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: ENST00000249389
Querying Taster for transcript #2: ENST00000249364
Querying Taster for transcript #3: ENST00000449187
Querying Taster for transcript #4: ENST00000542996
MT speed 0.26 s - this script 2.665968 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
ENST00000249389(MANE Select)	OPN1SW	Deleterious	59\|41	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000249364(MANE Select)	CALU	Benign	3\|97	3utr	No	Single base exchange	N/A
ENST00000449187	CALU	Benign	3\|97	3utr	No	Single base exchange	N/A
ENST00000542996	CALU	Benign	4\|96	3utr	No	Single base exchange	N/A

MutationT@ster 2025

Variant:

7:128772550C>T_1_ENST00000249389

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 59|41 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr7:128772550C>T (GRCh38)

Gene symbol

OPN1SW

Gene constraints

LOEUF: 1.03, LOF (oe): 0.74, misssense (oe): 0.90, synonymous (oe): 1.05 ? (gnomAD)

Ensembl transcript ID

ENST00000249389.3

Genbank transcript ID

NM_001385125 (exact from MANE)

UniProt / AlphaMissense peptide

OPSB_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1028G>A
g.3245G>A

AA changes

AAE:	G343D	?
Score:	94

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

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

Protein conservation

Species	Match	AA	Alignment
Human		343	T	E	V	S	T	V	S	S	T	Q	V	G	P	N	*
mutated	not conserved	343	T	E	V	S	T	V	S	S	T	Q	V	D	P	N
Ptroglodytes	all identical	346	T	E	V	S	T	V	S	S	T	Q	V	G	P	N
Mmulatta	all identical	347	T	E	V	S	T	V	S	S	S	Q	V	G	P	N
Fcatus	all identical	347	T	E	V	S	A	L	S	S	S	Q	V	G	P	N
Mmusculus	all identical	344	T	E	V	S	T	V	S	S	S	K	V	G	P	H
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	not conserved	346	T	E	V	S	T	V	S	S	S	Q	V	S	P

Protein features

Start (aa)	End (aa)	Feature	Details
1	345	CHAIN		lost
304	345	TOPO_DOM	Cytoplasmic	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	2.197	1
	1.649	1
(flanking)	1.886	1

?

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

7

Strand

-1

Original gDNA sequence snippet

TGTCTCGTCTACCCAAGTTGGCCCCAACTGAGGACCCAATA

Altered gDNA sequence snippet

TGTCTCGTCTACCCAAGTTGACCCCAACTGAGGACCCAATA

Original cDNA sequence snippet

TGTCTCGTCTACCCAAGTTGGCCCCAACTGAGGACCCAATA

Altered cDNA sequence snippet

TGTCTCGTCTACCCAAGTTGACCCCAACTGAGGACCCAATA

Wildtype AA sequence

MSEEEFYLFK NISSVGPWDG PQYHIAPVWA FYLQAAFMGT VFLIGFPLNA MVLVATLRYK
KLRQPLNYIL VNVSFGGFLL CIFSVFPVFV ASCNGYFVFG RHVCALEGFL GTVAGLVTGW
SLAFLAFERY IVICKPFGNF RFSSKHALTV VLATWTIGIG VSIPPFFGWS RFIPEGLQCS
CGPDWYTVGT KYRSESYTWF LFIFCFIVPL SLICFSYTQL LRALKAVAAQ QQESATTQKA
EREVSRMVVV MVGSFCVCYV PYAAFAMYMV NNRNHGLDLR LVTIPSFFSK SACIYNPIIY
CFMNKQFQAC IMKMVCGKAM TDESDTCSSQ KTEVSTVSST QVGPN*

Mutated AA sequence

MSEEEFYLFK NISSVGPWDG PQYHIAPVWA FYLQAAFMGT VFLIGFPLNA MVLVATLRYK
KLRQPLNYIL VNVSFGGFLL CIFSVFPVFV ASCNGYFVFG RHVCALEGFL GTVAGLVTGW
SLAFLAFERY IVICKPFGNF RFSSKHALTV VLATWTIGIG VSIPPFFGWS RFIPEGLQCS
CGPDWYTVGT KYRSESYTWF LFIFCFIVPL SLICFSYTQL LRALKAVAAQ QQESATTQKA
EREVSRMVVV MVGSFCVCYV PYAAFAMYMV NNRNHGLDLR LVTIPSFFSK SACIYNPIIY
CFMNKQFQAC IMKMVCGKAM TDESDTCSSQ KTEVSTVSST QVDPN*

Position of stopcodon in wt / mu CDS

1038 / 1038

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

346 / 346

Position of stopcodon in wt / mu cDNA

1051 / 1051

Position of start ATG in wt / mu cDNA

14 / 14

Last intron/exon boundary

931

Theoretical NMD boundary in CDS

867

Length of CDS

1038

Coding sequence (CDS) position

1028

cDNA position

1041

gDNA position

3245

Chromosomal position

128772550

Speed

0.06 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:

7:128772550C>T_2_ENST00000249364

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Prediction:

BenignPermalink

Summary:

Model: 3utr
Tree vote: 3|97 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr7:128772550C>T (GRCh38)

Gene symbol

CALU

Gene constraints

LOEUF: 0.56, LOF (oe): 0.32, misssense (oe): 0.69, synonymous (oe): 0.79 ? (gnomAD)

Ensembl transcript ID

ENST00000249364.9

Genbank transcript ID

NM_001219 (exact from MANE)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

3'UTR

DNA changes

cDNA.4416C>T
g.33259C>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

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

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	2.197	1
	1.649	1
(flanking)	1.886	1

?

