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: ENST00000711098
Querying Taster for transcript #2: ENST00000711099
Querying Taster for transcript #3: ENST00000480945
Querying Taster for transcript #4: ENST00000345034
MT speed 1.18 s - this script 3.571875 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
ENST00000345034(MANE Select)	RSC1A1	Deleterious	69\|31	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000711099	DDI2	Benign	0\|100	3utr	No	Single base exchange	N/A
ENST00000480945(MANE Select)	DDI2	Benign	0\|100	3utr	No	Single base exchange	N/A
ENST00000711098	DDI2	Benign	42\|58	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed

MutationT@ster 2025

Variant:

1:15660197T>C_4_ENST00000345034

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 69|31 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr1:15660197T>C (GRCh38)

Gene symbol

RSC1A1

Gene constraints

LOEUF: 1.45, LOF (oe): 0.78, misssense (oe): 0.95, synonymous (oe): 0.90 ? (gnomAD)

Ensembl transcript ID

ENST00000345034.2

Genbank transcript ID

NM_006511 (exact from MANE)

UniProt / AlphaMissense peptide

RSCA1_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.329T>C
g.485T>C

AA changes

AAE:	L110P	?
Score:	98

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

	Not in dbSNP
	Allele 'C' was not found in gnomAD

Protein conservation

Species	Match	AA	Alignment
Human		110	N	S	S	E	E	I	T	V	A	G	N	L	E	K	S	A	E	R	S	T	Q	G	L	K
mutated	not conserved	110	N	S	S	E	E	I	T	V	A	G	N	P	E	K	S	A	E	R	S	T	Q	G
Ptroglodytes	no homologue
Mmulatta	all identical	515	N	S	S	E	E	T	T	V	A	G	N	L	E	K	S	A	E	R	S	T	Q	G
Fcatus	all conserved	515	N	S	S	E	E	A	I	V	A	E	N	M	A	K	S	A	E	R	S	T	Q	G
Mmusculus	all identical	109	K	S	S	K	E	A	V	V	A	G	N	L	E	K	S	V	E	K	G	T	Q	G
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	617	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.12	0.001
	0.101	0.006
(flanking)	0.306	0.093

?

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

1

Strand

1

Original gDNA sequence snippet

AATAACTGTTGCAGGTAATCTGGAGAAATCTGCTGAAAGAA

Altered gDNA sequence snippet

AATAACTGTTGCAGGTAATCCGGAGAAATCTGCTGAAAGAA

Original cDNA sequence snippet

AATAACTGTTGCAGGTAATCTGGAGAAATCTGCTGAAAGAA

Altered cDNA sequence snippet

AATAACTGTTGCAGGTAATCCGGAGAAATCTGCTGAAAGAA

Wildtype AA sequence

MSSLPTSDGF NHPARSSGQS PDVGNPMSLA RSVSASVCPI KPSDSDRIEP KAVKALKASA
EFQLNSEKKE HLSLQDLSDH ASSADHAPTD QSPAMPMQNS SEEITVAGNL EKSAERSTQG
LKFHLHTRQE ASLSVTSTRM HEPQMFLGEK DWHPENQNLS QVSDPQQHEE PGNEQYEVAQ
QKASHDQEYL CNIGDLELPE ERQQNQHKIV DLEATMKGNG LPQNVDPPSA KKSIPSSECS
GCSNSETFME IDTAQQSLVT LLNSTGRQNA NVKNIGALDL TLDNPLMEVE TSKCNPSSEI
LNDSISTQDL QPPETNVEIP GTNKEYGHYS SPSLCGSCQP SVESAEESCP SITAALKELH
ELLVVSSKPA SENTSEEVIC QSETIAEGQT SIKDLSERWT QNEHLTQNEQ CPQVSFHQAI
SVSVETEKLT GTSSDTGREA VENVNFRSLG DGLSTDKEGV PKSRESINKN RSVTVTSAKT
SNQLHCTLGV EISPKLLAGE EDALNQTSEQ TKSLSSNFIL VKDLGQGIQN SVTDRPETRE
NVCPDASRPL LEYEPPTSHP SSSPAILPPL IFPATDIDRI LRAGFTLQEA LGALHRVGGN
ADLALLVLLA KNIVVPT*

