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: ENST00000551245
Querying Taster for transcript #2: ENST00000547923
Querying Taster for transcript #3: ENST00000257909
MT speed 0.77 s - this script 3.205271 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
ENST00000547923	TROAP	Deleterious	53\|46	5utr	No	Single base exchange	N/A
ENST00000551245	TROAP	Deleterious	91\|9	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed
ENST00000257909(MANE Select)	TROAP	Deleterious	95\|5	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected

MutationT@ster 2025

Variant:

12:49327250T>C_2_ENST00000547923

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Prediction:

DeleteriousPermalink

Summary:

Model: 5utr
Tree vote: 53|46 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr12:49327250T>C (GRCh38)

Gene symbol

TROAP

Gene constraints

LOEUF: 0.92, LOF (oe): 0.69, misssense (oe): 0.87, synonymous (oe): 0.88 ? (gnomAD)

Ensembl transcript ID

ENST00000547923.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

5'UTR

DNA changes

cDNA.122T>C
g.4015T>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	rs142606809
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	0	62	62

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.574	0.011
	1.948	0.965
(flanking)	3.256	0.996

?

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

N/A

Chromosome

12

Strand

1

Original gDNA sequence snippet

AACGCGAGGTTGTCACTCACTCAGATGAAGGAGGTGTGGCC

Altered gDNA sequence snippet

AACGCGAGGTTGTCACTCACCCAGATGAAGGAGGTGTGGCC

Original cDNA sequence snippet

AACGCGAGGTTGTCACTCACTCAGATGAAGGAGGTGTGGCC

Altered cDNA sequence snippet

AACGCGAGGTTGTCACTCACCCAGATGAAGGAGGTGTGGCC

Wildtype AA sequence

MSHTRDSHDS HLMPSPAPVA QPLPGHVVPC PSPFGRAQRV PSPGPPTLTS YSVLRRLTVQ
PKTRFTPMPS TPRVQQAQWL RGVSPQSCSE DPALPWEQVA VRLFDQESCI RSLEGSGKPP
VATPSGPHSN RTPSLQEVKI QRIGILQQLL RQEVEGLVGG QCVPLNGGSS LDMVELQPLL
TEISRTLNAT EHNSGTSHLP GLLKHSGLPK PCLPEECGEP QPCPPAEPGP PEAFCRSEPE
IPEPSLQEQL EVPEPYPPAE PRPLESCCRS EPEIPESSRQ EQLEEQLEVP EPCPPAEPGP
LQPSTQGQSG PPGPCPRVEL GASEPCTLEH RSLESSLPPC CSQWAPATTS LIFSSQHPLC
ASPPICSLQS LRPPAGQAGL SNLAPRTLAL RERLKSCLTA IHCFHEARLD DECAFYTSRA
PPSGPTRVCT NPVATLLEWQ DALCFIPVGS AAPQGSP*

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

188 / 188

Last intron/exon boundary

1516

Theoretical NMD boundary in CDS

1278

Length of CDS

1374

Coding sequence (CDS) position

N/A

cDNA position

122

gDNA position

4015

Chromosomal position

49327250

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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MutationT@ster 2025

Variant:

12:49327250T>C_1_ENST00000551245

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed

Model: simple_aae
Tree vote: 91|9 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr12:49327250T>C (GRCh38)

Gene symbol

TROAP

Gene constraints

LOEUF: 0.96, LOF (oe): 0.79, misssense (oe): 0.86, synonymous (oe): 0.87 ? (gnomAD)

Ensembl transcript ID

ENST00000551245.5

Genbank transcript ID

NM_001410976 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.811T>C
g.4015T>C

AA changes

AAE:	S271P	?
Score:	74

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs142606809
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	0	62	62

Protein conservation

Species	Match	AA	Alignment
Human		271	L	P	K	G	E	R	E	V	V	T	H	S	D	E	G	G	V	A	S	L	G	L	A	Q
mutated	not conserved	271	L	P	K	G	E	R	E	V	V	T	H	P	D	E	G	G	V	A	S	L	G	L	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

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.574	0.011
	1.948	0.965
(flanking)	3.256	0.996

?

