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: ENST00000549275
Querying Taster for transcript #2: ENST00000551245
Querying Taster for transcript #3: ENST00000380327
Querying Taster for transcript #4: ENST00000548311
Querying Taster for transcript #5: ENST00000549534
Querying Taster for transcript #6: ENST00000550709
Querying Taster for transcript #7: ENST00000257909
MT speed 3.1 s - this script 5.538671 s

Transcript summary:

Permalink

Transcript	Gene symbol	Prediction	Tree vote	Model	Splice site change	Variant type	Protein length	Features at a glance
ENST00000550709	TROAP	Undetermined	50\|50	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed
ENST00000551245	TROAP	Deleterious	52\|48	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed
ENST00000257909(MANE Select)	TROAP	Deleterious	52\|48	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000548311	TROAP	Deleterious	53\|47	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000380327	TROAP	Deleterious	57\|43	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000549534	TROAP	Benign	39\|61	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed
ENST00000549275	TROAP	Benign	46\|54	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed

MutationT@ster 2025

Variant:

12:49323646G>A_6_ENST00000550709

Back to summary table

Prediction:

UndeterminedPermalink

Summary:

Amino acid sequence changed

Model: simple_aae
Tree vote: 50|50 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr12:49323646G>A (GRCh38)

Gene symbol

TROAP

Gene constraints

LOEUF: 1.95, LOF (oe): 1.75, misssense (oe): 0.88, synonymous (oe): 0.89 ? (gnomAD)

Ensembl transcript ID

ENST00000550709.5

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.38G>A
g.411G>A

AA changes

AAE:	R13Q	?
Score:	43

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs376455925
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	13	13

Protein conservation

Species	Match	AA	Alignment
Human		13	T	T	R	Q	A	T	K	D	P	L	L	R	G	V	S	P	T	P	S	K	I	P	V	R
mutated	all conserved	13	T	T	R	Q	A	T	K	D	P	L	L	Q	G	V	S	P	T	P	S	K	I	P	V
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)	0.471	0.37
	1.422	0.933
(flanking)	0.548	0.968

?

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

CACGAAGGATCCCCTCCTCCGGGGTGTATCTCCTACCCCTA

Altered gDNA sequence snippet

CACGAAGGATCCCCTCCTCCAGGGTGTATCTCCTACCCCTA

Original cDNA sequence snippet

CACGAAGGATCCCCTCCTCCGGGGTGTATCTCCTACCCCTA

Altered cDNA sequence snippet

CACGAAGGATCCCCTCCTCCAGGGTGTATCTCCTACCCCTA

Wildtype AA sequence

MTTRQATKDP LLRGVSPTPS KIPVRSQKRT PFPTVTSCAV DQENQDPRRW VQKPPLNIQR
PLVDSAGPRP KARHQAETSQ RLVGISQPRN PLEELRPSPR GQNVGPGPPA QTGTCWSHGN
TASMAE*

Mutated AA sequence

MTTRQATKDP LLQGVSPTPS KIPVRSQKRT PFPTVTSCAV DQENQDPRRW VQKPPLNIQR
PLVDSAGPRP KARHQAETSQ RLVGISQPRN PLEELRPSPR GQNVGPGPPA QTGTCWSHGN
TASMAE*

Position of stopcodon in wt / mu CDS

381 / 381

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

127 / 127

Position of stopcodon in wt / mu cDNA

479 / 479

Position of start ATG in wt / mu cDNA

99 / 99

Last intron/exon boundary

242

Theoretical NMD boundary in CDS

93

Length of CDS

381

Coding sequence (CDS) position

38

cDNA position

136

gDNA position

411

Chromosomal position

49323646

Speed

0.44 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:

12:49323646G>A_2_ENST00000551245

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed

Model: simple_aae
Tree vote: 52|48 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr12:49323646G>A (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.38G>A
g.411G>A

AA changes

AAE:	R13Q	?
Score:	43

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs376455925
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	13	13

Protein conservation

Species	Match	AA	Alignment
Human		13	T	T	R	Q	A	T	K	D	P	L	L	R	G	V	S	P	T	P	S	K	I	P	V	R
mutated	all conserved	13	T	T	R	Q	A	T	K	D	P	L	L	Q	G	V	S	P	T	P	S	K	I	P	V
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)	0.471	0.37
	1.422	0.933
(flanking)	0.548	0.968

?

