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: ENST00000309424
Querying Taster for transcript #2: ENST00000589804
MT speed 0.11 s - this script 2.4951 s

Transcript summary:

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Transcript	Gene symbol	Prediction	Tree vote	Model	Prediction problem	Splice site change	Known ClinVar disease mutation	Potential ClinVar disease mutation	Amino acid changes	Variant type	dbSNP ID	Protein length	Features at a glance
ENST00000589804	POLR1G	Deleterious	66\|34	simple_aae		No				Single base exchange		Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000309424(MANE Select)	POLR1G	Benign	45\|55	simple_aae		No				Single base exchange		Normal	Amino acid sequence changed Protein features (might be) affected

MutationT@ster 2025

Variant:

19:45406703G>A_2_ENST00000589804

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 66|34 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr19:45406703G>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.7G>A
g.60G>A

AA changes

AAE:	E3K	?
Score:	56

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs1018663455
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	25	25

Protein conservation

Species	Match	AA
Human		3	M	E	E	P	Q	A	G	G	E	D	A	A	R	F	S
mutated	all conserved	3	M	E	K	P	Q	A	G	G	E	D	A	A	R	F	S	C	P	P	N	F	T	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
1	31	REGION		lost
1	510	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	2.228	1
	2.216	0.997
(flanking)	0.017	0.01

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

22

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

19

Strand

1

Original gDNA sequence snippet

GTGTGGGTCCCAGGATGGAGGAGCCCCAGGCCGGCGGTGAG

Altered gDNA sequence snippet

GTGTGGGTCCCAGGATGGAGAAGCCCCAGGCCGGCGGTGAG

Original cDNA sequence snippet

CCCAGGATGGAGGAGCCCCAGGCCGGCGGTGAG

Altered cDNA sequence snippet

CCCAGGATGGAGAAGCCCCAGGCCGGCGGTGAG

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

MEKPQAGGED 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*

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

7

cDNA position

13

gDNA position

60

Chromosomal position

45406703

Speed

0.04 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:

19:45406703G>A_1_ENST00000309424

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Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 45|55 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr19:45406703G>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.7G>A
g.60G>A

AA changes

AAE:	E3K	?
Score:	56

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs1018663455
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	25	25

Protein conservation

Species	Match	AA
Human		3	M	E	E	P	Q	A	G	D	A	A	R	F	S	C	P
mutated	all conserved	3	M	E	K	P	Q	A	G	D	A	A	R	F	S	C	P	P	N	F	T	A	K	P
Ptroglodytes	all identical	3	M	E	E	P	Q	A	G	D	A	A	R	F	S	C	P	P	N	F	T	A	K	P
Mmulatta	all identical	3	M	E	E	P	Q	A	G	GER	A	A	R	F	S	C	P	P	N	F	I	A	K	P
Fcatus	no alignment	n/a
Mmusculus	not conserved	3	M	A	G	T	Q	A	C	S	A	T	R	F	S	C	P	P	H	F	T	E	M	S
Ggallus	no homologue
Trubripes	all identical	19			E	S	Q	P	K	Q	L	G	T	Y	E	C	P	V	D	F	V	S	V	S
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no alignment	n/a

Protein features

Start (aa)	End (aa)	Feature	Details
1	31	REGION		lost
1	510	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	2.228	1
	2.216	0.997
(flanking)	0.017	0.01

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

16

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

19

Strand

1

Original gDNA sequence snippet

GTGTGGGTCCCAGGATGGAGGAGCCCCAGGCCGGCGGTGAG

Altered gDNA sequence snippet

GTGTGGGTCCCAGGATGGAGAAGCCCCAGGCCGGCGGTGAG

Original cDNA sequence snippet

GTGTGGGTCCCAGGATGGAGGAGCCCCAGGCCGGCGATGCT

Altered cDNA sequence snippet

GTGTGGGTCCCAGGATGGAGAAGCCCCAGGCCGGCGATGCT

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

MEKPQAGDAA 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 *

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

7

cDNA position

60

gDNA position

60

Chromosomal position

45406703

Speed

0.07 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