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

12

Strand

1

Original gDNA sequence snippet

AACGCGAGGTTGTCACTCACTCAGATGAAGGAGGTGTGGCC

Altered gDNA sequence snippet

AACGCGAGGTTGTCACTCACCCAGATGAAGGAGGTGTGGCC

Original cDNA sequence snippet

AACGCGAGGTTGTCACTCACTCAGATGAAGGAGGTGTGGCC

Altered cDNA sequence snippet

AACGCGAGGTTGTCACTCACCCAGATGAAGGAGGTGTGGCC

Wildtype AA sequence

MTTRQATKDP LLRGVSPTPS KIPVRSQKRT PFPTVTSCAV DQENQDPRRW VQKPPLNIQR
PLVDSAGPRP KARHQAETSQ RLVGISQPRN PLEELRPSPR GQNVGPGPPA QTEAPGTIEF
VADPAALATI LSGEGVKSCH LGRQPSLAKR VLVRGSQGGT TQRVQGVRAS AYLAPRTPTH
RLDPARASCF SRLEGPGPRG RTLCPQRLQA LISPSGPSFH PSTRPSFQEL RRETAGSSRT
SVSQASGLLL ETPVQPAFSL PKGEREVVTH SDEGGVASLG LAQRVPLREN REMSHTRDSH
DSHLMPSPAP VAQPLPGHVV PCPSPFGRAQ RVPSPGPPTL TSYSVLRRLT VQPKTRFTPM
PSTPRVQQAQ WLRGVSPQSC SEDPALPWEQ VAVRLFDQES CIRSLEGSGK PPVATPSGPH
SNRTPSLQEV KIQRIGILQQ LLRQEVEGLV GGQCVPLNGG SSLDMVELQP LLTEISRTLN
ATEHNSGTSH LPGLLKHSGL PKPCLPEECG EPQPCPPAEP GPPEAFCRSE PEIPEPSLQE
QLEVPEPYPP AEPRPLESCC RSEPEIPESS RQEQLEVPEP CPPAEPRPLE SYCRIEPEIP
ESSRQEQLEV PEPCPPAEPG PLQPSTQGQS GPPGPCPRVE LGASEPCTLE HRSLESSLPP
CCSQWAPATT SLIFSSQHPL CASPPICSLQ SLRPPAGQAG KELAGKECEH KRSSPHCELH
TCPAPTPGNL MLPHLPPWPS LALPQEEGRG CTSSPVLLIG LAVGGGGGED STWWKYRTPD
LPLNFPCPSG LSNLAPRTLA LRERLKSCLT AIHCFHEARL DDECAFYTSR APPSGPTRVC
TNPVATLLEW QDALCFIPVG SAAPQGSP*

Mutated AA sequence

MTTRQATKDP LLRGVSPTPS KIPVRSQKRT PFPTVTSCAV DQENQDPRRW VQKPPLNIQR
PLVDSAGPRP KARHQAETSQ RLVGISQPRN PLEELRPSPR GQNVGPGPPA QTEAPGTIEF
VADPAALATI LSGEGVKSCH LGRQPSLAKR VLVRGSQGGT TQRVQGVRAS AYLAPRTPTH
RLDPARASCF SRLEGPGPRG RTLCPQRLQA LISPSGPSFH PSTRPSFQEL RRETAGSSRT
SVSQASGLLL ETPVQPAFSL PKGEREVVTH PDEGGVASLG LAQRVPLREN REMSHTRDSH
DSHLMPSPAP VAQPLPGHVV PCPSPFGRAQ RVPSPGPPTL TSYSVLRRLT VQPKTRFTPM
PSTPRVQQAQ WLRGVSPQSC SEDPALPWEQ VAVRLFDQES CIRSLEGSGK PPVATPSGPH
SNRTPSLQEV KIQRIGILQQ LLRQEVEGLV GGQCVPLNGG SSLDMVELQP LLTEISRTLN
ATEHNSGTSH LPGLLKHSGL PKPCLPEECG EPQPCPPAEP GPPEAFCRSE PEIPEPSLQE
QLEVPEPYPP AEPRPLESCC RSEPEIPESS RQEQLEVPEP CPPAEPRPLE SYCRIEPEIP
ESSRQEQLEV PEPCPPAEPG PLQPSTQGQS GPPGPCPRVE LGASEPCTLE HRSLESSLPP
CCSQWAPATT SLIFSSQHPL CASPPICSLQ SLRPPAGQAG KELAGKECEH KRSSPHCELH
TCPAPTPGNL MLPHLPPWPS LALPQEEGRG CTSSPVLLIG LAVGGGGGED STWWKYRTPD
LPLNFPCPSG LSNLAPRTLA LRERLKSCLT AIHCFHEARL DDECAFYTSR APPSGPTRVC
TNPVATLLEW QDALCFIPVG SAAPQGSP*