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

CACGAAGGATCCCCTCCTCCGGGGTGTATCTCCTACCCCTA

Altered gDNA sequence snippet

CACGAAGGATCCCCTCCTCCAGGGTGTATCTCCTACCCCTA

Original cDNA sequence snippet

CACGAAGGATCCCCTCCTCCGGGGTGTATCTCCTACCCCTA

Altered cDNA sequence snippet

CACGAAGGATCCCCTCCTCCAGGGTGTATCTCCTACCCCTA

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 LLQGVSPTPS 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*

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

38

cDNA position

149

gDNA position

411

Chromosomal position

49323646

Speed

0.51 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:

12:49323646G>A_7_ENST00000257909

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 52|48 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr12:49323646G>A (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.38G>A
g.411G>A

AA changes

AAE:	R13Q	?
Score:	43

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs376455925
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	13	13

Protein conservation

Species	Match	AA	Alignment
Human		13	T	T	R	Q	A	T	K	D	P	L	L	R	G	V	S	P	T	P	S	K	I	P	V	R
mutated	all conserved	13	T	T	R	Q	A	T	K	D	P	L	L	Q	G	V	S	P	T	P	S	K	I	P	V
Ptroglodytes	all identical	13	T	T	R	Q	A	T	K	D	P	L	L	R	G	V	S	P	T	P	S	K	I	P	V
Mmulatta	all identical	13	T	T	R	Q	A	T	R	D	P	L	L	R	G	V	S	P	T	P	S	K	I	P	V
Fcatus	all identical	13	T	T	L	Q	A	T	K	E	P	L	L	R	G	V	S	P	T	P	S	K	I	P	V
Mmusculus	all identical	13	T	T	L	Q	T	N	K	D	P	H	L	R	G	V	S	P	N	P	S	K	I	P	V
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	115	REGION		lost
1	778	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.471	0.37
	1.422	0.933
(flanking)	0.548	0.968

?

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

CACGAAGGATCCCCTCCTCCGGGGTGTATCTCCTACCCCTA

Altered gDNA sequence snippet

CACGAAGGATCCCCTCCTCCAGGGTGTATCTCCTACCCCTA

Original cDNA sequence snippet

CACGAAGGATCCCCTCCTCCGGGGTGTATCTCCTACCCCTA

Altered cDNA sequence snippet

CACGAAGGATCCCCTCCTCCAGGGTGTATCTCCTACCCCTA

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 LLQGVSPTPS 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*

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

38

cDNA position

138

gDNA position

411

Chromosomal position

49323646

Speed

0.43 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:

12:49323646G>A_4_ENST00000548311

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 53|47 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr12:49323646G>A (GRCh38)

Gene symbol

TROAP

Gene constraints

LOEUF: 1.83, LOF (oe): 1.25, misssense (oe): 0.85, synonymous (oe): 0.90 ? (gnomAD)

Ensembl transcript ID

ENST00000548311.5

Genbank transcript ID

NM_001278324 (by similarity)

UniProt / AlphaMissense peptide

TROAP_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.38G>A
g.411G>A

AA changes

AAE:	R13Q	?
Score:	43

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs376455925
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	13	13

Protein conservation

Species	Match	AA	Alignment
Human		13	T	T	R	Q	A	T	K	D	P	L	L	R	G	V	S	P	T	P	S	K	I	P	V	R
mutated	all conserved	13	T	T	R	Q	A	T	K	D	P	L	L	Q	G	V	S	P	T	P	S	K	I	P	V
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
1	115	REGION		lost
1	778	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.471	0.37
	1.422	0.933
(flanking)	0.548	0.968

?

