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: ENST00000300853
Querying Taster for transcript #2: ENST00000423698
Querying Taster for transcript #3: ENST00000309424
Querying Taster for transcript #4: ENST00000589804
MT speed 1.39 s - this script 3.800115 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
ENST00000423698	ERCC1	Benign	2\|98	3utr	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000300853(MANE Select)	ERCC1	Benign	3\|97	3utr	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000309424(MANE Select)	POLR1G	Benign	31\|69	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Homozygous in gnomAD Protein features (might be) affected
ENST00000589804	POLR1G	Benign	33\|67	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Homozygous in gnomAD Protein features (might be) affected

MutationT@ster 2025

Variant:

19:45409478C>A_2_ENST00000423698

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Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: 3utr
Tree vote: 2|98 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr19:45409478C>A (GRCh38)

Gene symbol

ERCC1

Gene constraints

LOEUF: 1.28, LOF (oe): 0.92, misssense (oe): 0.86, synonymous (oe): 0.96 ? (gnomAD)

Ensembl transcript ID

ENST00000423698.6

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

3'UTR

DNA changes

cDNA.975G>T
g.69351G>T

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	rs3212986
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	>32000	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.88	0.003
	-1.507	0
(flanking)	0.703	0.012

?

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

19

Strand

-1

Original gDNA sequence snippet

CACAGGCTGCTGCTGCTGCTGCTTCCGCTTCTTGTCCCGGC

Altered gDNA sequence snippet

CACAGGCTGCTGCTGCTGCTTCTTCCGCTTCTTGTCCCGGC

Original cDNA sequence snippet

CACAGGCTGCTGCTGCTGCTGCTTCCGCTTCTTGTCCCGGC

Altered cDNA sequence snippet

CACAGGCTGCTGCTGCTGCTTCTTCCGCTTCTTGTCCCGGC

Wildtype AA sequence

MDPGKDKEGV PQPSGPPARK KFVIPLDEDE VPPGVRGNPV LKFVRNVPWE FGDVIPDYVL
GQSTCALFLS LRYHNLHPDY IHGRLQSLGK NFALRVLLVQ VDVKDPQQAL KELAKMCILA
DCTLILAWSP EEAGRYLETY KAYEQKPADL LMEKLEQDFV SRVTECLTTV KSVNKTDSQT
LLTTFGSLEQ LIAASREDLA LCPGLGPQKA RRLFDVLHEP FLKVP*

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

101 / 101

Last intron/exon boundary

727

Theoretical NMD boundary in CDS

576

Length of CDS

678

Coding sequence (CDS) position

N/A

cDNA position

975

gDNA position

69351

Chromosomal position

45409478

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

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MutationT@ster 2025

Variant:

19:45409478C>A_1_ENST00000300853

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Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: 3utr
Tree vote: 3|97 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr19:45409478C>A (GRCh38)

Gene symbol

ERCC1

Gene constraints

LOEUF: 1.31, LOF (oe): 0.99, misssense (oe): 0.88, synonymous (oe): 0.95 ? (gnomAD)

Ensembl transcript ID

ENST00000300853.8

Genbank transcript ID

NM_001983 (exact from MANE), NM_001369412 (by similarity), NM_001369413 (by similarity), NM_001369414 (by similarity), NM_001369415 (by similarity), NM_001369416 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

3'UTR

DNA changes

cDNA.1235G>T
g.69351G>T

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	rs3212986
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	>32000	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.88	0.003
	-1.507	0
(flanking)	0.703	0.012

?

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

19

Strand

-1

Original gDNA sequence snippet

CACAGGCTGCTGCTGCTGCTGCTTCCGCTTCTTGTCCCGGC

Altered gDNA sequence snippet

CACAGGCTGCTGCTGCTGCTTCTTCCGCTTCTTGTCCCGGC

Original cDNA sequence snippet

CACAGGCTGCTGCTGCTGCTGCTTCCGCTTCTTGTCCCGGC

Altered cDNA sequence snippet

CACAGGCTGCTGCTGCTGCTTCTTCCGCTTCTTGTCCCGGC

Wildtype AA sequence

MDPGKDKEGV PQPSGPPARK KFVIPLDEDE VPPGVAKPLF RSTQSLPTVD TSAQAAPQTY
AEYAISQPLE GAGATCPTGS EPLAGETPNQ ALKPGAKSNS IIVSPRQRGN PVLKFVRNVP
WEFGDVIPDY VLGQSTCALF LSLRYHNLHP DYIHGRLQSL GKNFALRVLL VQVDVKDPQQ
ALKELAKMCI LADCTLILAW SPEEAGRYLE TYKAYEQKPA DLLMEKLEQD FVSRVTECLT
TVKSVNKTDS QTLLTTFGSL EQLIAASRED LALCPGLGPQ KARRLFDVLH EPFLKVP*

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

145 / 145

Last intron/exon boundary

987

Theoretical NMD boundary in CDS

792

Length of CDS

894

Coding sequence (CDS) position

N/A

cDNA position

1235

gDNA position

69351

Chromosomal position

45409478

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

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MutationT@ster 2025

Variant:

19:45409478C>A_3_ENST00000309424

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Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Homozygous in gnomAD
Protein features (might be) affected

Model: simple_aae
Tree vote: 31|69 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr19:45409478C>A (GRCh38)

Gene symbol

POLR1G

Gene constraints

LOEUF: 1.91, LOF (oe): 1.40, misssense (oe): 0.93, synonymous (oe): 0.92 ? (gnomAD)

Ensembl transcript ID

ENST00000309424.8

Genbank transcript ID

NM_012099 (exact from MANE)

UniProt / AlphaMissense peptide

RPA34_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1510C>A
g.2835C>A

AA changes

AAE:	Q504K	?
Score:	53

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs3212986
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	>32000	>32000	>32000

Protein conservation

Species	Match	AA	Alignment
Human		504	E	A	P	T	G	R	D	K	K	R	K	Q	Q	Q	Q	Q	P	V	*
mutated	all conserved	504	E	A	P	T	G	R	D	K	K	R	K	K	Q	Q	Q	Q	P	V
Ptroglodytes	all conserved	505	E	A	P	T	G	R	D	K	K	R	K	K	Q	Q	Q	Q	P	V
Mmulatta	all conserved	510	E	A	P	T	V	R	D	K	K	R	R	K	Q	Q	Q
Fcatus	all conserved	472	V	A	S	T	G	R	E	K	K	S	K	R	L	Q	P	D	P	V
Mmusculus	not conserved	362	Q	A	E	V	A	L	V	S	P	K	K	T	K	K	K	K
Ggallus	no homologue
Trubripes	no alignment	n/a
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	all conserved	181	L	A	I	V	H	K	K	K	K	K	K	R	K	R	E	E

Protein features

Start (aa)	End (aa)	Feature	Details
1	510	CHAIN		lost
203	510	REGION		lost
493	510	COMPBIAS	Basic and acidic residues	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.88	0.003
	-1.507	0
(flanking)	0.703	0.012

?

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

GCCGGGACAAGAAGCGGAAGCAGCAGCAGCAGCAGCCTGTG

Altered gDNA sequence snippet

GCCGGGACAAGAAGCGGAAGAAGCAGCAGCAGCAGCCTGTG

Original cDNA sequence snippet

GCCGGGACAAGAAGCGGAAGCAGCAGCAGCAGCAGCCTGTG

Altered cDNA sequence snippet

GCCGGGACAAGAAGCGGAAGAAGCAGCAGCAGCAGCCTGTG

Wildtype AA sequence

MEEPQAGDAA RFSCPPNFTA KPPASESPRF SLEALTGPDT ELWLIQAPAD FAPECFNGRH
VPLSGSQIVK GKLAGKRHRY RVLSSCPQAG EATLLAPSTE AGGGLTCASA PQGTLRILEG
PQQSLSGSPL QPIPASPPPQ IPPGLRPRFC AFGGNPPVTG PRSALAPNLL TSGKKKKEMQ
VTEAPVTQEA VNGHGALEVD MALGSPEMDV RKKKKKKNQQ LKEPEAAGPV GTEPTVETLE
PLGVLFPSTT KKRKKPKGKE TFEPEDKTVK QEQINTEPLE DTVLSPTKKR KRQKGTEGME
PEEGVTVESQ PQVKVEPLEE AIPLPPTKKR KKEKGQMAMM EPGTEAMEPV EPEMKPLESP
GGTMAPQQPE GAKPQAQAAL AAPKKKTKKE KQQDATVEPE TEVVGPELPD DLEPQAAPTS
TKKKKKKKER GHTVTEPIQP LEPELPGEGQ PEARATPGST KKRKKQSQES RMPETVPQEE
MPGPPLNSES GEEAPTGRDK KRKQQQQQPV *

Mutated AA sequence

MEEPQAGDAA RFSCPPNFTA KPPASESPRF SLEALTGPDT ELWLIQAPAD FAPECFNGRH
VPLSGSQIVK GKLAGKRHRY RVLSSCPQAG EATLLAPSTE AGGGLTCASA PQGTLRILEG
PQQSLSGSPL QPIPASPPPQ IPPGLRPRFC AFGGNPPVTG PRSALAPNLL TSGKKKKEMQ
VTEAPVTQEA VNGHGALEVD MALGSPEMDV RKKKKKKNQQ LKEPEAAGPV GTEPTVETLE
PLGVLFPSTT KKRKKPKGKE TFEPEDKTVK QEQINTEPLE DTVLSPTKKR KRQKGTEGME
PEEGVTVESQ PQVKVEPLEE AIPLPPTKKR KKEKGQMAMM EPGTEAMEPV EPEMKPLESP
GGTMAPQQPE GAKPQAQAAL AAPKKKTKKE KQQDATVEPE TEVVGPELPD DLEPQAAPTS
TKKKKKKKER GHTVTEPIQP LEPELPGEGQ PEARATPGST KKRKKQSQES RMPETVPQEE
MPGPPLNSES GEEAPTGRDK KRKKQQQQPV *