Mutated AA sequence

MSSLPTSDGF NHPARSSGQS PDVGNPMSLA RSVSASVCPI KPSDSDRIEP KAVKALKASA
EFQLNSEKKE HLSLQDLSDH ASSADHAPTD QSPAMPMQNS SEEITVAGNP EKSAERSTQG
LKFHLHTRQE ASLSVTSTRM HEPQMFLGEK DWHPENQNLS QVSDPQQHEE PGNEQYEVAQ
QKASHDQEYL CNIGDLELPE ERQQNQHKIV DLEATMKGNG LPQNVDPPSA KKSIPSSECS
GCSNSETFME IDTAQQSLVT LLNSTGRQNA NVKNIGALDL TLDNPLMEVE TSKCNPSSEI
LNDSISTQDL QPPETNVEIP GTNKEYGHYS SPSLCGSCQP SVESAEESCP SITAALKELH
ELLVVSSKPA SENTSEEVIC QSETIAEGQT SIKDLSERWT QNEHLTQNEQ CPQVSFHQAI
SVSVETEKLT GTSSDTGREA VENVNFRSLG DGLSTDKEGV PKSRESINKN RSVTVTSAKT
SNQLHCTLGV EISPKLLAGE EDALNQTSEQ TKSLSSNFIL VKDLGQGIQN SVTDRPETRE
NVCPDASRPL LEYEPPTSHP SSSPAILPPL IFPATDIDRI LRAGFTLQEA LGALHRVGGN
ADLALLVLLA KNIVVPT*

Position of stopcodon in wt / mu CDS

1854 / 1854

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

618 / 618

Position of stopcodon in wt / mu cDNA

2010 / 2010

Position of start ATG in wt / mu cDNA

157 / 157

Last intron/exon boundary

0

Theoretical NMD boundary in CDS

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

Length of CDS

1854

Coding sequence (CDS) position

329

cDNA position

485

gDNA position

485

Chromosomal position

15660197

Speed

0.37 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:

1:15660197T>C_2_ENST00000711099

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Prediction:

BenignPermalink

Summary:

Model: 3utr
Tree vote: 0|100 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr1:15660197T>C (GRCh38)

Gene symbol

DDI2

Gene constraints

no data

Ensembl transcript ID

ENST00000711099.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

3'UTR

DNA changes

cDNA.1818T>C
g.42740T>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

	Not in dbSNP
	Allele 'C' was not found in gnomAD

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.12	0.001
	0.101	0.006
(flanking)	0.306	0.093

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

polyA signal ok

AA sequence altered

N/A

Chromosome

1

Strand

1

Original gDNA sequence snippet

AATAACTGTTGCAGGTAATCTGGAGAAATCTGCTGAAAGAA

Altered gDNA sequence snippet

AATAACTGTTGCAGGTAATCCGGAGAAATCTGCTGAAAGAA

Original cDNA sequence snippet

AATAACTGTTGCAGGTAATCTGGAGAAATCTGCTGAAAGAA

Altered cDNA sequence snippet

AATAACTGTTGCAGGTAATCCGGAGAAATCTGCTGAAAGAA

Wildtype AA sequence

MLLTVYCVRR DLSEVTFSLQ VDADFELHNF RALCELESGI PAAESQIVYA ERPLTDNHRS
LASYGLKDGD VVILRQKENA DPRPPVQFPN LPRIDFSSIA VPGTSSPRQR QPPGTQQSHS
SPGEITSSPQ GLDNPALLRD MLLANPHELS LLKERNPPLA EALLSGDLEK FSRVLVEQQQ
DRARREQERI RLFSADPFDL EAQAKIEEDI RQQNIEENMT IAMEEAPESF GQVVMLYINC
KVNGHPVKAF VDSGAQMTIM SQACAERCNI MRLVDRRWAG IAKGVGTQKI IGRVHLAQVQ
IEGDFLPCSF SILEEQPMDM LLGLDMLKRH QCSIDLKKNV LVIGTTGSQT TFLPEGELPE
CARLAYGAGR EDVRPEEIAD QELAEALQKS AEDAASEAMM HVVCVYCSWS GPQTREKW*

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

214 / 214

Last intron/exon boundary

1457

Theoretical NMD boundary in CDS

1193

Length of CDS

1257

Coding sequence (CDS) position

N/A

cDNA position

1818

gDNA position

42740

Chromosomal position

15660197

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

MutationT@ster 2025

Variant:

1:15660197T>C_3_ENST00000480945

Back to summary table

Prediction:

BenignPermalink

Summary:

Model: 3utr
Tree vote: 0|100 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr1:15660197T>C (GRCh38)

Gene symbol

DDI2

Gene constraints

LOEUF: 0.22, LOF (oe): 0.11, misssense (oe): 0.55, synonymous (oe): 1.07 ? (gnomAD)