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

CACGAAGGATCCCCTCCTCCGGGGTGTATCTCCTACCCCTA

Altered gDNA sequence snippet

CACGAAGGATCCCCTCCTCCAGGGTGTATCTCCTACCCCTA

Original cDNA sequence snippet

CACGAAGGATCCCCTCCTCCGGGGTGTATCTCCTACCCCTA

Altered cDNA sequence snippet

CACGAAGGATCCCCTCCTCCAGGGTGTATCTCCTACCCCTA

Wildtype AA sequence

MTTRQATKDP LLRGVSPTPS KIPVRSQKRT PFPTVTSCAV DQENQDPRRW VQKPPLNIQR
PLVDSAGPRP KARHQAETSQ RLVGISQPRN PLEELRPSPR GQNVGPGPPA QTGAMACTCN
HSYSGG*

Mutated AA sequence

MTTRQATKDP LLQGVSPTPS KIPVRSQKRT PFPTVTSCAV DQENQDPRRW VQKPPLNIQR
PLVDSAGPRP KARHQAETSQ RLVGISQPRN PLEELRPSPR GQNVGPGPPA QTGAMACTCN
HSYSGG*

Position of stopcodon in wt / mu CDS

381 / 381

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

127 / 127

Position of stopcodon in wt / mu cDNA

481 / 481

Position of start ATG in wt / mu cDNA

101 / 101

Last intron/exon boundary

437

Theoretical NMD boundary in CDS

286

Length of CDS

381

Coding sequence (CDS) position

38

cDNA position

138

gDNA position

411

Chromosomal position

49323646

Speed

0.53 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:

12:49323646G>A_3_ENST00000380327

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 57|43 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr12:49323646G>A (GRCh38)

Gene symbol

TROAP

Gene constraints

LOEUF: 1.70, LOF (oe): 1.09, misssense (oe): 0.85, synonymous (oe): 0.93 ? (gnomAD)

Ensembl transcript ID

ENST00000380327.9

Genbank transcript ID

NM_001100620 (by similarity)

UniProt / AlphaMissense peptide

TROAP_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.38G>A
g.411G>A

AA changes

AAE:	R13Q	?
Score:	43

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs376455925
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	13	13

Protein conservation

Species	Match	AA	Alignment
Human		13	T	T	R	Q	A	T	K	D	P	L	L	R	G	V	S	P	T	P	S	K	I	P	V	R
mutated	all conserved	13	T	T	R	Q	A	T	K	D	P	L	L	Q	G	V	S	P	T	P	S	K	I	P	V
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
1	115	REGION		lost
1	778	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.471	0.37
	1.422	0.933
(flanking)	0.548	0.968

?

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

CACGAAGGATCCCCTCCTCCGGGGTGTATCTCCTACCCCTA

Altered gDNA sequence snippet

CACGAAGGATCCCCTCCTCCAGGGTGTATCTCCTACCCCTA

Original cDNA sequence snippet

CACGAAGGATCCCCTCCTCCGGGGTGTATCTCCTACCCCTA

Altered cDNA sequence snippet

CACGAAGGATCCCCTCCTCCAGGGTGTATCTCCTACCCCTA

Wildtype AA sequence

MTTRQATKDP LLRGVSPTPS KIPVRSQKRT PFPTVTSCAV DQENQDPRRW VQKPPLNIQR
PLVDSAGPRP KARHQAETSQ RLVGISQPRN PLEELRPSPR GQNVGPGPPA QTVLVPAPGK
LFALRRSPFP PAKCHLARCH GLYL*

Mutated AA sequence

MTTRQATKDP LLQGVSPTPS KIPVRSQKRT PFPTVTSCAV DQENQDPRRW VQKPPLNIQR
PLVDSAGPRP KARHQAETSQ RLVGISQPRN PLEELRPSPR GQNVGPGPPA QTVLVPAPGK
LFALRRSPFP PAKCHLARCH GLYL*

Position of stopcodon in wt / mu CDS

435 / 435

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

145 / 145

Position of stopcodon in wt / mu cDNA

535 / 535

Position of start ATG in wt / mu cDNA

101 / 101

Last intron/exon boundary

437

Theoretical NMD boundary in CDS

286

Length of CDS

435

Coding sequence (CDS) position

38

cDNA position

138

gDNA position

411

Chromosomal position

49323646

Speed

0.52 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:

12:49323646G>A_5_ENST00000549534

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Prediction:

BenignPermalink

Summary:

Amino acid sequence changed

Model: simple_aae
Tree vote: 39|61 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr12:49323646G>A (GRCh38)

Gene symbol

TROAP

Gene constraints

LOEUF: 1.81, LOF (oe): 0.78, misssense (oe): 0.96, synonymous (oe): 0.93 ? (gnomAD)

