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: ENST00000334744
Querying Taster for transcript #2: ENST00000394450
Querying Taster for transcript #3: ENST00000505416
Querying Taster for transcript #4: ENST00000511435
Querying Taster for transcript #5: ENST00000683046
MT speed 0.1 s - this script 2.523729 s

Transcript summary:

Permalink

Transcript	Gene symbol	Prediction	Tree vote	Model	Splice site change	Variant type	Protein length	Features at a glance
ENST00000334744	PRELID2	Benign	0\|200	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000394450	PRELID2	Benign	0\|200	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000505416	PRELID2	Benign	0\|200	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000511435	PRELID2	Benign	0\|200	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000683046(MANE Select)	PRELID2	Benign	0\|200	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD

MutationT@ster 2025

Variant:

5:145830478C>T_1_ENST00000334744

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 0|200 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr5:145830478C>T (GRCh38)

Gene symbol

PRELID2

Gene constraints

LOEUF: 1.64, LOF (oe): 0.94, misssense (oe): 1.03, synonymous (oe): 1.09 ? (gnomAD)

Ensembl transcript ID

ENST00000334744.8

Genbank transcript ID

NM_182960 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.75+4699G>A
g.4892G>A

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	rs443033
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	>32000	28668	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.156	0
	-0.25	0
(flanking)	-3.014	0

?

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

N/A

AA sequence altered

N/A

Chromosome

5

Strand

-1

Original gDNA sequence snippet

TGTAGCAGTGTAGAAAGTGGGTCTTCTCTGGAATCTCACTT

Altered gDNA sequence snippet

TGTAGCAGTGTAGAAAGTGGATCTTCTCTGGAATCTCACTT

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MGVSVDVHQV YKYPFEQVVA SFLRKYPNPM DKNVISVKIM EEKRDESTGV IYRKRIAICQ
NVVPEILRKS LSTLVILCWK KVSILKVPNI QLEEESWLNP RERNMAIRSH CLTWTQYASM
KEESVFRESM ENPNWTEFIQ RGRISITGVG FLNCVLETFA STFLRQGAQK GIRIMEMLLK
EQCGAPLAE*

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

54 / 54

Last intron/exon boundary

633

Theoretical NMD boundary in CDS

529

Length of CDS

570

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

4892

Chromosomal position

145830478

Speed

0.02 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:

5:145830478C>T_2_ENST00000394450

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 0|200 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr5:145830478C>T (GRCh38)

Gene symbol

PRELID2

Gene constraints

LOEUF: 1.67, LOF (oe): 0.93, misssense (oe): 0.98, synonymous (oe): 0.99 ? (gnomAD)

Ensembl transcript ID

ENST00000394450.6

Genbank transcript ID

NM_138492 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.-215-4278G>A
g.4892G>A

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	rs443033
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	>32000	28668	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.156	0
	-0.25	0
(flanking)	-3.014	0

?

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

N/A

AA sequence altered

N/A

Chromosome

5

Strand

-1

Original gDNA sequence snippet

TGTAGCAGTGTAGAAAGTGGGTCTTCTCTGGAATCTCACTT

Altered gDNA sequence snippet

TGTAGCAGTGTAGAAAGTGGATCTTCTCTGGAATCTCACTT

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MDKNVISVKI MEEKRDESTG VIYRKRIAIC QNVVPEILRK VSILKVPNIQ LEEESWLNPR
ERNMAIRSHC LTWTQYASMK EESVFRESME NPNWTEFIQR GRISITGVGF LNCVLETFAS
TFLRQGAQKG IRIMEMLLKE QCGAPLAE*

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

376 / 376

Last intron/exon boundary

832

Theoretical NMD boundary in CDS

406

Length of CDS

447

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

4892

Chromosomal position

145830478

Speed

0.02 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:

5:145830478C>T_3_ENST00000505416

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 0|200 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr5:145830478C>T (GRCh38)

Gene symbol

PRELID2

Gene constraints

LOEUF: 1.64, LOF (oe): 0.94, misssense (oe): 1.03, synonymous (oe): 1.09 ? (gnomAD)

Ensembl transcript ID

ENST00000505416.5

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.75+4699G>A
g.4892G>A

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	rs443033
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	>32000	28668	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.156	0
	-0.25	0
(flanking)	-3.014	0

?