Ensembl transcript ID

ENST00000480945.6

Genbank transcript ID

NM_032341 (exact from MANE)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

3'UTR

DNA changes

cDNA.1820T>C
g.42740T>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

	Not in dbSNP
	Allele 'C' was not found in gnomAD

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.12	0.001
	0.101	0.006
(flanking)	0.306	0.093

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

polyA signal ok

AA sequence altered

N/A

Chromosome

1

Strand

1

Original gDNA sequence snippet

AATAACTGTTGCAGGTAATCTGGAGAAATCTGCTGAAAGAA

Altered gDNA sequence snippet

AATAACTGTTGCAGGTAATCCGGAGAAATCTGCTGAAAGAA

Original cDNA sequence snippet

AATAACTGTTGCAGGTAATCTGGAGAAATCTGCTGAAAGAA

Altered cDNA sequence snippet

AATAACTGTTGCAGGTAATCCGGAGAAATCTGCTGAAAGAA

Wildtype AA sequence

MLLTVYCVRR DLSEVTFSLQ VDADFELHNF RALCELESGI PAAESQIVYA ERPLTDNHRS
LASYGLKDGD VVILRQKENA DPRPPVQFPN LPRIDFSSIA VPGTSSPRQR QPPGTQQSHS
SPGEITSSPQ GLDNPALLRD MLLANPHELS LLKERNPPLA EALLSGDLEK FSRVLVEQQQ
DRARREQERI RLFSADPFDL EAQAKIEEDI RQQNIEENMT IAMEEAPESF GQVVMLYINC
KVNGHPVKAF VDSGAQMTIM SQACAERCNI MRLVDRRWAG IAKGVGTQKI IGRVHLAQVQ
IEGDFLPCSF SILEEQPMDM LLGLDMLKRH QCSIDLKKNV LVIGTTGSQT TFLPEGELPE
CARLAYGAGR EDVRPEEIAD QELAEALQKS AEDAERQKP*

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

214 / 214

Last intron/exon boundary

1459

Theoretical NMD boundary in CDS

1195

Length of CDS

1200

Coding sequence (CDS) position

N/A

cDNA position

1820

gDNA position

42740

Chromosomal position

15660197

Speed

0.35 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:

1:15660197T>C_1_ENST00000711098

Back to summary table

Prediction:

BenignPermalink

Summary:

Amino acid sequence changed

Model: simple_aae
Tree vote: 42|58 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr1:15660197T>C (GRCh38)

Gene symbol

DDI2

Gene constraints

no data

Ensembl transcript ID

ENST00000711098.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1544T>C
g.42740T>C

AA changes

AAE:	L515P	?
Score:	98

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

	Not in dbSNP
	Allele 'C' was not found in gnomAD

Protein conservation

Species	Match	AA	Alignment
Human		515	N	S	S	E	E	I	T	V	A	G	N	L	E	K	S	A	E	R	S	T	Q	G	L	K
mutated	not conserved	515	N	S	S	E	E	I	T	V	A	G	N	P	E	K	S	A	E	R	S	T	Q	G	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

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.12	0.001
	0.101	0.006
(flanking)	0.306	0.093

?

