundary

123

Theoretical NMD boundary in CDS

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

Length of CDS

417

Coding sequence (CDS) position

139

cDNA position

213

gDNA position

1479

Chromosomal position

38932422

Speed

0.12 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