Position of stopcodon in wt / mu CDS

2607 / 2607

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

869 / 869

Position of stopcodon in wt / mu cDNA

2718 / 2718

Position of start ATG in wt / mu cDNA

112 / 112

Last intron/exon boundary

2673

Theoretical NMD boundary in CDS

2511

Length of CDS

2607

Coding sequence (CDS) position

811

cDNA position

922

gDNA position

4015

Chromosomal position

49327250

Speed

0.27 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:

12:49327250T>C_3_ENST00000257909

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 95|5 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr12:49327250T>C (GRCh38)

Gene symbol

TROAP

Gene constraints

LOEUF: 0.91, LOF (oe): 0.74, misssense (oe): 0.86, synonymous (oe): 0.88 ? (gnomAD)

Ensembl transcript ID

ENST00000257909.8

Genbank transcript ID

NM_005480 (exact from MANE)

UniProt / AlphaMissense peptide

TROAP_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.811T>C
g.4015T>C

AA changes

AAE:	S271P	?
Score:	74

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs142606809
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	0	62	62

Protein conservation

Species	Match	AA	Alignment
Human		271	L	P	K	G	E	R	E	V	V	T	H	S	D	E	G	G	V	A	S	L	G	L	A	Q
mutated	not conserved	271	L	P	K	G	E	R	E	V	V	T	H	P	D	E	G	G	V	A	S	L	G	L	A
Ptroglodytes	all identical	271	L	P	K	G	E	R	E	V	V	T	H	S	D	E	G	G	V	A	S	L	G	L	A
Mmulatta	all identical	271	L	P	K	G	E	H	E	V	V	T	R	S	D	E	G	S	V	A	S	L	G	L	A
Fcatus	all identical	268	L	P	E	G	E	H	E	V	V	T	H	S	D	E	G	G	G	G	P	L	G	L	A
Mmusculus	all identical	269	L	PL	R	G	E	Q	E	A	V	P	H	S	D	D	G	G	G	RH	H	L	G	L	A
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
1	778	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.574	0.011
	1.948	0.965
(flanking)	3.256	0.996

?