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

1

Strand

1

Original gDNA sequence snippet

AATAACTGTTGCAGGTAATCTGGAGAAATCTGCTGAAAGAA

Altered gDNA sequence snippet

AATAACTGTTGCAGGTAATCCGGAGAAATCTGCTGAAAGAA

Original cDNA sequence snippet

AATAACTGTTGCAGGTAATCTGGAGAAATCTGCTGAAAGAA

Altered cDNA sequence snippet

AATAACTGTTGCAGGTAATCCGGAGAAATCTGCTGAAAGAA

Wildtype AA sequence

MLLTVYCVRR DLSEVTFSLQ VDADFELHNF RALCELESGI PAAESQIVYA ERPLTDNHRS
LASYGLKDGD VVILRQKENA DPRPPVQFPN LPRIDFSSIA VPGTSSPRQR QPPGTQQSHS
SPGEITSSPQ GLDNPALLRD MLLANPHELS LLKERNPPLA EALLSGDLEK FSRVLVEQQQ
DRARREQERI RLFSADPFDL EAQAKIEEDI RQQNIEENMT IAMEEAPESF GQVVMLYINC
KVNGHPVKAF VDSGAQMTIM SQACAERCNI MRLVDRRWAG IAKGVGTQKI IGRVHLAQVQ
IEGDFLPCSF SILEEQPMDM LLGLDMLKRH QCSIDLKKNV LVIGTTGSQT TFLPEGELPE
CARLAYGAGR EDVRPEEIAD QELAEALQKS AEDAEKSGKE STSLGMSSLP TSDGFNHPAR
SSGQSPDVGN PMSLARSVSA SVCPIKPSDS DRIEPKAVKA LKASAEFQLN SEKKEHLSLQ
DLSDHASSAD HAPTDQSPAM PMQNSSEEIT VAGNLEKSAE RSTQGLKFHL HTRQEASLSV
TSTRMHEPQM FLGEKDWHPE NQNLSQVSDP QQHEEPGNEQ YEVAQQKASH DQEYLCNIGD
LELPEERQQN QHKIVDLEAT MKGNGLPQNV DPPSAKKSIP SSECSGCSNS ETFMEIDTAQ
QSLVTLLNST GRQNANVKNI GALDLTLDNP LMEVETSKCN PSSEILNDSI STQDLQPPET
NVEIPGTNKE YGHYSSPSLC GSCQPSVESA EESCPSITAA LKELHELLVV SSKPASENTS
EEVICQSETI AEGQTSIKDL SERWTQNEHL TQNEQCPQVS FHQAISVSVE TEKLTGTSSD
TGREAVENVN FRSLGDGLST DKEGVPKSRE SINKNRSVTV TSAKTSNQLH CTLGVEISPK
LLAGEEDALN QTSEQTKSLS SNFILVKDLG QGIQNSVTDR PETRENVCPD ASRPLLEYEP
PTSHPSSSPA ILPPLIFPAT DIDRILRAGF TLQEALGALH RVGGNADLAL LVLLAKNIVV
PT*

Mutated AA sequence

MLLTVYCVRR DLSEVTFSLQ VDADFELHNF RALCELESGI PAAESQIVYA ERPLTDNHRS
LASYGLKDGD VVILRQKENA DPRPPVQFPN LPRIDFSSIA VPGTSSPRQR QPPGTQQSHS
SPGEITSSPQ GLDNPALLRD MLLANPHELS LLKERNPPLA EALLSGDLEK FSRVLVEQQQ
DRARREQERI RLFSADPFDL EAQAKIEEDI RQQNIEENMT IAMEEAPESF GQVVMLYINC
KVNGHPVKAF VDSGAQMTIM SQACAERCNI MRLVDRRWAG IAKGVGTQKI IGRVHLAQVQ
IEGDFLPCSF SILEEQPMDM LLGLDMLKRH QCSIDLKKNV LVIGTTGSQT TFLPEGELPE
CARLAYGAGR EDVRPEEIAD QELAEALQKS AEDAEKSGKE STSLGMSSLP TSDGFNHPAR
SSGQSPDVGN PMSLARSVSA SVCPIKPSDS DRIEPKAVKA LKASAEFQLN SEKKEHLSLQ
DLSDHASSAD HAPTDQSPAM PMQNSSEEIT VAGNPEKSAE RSTQGLKFHL HTRQEASLSV
TSTRMHEPQM FLGEKDWHPE NQNLSQVSDP QQHEEPGNEQ YEVAQQKASH DQEYLCNIGD
LELPEERQQN QHKIVDLEAT MKGNGLPQNV DPPSAKKSIP SSECSGCSNS ETFMEIDTAQ
QSLVTLLNST GRQNANVKNI GALDLTLDNP LMEVETSKCN PSSEILNDSI STQDLQPPET
NVEIPGTNKE YGHYSSPSLC GSCQPSVESA EESCPSITAA LKELHELLVV SSKPASENTS
EEVICQSETI AEGQTSIKDL SERWTQNEHL TQNEQCPQVS FHQAISVSVE TEKLTGTSSD
TGREAVENVN FRSLGDGLST DKEGVPKSRE SINKNRSVTV TSAKTSNQLH CTLGVEISPK
LLAGEEDALN QTSEQTKSLS SNFILVKDLG QGIQNSVTDR PETRENVCPD ASRPLLEYEP
PTSHPSSSPA ILPPLIFPAT DIDRILRAGF TLQEALGALH RVGGNADLAL LVLLAKNIVV
PT*

Position of stopcodon in wt / mu CDS

3069 / 3069

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

1023 / 1023

Position of stopcodon in wt / mu cDNA

3282 / 3282

Position of start ATG in wt / mu cDNA

214 / 214

Last intron/exon boundary

1396

Theoretical NMD boundary in CDS

1132

Length of CDS

3069

Coding sequence (CDS) position

1544

cDNA position

1757

gDNA position

42740

Chromosomal position

15660197

Speed

0.34 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