Position of stopcodon in wt / mu CDS

1533 / 1533

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

511 / 511

Position of stopcodon in wt / mu cDNA

1586 / 1586

Position of start ATG in wt / mu cDNA

54 / 54

Last intron/exon boundary

217

Theoretical NMD boundary in CDS

113

Length of CDS

1533

Coding sequence (CDS) position

1510

cDNA position

1563

gDNA position

2835

Chromosomal position

45409478

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

MutationT@ster 2025

Variant:

19:45409478C>A_4_ENST00000589804

Back to summary table

Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Homozygous in gnomAD
Protein features (might be) affected

Model: simple_aae
Tree vote: 33|67 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr19:45409478C>A (GRCh38)

Gene symbol

POLR1G

Gene constraints

LOEUF: 1.66, LOF (oe): 0.95, misssense (oe): 0.93, synonymous (oe): 0.93 ? (gnomAD)

Ensembl transcript ID

ENST00000589804.1

Genbank transcript ID

NM_001297590 (by similarity)

UniProt / AlphaMissense peptide

RPA34_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1516C>A
g.2835C>A

AA changes

AAE:	Q506K	?
Score:	53

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs3212986
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	>32000	>32000	>32000

Protein conservation

Species	Match	AA	Alignment
Human		506	E	A	P	T	G	R	D	K	K	R	K	Q	Q	Q	Q	Q	P	V	*
mutated	all conserved	506	E	A	P	T	G	R	D	K	K	R	K	K	Q	Q	Q	Q	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	510	CHAIN		lost
203	510	REGION		lost
493	510	COMPBIAS	Basic and acidic residues	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.88	0.003
	-1.507	0
(flanking)	0.703	0.012

?

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

GCCGGGACAAGAAGCGGAAGCAGCAGCAGCAGCAGCCTGTG

Altered gDNA sequence snippet

GCCGGGACAAGAAGCGGAAGAAGCAGCAGCAGCAGCCTGTG

Original cDNA sequence snippet

GCCGGGACAAGAAGCGGAAGCAGCAGCAGCAGCAGCCTGTG

Altered cDNA sequence snippet

GCCGGGACAAGAAGCGGAAGAAGCAGCAGCAGCAGCCTGTG

Wildtype AA sequence

MEEPQAGGED AARFSCPPNF TAKPPASESP RFSLEALTGP DTELWLIQAP ADFAPECFNG
RHVPLSGSQI VKGKLAGKRH RYRVLSSCPQ AGEATLLAPS TEAGGGLTCA SAPQGTLRIL
EGPQQSLSGS PLQPIPASPP PQIPPGLRPR FCAFGGNPPV TGPRSALAPN LLTSGKKKKE
MQVTEAPVTQ EAVNGHGALE VDMALGSPEM DVRKKKKKKN QQLKEPEAAG PVGTEPTVET
LEPLGVLFPS TTKKRKKPKG KETFEPEDKT VKQEQINTEP LEDTVLSPTK KRKRQKGTEG
MEPEEGVTVE SQPQVKVEPL EEAIPLPPTK KRKKEKGQMA MMEPGTEAME PVEPEMKPLE
SPGGTMAPQQ PEGAKPQAQA ALAAPKKKTK KEKQQDATVE PETEVVGPEL PDDLEPQAAP
TSTKKKKKKK ERGHTVTEPI QPLEPELPGE GQPEARATPG STKKRKKQSQ ESRMPETVPQ
EEMPGPPLNS ESGEEAPTGR DKKRKQQQQQ PV*

Mutated AA sequence

MEEPQAGGED AARFSCPPNF TAKPPASESP RFSLEALTGP DTELWLIQAP ADFAPECFNG
RHVPLSGSQI VKGKLAGKRH RYRVLSSCPQ AGEATLLAPS TEAGGGLTCA SAPQGTLRIL
EGPQQSLSGS PLQPIPASPP PQIPPGLRPR FCAFGGNPPV TGPRSALAPN LLTSGKKKKE
MQVTEAPVTQ EAVNGHGALE VDMALGSPEM DVRKKKKKKN QQLKEPEAAG PVGTEPTVET
LEPLGVLFPS TTKKRKKPKG KETFEPEDKT VKQEQINTEP LEDTVLSPTK KRKRQKGTEG
MEPEEGVTVE SQPQVKVEPL EEAIPLPPTK KRKKEKGQMA MMEPGTEAME PVEPEMKPLE
SPGGTMAPQQ PEGAKPQAQA ALAAPKKKTK KEKQQDATVE PETEVVGPEL PDDLEPQAAP
TSTKKKKKKK ERGHTVTEPI QPLEPELPGE GQPEARATPG STKKRKKQSQ ESRMPETVPQ
EEMPGPPLNS ESGEEAPTGR DKKRKKQQQQ PV*

Position of stopcodon in wt / mu CDS

1539 / 1539

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

513 / 513

Position of stopcodon in wt / mu cDNA

1545 / 1545

Position of start ATG in wt / mu cDNA

7 / 7

Last intron/exon boundary

176

Theoretical NMD boundary in CDS

119

Length of CDS

1539

Coding sequence (CDS) position

1516

cDNA position

1522

gDNA position

2835

Chromosomal position

45409478

Speed

0.36 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