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 0.29 s - this script 2.719395 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
ENST00000308018(MANE Select)	MRPS12	Deleterious	75\|25	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000407800	MRPS12	Deleterious	96\|4	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000402029	MRPS12	Deleterious	96\|4	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected

MutationT@ster 2025

Variant:

19:38932476A>G_1_ENST00000308018

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 75|25 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr19:38932476A>G (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.193A>G
g.1533A>G

AA changes

AAE:	T65A	?
Score:	58

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs1703196611
gnomAD	homozygous (G/G)	heterozygous	allele carriers
	0	14	14

Protein conservation

Species	Match	AA	Alignment
Human		65	G	R	P	Q	L	K	G	V	V	L	C	T	F	T	R	K	P	K	K	P	N	S	A	N
mutated	not conserved	65								V	V	L	C	A	F	T	R	K	P	K	K	P	N	S	A
Ptroglodytes	all identical	65								V	V	L	C	T	F	T	R	K	P	K	K	P	N	S	A
Mmulatta	all identical	65								V	V	L	S	T	F	T	L	K	P	K	K	P	N	S	A
Fcatus	all identical	65								V	V	L	R	T	F	I	R	K	P	K	K	P	N	S	A
Mmusculus	all identical	65								V	V	L	R	T	F	I	R	K	P	K	K	P	N	S	A
Ggallus	not conserved	142	G	R	P	Q	L	K	G	V	V	V	R	N	L	I	R	K	P	K	K	P	N	S	A
Trubripes	all identical	68	G	C	P	Q	L	K	A	V	V	L	K	T	M	I	R	K	P	K	K	P	N	S	A
Drerio	no homologue
Dmelanogaster	all identical	79											K	T	L	I	K	K	P	K	K	P	N	S	A
Celegans	all identical	81	G	Y	S	H	Y	K	G	I	V	L	K	T	V	I	R	H	P	K	K	P	N	S	G
Xtropicalis	all identical	98	G	C	P	Q	L	K	G	V	V	L	K	T	M	I	R	K	P	K	K	P	N	S	A

Protein features

Start (aa)	End (aa)	Feature	Details
30	138	CHAIN		lost
56	68	STRAND		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	4.063	1
	7.2	1
(flanking)	4.012	0.997

?

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

TGAAGGGTGTGGTCCTGTGCACGTTTACCCGCAAGCCGAAG

Altered gDNA sequence snippet

TGAAGGGTGTGGTCCTGTGCGCGTTTACCCGCAAGCCGAAG

Original cDNA sequence snippet

TGAAGGGTGTGGTCCTGTGCACGTTTACCCGCAAGCCGAAG

Altered cDNA sequence snippet

TGAAGGGTGTGGTCCTGTGCGCGTTTACCCGCAAGCCGAAG

Wildtype AA sequence

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

Mutated AA sequence

MSWSGLLHGL NTSLTCGPAL VPRLWATCSM ATLNQMHRLG PPKRPPRKLG PTEGRPQLKG
VVLCAFTRKP 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

193

cDNA position

267

gDNA position

1533

Chromosomal position

38932476

Speed

0.10 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:

19:38932476A>G_2_ENST00000407800

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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

Chr19:38932476A>G (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.193A>G
g.1533A>G

AA changes

AAE:	T65A	?
Score:	58

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs1703196611
gnomAD	homozygous (G/G)	heterozygous	allele carriers
	0	14	14

Protein conservation

Species	Match	AA	Alignment
Human		65	G	R	P	Q	L	K	G	V	V	L	C	T	F	T	R	K	P	K	K	P	N	S	A	N
mutated	not conserved	65								V	V	L	C	A	F	T	R	K	P	K	K	P	N	S	A
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
56	68	STRAND		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	4.063	1
	7.2	1
(flanking)	4.012	0.997

?

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

TGAAGGGTGTGGTCCTGTGCACGTTTACCCGCAAGCCGAAG

Altered gDNA sequence snippet

TGAAGGGTGTGGTCCTGTGCGCGTTTACCCGCAAGCCGAAG

Original cDNA sequence snippet

TGAAGGGTGTGGTCCTGTGCACGTTTACCCGCAAGCCGAAG

Altered cDNA sequence snippet

TGAAGGGTGTGGTCCTGTGCGCGTTTACCCGCAAGCCGAAG

Wildtype AA sequence

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

Mutated AA sequence

MSWSGLLHGL NTSLTCGPAL VPRLWATCSM ATLNQMHRLG PPKRPPRKLG PTEGRPQLKG
VVLCAFTRKP 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

193

cDNA position

534

gDNA position

1533

Chromosomal position

38932476

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:

19:38932476A>G_3_ENST00000402029

Back to summary table

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

Chr19:38932476A>G (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.193A>G
g.1533A>G

AA changes

AAE:	T65A	?
Score:	58

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs1703196611
gnomAD	homozygous (G/G)	heterozygous	allele carriers
	0	14	14

Protein conservation

Species	Match	AA	Alignment
Human		65	G	R	P	Q	L	K	G	V	V	L	C	T	F	T	R	K	P	K	K	P	N	S	A	N
mutated	not conserved	65								V	V	L	C	A	F	T	R	K	P	K	K	P	N	S	A
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
56	68	STRAND		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	4.063	1
	7.2	1
(flanking)	4.012	0.997

?

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

TGAAGGGTGTGGTCCTGTGCACGTTTACCCGCAAGCCGAAG

Altered gDNA sequence snippet

TGAAGGGTGTGGTCCTGTGCGCGTTTACCCGCAAGCCGAAG

Original cDNA sequence snippet

TGAAGGGTGTGGTCCTGTGCACGTTTACCCGCAAGCCGAAG

Altered cDNA sequence snippet

TGAAGGGTGTGGTCCTGTGCGCGTTTACCCGCAAGCCGAAG

Wildtype AA sequence

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

Mutated AA sequence

MSWSGLLHGL NTSLTCGPAL VPRLWATCSM ATLNQMHRLG PPKRPPRKLG PTEGRPQLKG
VVLCAFTRKP 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

193

cDNA position

385

gDNA position

1533

Chromosomal position

38932476

Speed

0.10 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