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

12

Strand

1

Original gDNA sequence snippet

AACGCGAGGTTGTCACTCACTCAGATGAAGGAGGTGTGGCC

Altered gDNA sequence snippet

AACGCGAGGTTGTCACTCACCCAGATGAAGGAGGTGTGGCC

Original cDNA sequence snippet

AACGCGAGGTTGTCACTCACTCAGATGAAGGAGGTGTGGCC

Altered cDNA sequence snippet

AACGCGAGGTTGTCACTCACCCAGATGAAGGAGGTGTGGCC

Wildtype AA sequence

MTTRQATKDP LLRGVSPTPS KIPVRSQKRT PFPTVTSCAV DQENQDPRRW VQKPPLNIQR
PLVDSAGPRP KARHQAETSQ RLVGISQPRN PLEELRPSPR GQNVGPGPPA QTEAPGTIEF
VADPAALATI LSGEGVKSCH LGRQPSLAKR VLVRGSQGGT TQRVQGVRAS AYLAPRTPTH
RLDPARASCF SRLEGPGPRG RTLCPQRLQA LISPSGPSFH PSTRPSFQEL RRETAGSSRT
SVSQASGLLL ETPVQPAFSL PKGEREVVTH SDEGGVASLG LAQRVPLREN REMSHTRDSH
DSHLMPSPAP VAQPLPGHVV PCPSPFGRAQ RVPSPGPPTL TSYSVLRRLT VQPKTRFTPM
PSTPRVQQAQ WLRGVSPQSC SEDPALPWEQ VAVRLFDQES CIRSLEGSGK PPVATPSGPH
SNRTPSLQEV KIQRIGILQQ LLRQEVEGLV GGQCVPLNGG SSLDMVELQP LLTEISRTLN
ATEHNSGTSH LPGLLKHSGL PKPCLPEECG EPQPCPPAEP GPPEAFCRSE PEIPEPSLQE
QLEVPEPYPP AEPRPLESCC RSEPEIPESS RQEQLEVPEP CPPAEPRPLE SYCRIEPEIP
ESSRQEQLEV PEPCPPAEPG PLQPSTQGQS GPPGPCPRVE LGASEPCTLE HRSLESSLPP
CCSQWAPATT SLIFSSQHPL CASPPICSLQ SLRPPAGQAG LSNLAPRTLA LRERLKSCLT
AIHCFHEARL DDECAFYTSR APPSGPTRVC TNPVATLLEW QDALCFIPVG SAAPQGSP*

Mutated AA sequence

MTTRQATKDP LLRGVSPTPS KIPVRSQKRT PFPTVTSCAV DQENQDPRRW VQKPPLNIQR
PLVDSAGPRP KARHQAETSQ RLVGISQPRN PLEELRPSPR GQNVGPGPPA QTEAPGTIEF
VADPAALATI LSGEGVKSCH LGRQPSLAKR VLVRGSQGGT TQRVQGVRAS AYLAPRTPTH
RLDPARASCF SRLEGPGPRG RTLCPQRLQA LISPSGPSFH PSTRPSFQEL RRETAGSSRT
SVSQASGLLL ETPVQPAFSL PKGEREVVTH PDEGGVASLG LAQRVPLREN REMSHTRDSH
DSHLMPSPAP VAQPLPGHVV PCPSPFGRAQ RVPSPGPPTL TSYSVLRRLT VQPKTRFTPM
PSTPRVQQAQ WLRGVSPQSC SEDPALPWEQ VAVRLFDQES CIRSLEGSGK PPVATPSGPH
SNRTPSLQEV KIQRIGILQQ LLRQEVEGLV GGQCVPLNGG SSLDMVELQP LLTEISRTLN
ATEHNSGTSH LPGLLKHSGL PKPCLPEECG EPQPCPPAEP GPPEAFCRSE PEIPEPSLQE
QLEVPEPYPP AEPRPLESCC RSEPEIPESS RQEQLEVPEP CPPAEPRPLE SYCRIEPEIP
ESSRQEQLEV PEPCPPAEPG PLQPSTQGQS GPPGPCPRVE LGASEPCTLE HRSLESSLPP
CCSQWAPATT SLIFSSQHPL CASPPICSLQ SLRPPAGQAG LSNLAPRTLA LRERLKSCLT
AIHCFHEARL DDECAFYTSR APPSGPTRVC TNPVATLLEW QDALCFIPVG SAAPQGSP*

Position of stopcodon in wt / mu CDS

2337 / 2337

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

779 / 779

Position of stopcodon in wt / mu cDNA

2437 / 2437

Position of start ATG in wt / mu cDNA

101 / 101

Last intron/exon boundary

2392

Theoretical NMD boundary in CDS

2241

Length of CDS

2337

Coding sequence (CDS) position

811

cDNA position

911

gDNA position

4015

Chromosomal position

49327250

Speed

0.49 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