Ensembl transcript ID

ENST00000549534.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.38G>A
g.411G>A

AA changes

AAE:	R13Q	?
Score:	43

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs376455925
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	13	13

Protein conservation

Species	Match	AA	Alignment
Human		13	T	T	R	Q	A	T	K	D	P	L	L	R	G	V	S	P	T	P	S	K	I	P	V	R
mutated	all conserved	13	T	T	R	Q	A	T	K	D	P	L	L	Q	G	V	S	P	T	P	S	K	I	P	V
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)	0.471	0.37
	1.422	0.933
(flanking)	0.548	0.968

?

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

CACGAAGGATCCCCTCCTCCGGGGTGTATCTCCTACCCCTA

Altered gDNA sequence snippet

CACGAAGGATCCCCTCCTCCAGGGTGTATCTCCTACCCCTA

Original cDNA sequence snippet

CACGAAGGATCCCCTCCTCCGGGGTGTATCTCCTACCCCTA

Altered cDNA sequence snippet

CACGAAGGATCCCCTCCTCCAGGGTGTATCTCCTACCCCTA

Wildtype AA sequence

MTTRQATKDP LLRGVSPTPS KIPVRSQKRT PFPTVTSCAV DQENQDPRVR GA*

Mutated AA sequence

MTTRQATKDP LLQGVSPTPS KIPVRSQKRT PFPTVTSCAV DQENQDPRVR GA*

Position of stopcodon in wt / mu CDS

159 / 159

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

53 / 53

Position of stopcodon in wt / mu cDNA

241 / 241

Position of start ATG in wt / mu cDNA

83 / 83

Last intron/exon boundary

77

Theoretical NMD boundary in CDS

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

Length of CDS

159

Coding sequence (CDS) position

38

cDNA position

120

gDNA position

411

Chromosomal position

49323646

Speed

0.39 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:

12:49323646G>A_1_ENST00000549275

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Prediction:

BenignPermalink

Summary:

Amino acid sequence changed

Model: simple_aae
Tree vote: 46|54 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr12:49323646G>A (GRCh38)

Gene symbol

TROAP

Gene constraints

LOEUF: 1.84, LOF (oe): 1.10, misssense (oe): 0.88, synonymous (oe): 0.96 ? (gnomAD)

Ensembl transcript ID

ENST00000549275.5

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.38G>A
g.411G>A

AA changes

AAE:	R13Q	?
Score:	43

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs376455925
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	13	13

Protein conservation

Species	Match	AA	Alignment
Human		13	T	T	R	Q	A	T	K	D	P	L	L	R	G	V	S	P	T	P	S	K	I	P	V	R
mutated	all conserved	13	T	T	R	Q	A	T	K	D	P	L	L	Q	G	V	S	P	T	P	S	K	I	P	V
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)	0.471	0.37
	1.422	0.933
(flanking)	0.548	0.968

?

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

CACGAAGGATCCCCTCCTCCGGGGTGTATCTCCTACCCCTA

Altered gDNA sequence snippet

CACGAAGGATCCCCTCCTCCAGGGTGTATCTCCTACCCCTA

Original cDNA sequence snippet

CACGAAGGATCCCCTCCTCCGGGGTGTATCTCCTACCCCTA

Altered cDNA sequence snippet

CACGAAGGATCCCCTCCTCCAGGGTGTATCTCCTACCCCTA

Wildtype AA sequence

MTTRQATKDP LLRGVSPTPS KIPVRSQKRT PFPTVTSCAV DQENQDPRQN VISPGAMACT
CNHSYSGG*

Mutated AA sequence

MTTRQATKDP LLQGVSPTPS KIPVRSQKRT PFPTVTSCAV DQENQDPRQN VISPGAMACT
CNHSYSGG*

Position of stopcodon in wt / mu CDS

207 / 207

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

69 / 69

Position of stopcodon in wt / mu cDNA

326 / 326

Position of start ATG in wt / mu cDNA

120 / 120

Last intron/exon boundary

263

Theoretical NMD boundary in CDS

93

Length of CDS

207

Coding sequence (CDS) position

38

cDNA position

157

gDNA position

411

Chromosomal position

49323646

Speed

0.28 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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