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

N/A

AA sequence altered

N/A

Chromosome

5

Strand

-1

Original gDNA sequence snippet

TGTAGCAGTGTAGAAAGTGGGTCTTCTCTGGAATCTCACTT

Altered gDNA sequence snippet

TGTAGCAGTGTAGAAAGTGGATCTTCTCTGGAATCTCACTT

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MGVSVDVHQV YKYPFEQVVA SFLRKYPNPM DKNVISVKIM EEKRDESTGV IYRKRIAICQ
NVVPEILRKV SILKVPNIQL EEESWLNPRE RNMAIRSHCL TWTQYASMKE ESVFRESMEN
PNWTEFIQRG RISITGVGFL NCVLETFAST FLRQGAQKGI RIMEMLLKEQ CGAPLAE*

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

35 / 35

Last intron/exon boundary

578

Theoretical NMD boundary in CDS

493

Length of CDS

534

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

4892

Chromosomal position

145830478

Speed

0.02 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:

5:145830478C>T_4_ENST00000511435

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 0|200 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr5:145830478C>T (GRCh38)

Gene symbol

PRELID2

Gene constraints

LOEUF: 1.64, LOF (oe): 0.94, misssense (oe): 1.03, synonymous (oe): 1.09 ? (gnomAD)

Ensembl transcript ID

ENST00000511435.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.75+4699G>A
g.4892G>A

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	rs443033
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	>32000	28668	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.156	0
	-0.25	0
(flanking)	-3.014	0

?

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

N/A

AA sequence altered

N/A

Chromosome

5

Strand

-1

Original gDNA sequence snippet

TGTAGCAGTGTAGAAAGTGGGTCTTCTCTGGAATCTCACTT

Altered gDNA sequence snippet

TGTAGCAGTGTAGAAAGTGGATCTTCTCTGGAATCTCACTT

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MGVSVDVHQV YKYPFEQVVA SFLRKYPNPM DKNVISVKIM EEKRDESTGV IYRKRIAICQ
NVVPEILRKV SILKVPNIQL EEESWLNPRE RNMAIRSHCL TWTQYASMKE ESVFRESMEN
PNWTEFIQRG RISITGVGFL NCVLETFAST FLRQGAQKVT IFLL*

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

54 / 54

Last intron/exon boundary

421

Theoretical NMD boundary in CDS

317

Length of CDS

495

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

4892

Chromosomal position

145830478

Speed

0.02 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:

5:145830478C>T_5_ENST00000683046

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 0|200 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr5:145830478C>T (GRCh38)

Gene symbol

PRELID2

Gene constraints

LOEUF: 1.64, LOF (oe): 0.94, misssense (oe): 1.03, synonymous (oe): 1.09 ? (gnomAD)

Ensembl transcript ID

ENST00000683046.1

Genbank transcript ID

NM_205846 (exact from MANE)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.75+4699G>A
g.4892G>A

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	rs443033
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	>32000	28668	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.156	0
	-0.25	0
(flanking)	-3.014	0

?

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

N/A

AA sequence altered

N/A

Chromosome

5

Strand

-1

Original gDNA sequence snippet

TGTAGCAGTGTAGAAAGTGGGTCTTCTCTGGAATCTCACTT

Altered gDNA sequence snippet

TGTAGCAGTGTAGAAAGTGGATCTTCTCTGGAATCTCACTT

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MGVSVDVHQV YKYPFEQVVA SFLRKYPNPM DKNVISVKIM EEKRDESTGV IYRKRIAICQ
NVVPEILRKV SILKVPNIQL EEESWLNPRE RNMAIRSHCL TWTQYASMKE ESVFRESMEN
PNWTEFIQRG RISITGVGFL NCVLETFAST FLRQGAQKGI RIMEMLLKEQ CGAPLAE*

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

92 / 92

Last intron/exon boundary

635

Theoretical NMD boundary in CDS

493

Length of CDS

534

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

4892

Chromosomal position

145830478

Speed

0.02 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