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

7

Strand

1

Original gDNA sequence snippet

TATTGGGTCCTCAGTTGGGGCCAACTTGGGTAGACGAGACA

Altered gDNA sequence snippet

TATTGGGTCCTCAGTTGGGGTCAACTTGGGTAGACGAGACA

Original cDNA sequence snippet

TATTGGGTCCTCAGTTGGGGCCAACTTGGGTAGACGAGACA

Altered cDNA sequence snippet

TATTGGGTCCTCAGTTGGGGTCAACTTGGGTAGACGAGACA

Wildtype AA sequence

MDLRQFLMCL SLCTAFALSK PTEKKDRVHH EPQLSDKVHN DAQSFDYDHD AFLGAEEAKT
FDQLTPEESK ERLGKIVSKI DGDKDGFVTV DELKDWIKFA QKRWIYEDVE RQWKGHDLNE
DGLVSWEEYK NATYGYVLDD PDPDDGFNYK QMMVRDERRF KMADKDGDLI ATKEEFTAFL
HPEEYDYMKD IVVQETMEDI DKNADGFIDL EEYIGDMYSH DGNTDEPEWV KTEREQFVEF
RDKNRDGKMD KEETKDWILP SDYDHAEAEA RHLVYESDQN KDGKLTKEEI VDKYDLFVGS
QATDFGEALV RHDEF*

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

86 / 86

Last intron/exon boundary

928

Theoretical NMD boundary in CDS

792

Length of CDS

948

Coding sequence (CDS) position

N/A

cDNA position

4416

gDNA position

33259

Chromosomal position

128772550

Speed

0.05 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:

7:128772550C>T_3_ENST00000449187

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Prediction:

BenignPermalink

Summary:

Model: 3utr
Tree vote: 3|97 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr7:128772550C>T (GRCh38)

Gene symbol

CALU

Gene constraints

LOEUF: 0.98, LOF (oe): 0.65, misssense (oe): 0.78, synonymous (oe): 0.84 ? (gnomAD)

Ensembl transcript ID

ENST00000449187.7

Genbank transcript ID

NM_001130674 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

3'UTR

DNA changes

cDNA.4416C>T
g.33259C>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

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

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	2.197	1
	1.649	1
(flanking)	1.886	1

?

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

7

Strand

1

Original gDNA sequence snippet

TATTGGGTCCTCAGTTGGGGCCAACTTGGGTAGACGAGACA

Altered gDNA sequence snippet

TATTGGGTCCTCAGTTGGGGTCAACTTGGGTAGACGAGACA

Original cDNA sequence snippet

TATTGGGTCCTCAGTTGGGGCCAACTTGGGTAGACGAGACA

Altered cDNA sequence snippet

TATTGGGTCCTCAGTTGGGGTCAACTTGGGTAGACGAGACA

Wildtype AA sequence

MDLRQFLMCL SLCTAFALSK PTEKKDRVHH EPQLSDKVHN DAQSFDYDHD AFLGAEEAKT
FDQLTPEESK ERLGMIVDKI DADKDGFVTE GELKSWIKHA QKKYIYDNVE NQWQEFDMNQ
DGLISWDEYR NVTYGTYLDD PDPDDGFNYK QMMVRDERRF KMADKDGDLI ATKEEFTAFL
HPEEYDYMKD IVVQETMEDI DKNADGFIDL EEYIGDMYSH DGNTDEPEWV KTEREQFVEF
RDKNRDGKMD KEETKDWILP SDYDHAEAEA RHLVYESDQN KDGKLTKEEI VDKYDLFVGS
QATDFGEALV RHDEF*

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

86 / 86

Last intron/exon boundary

928

Theoretical NMD boundary in CDS

792

Length of CDS

948

Coding sequence (CDS) position

N/A

cDNA position

4416

gDNA position

33259

Chromosomal position

128772550

Speed

0.05 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:

7:128772550C>T_4_ENST00000542996

Back to summary table

Prediction:

BenignPermalink

Summary:

Model: 3utr
Tree vote: 4|96 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr7:128772550C>T (GRCh38)

Gene symbol

CALU

Gene constraints

LOEUF: 0.98, LOF (oe): 0.65, misssense (oe): 0.78, synonymous (oe): 0.84 ? (gnomAD)

Ensembl transcript ID

ENST00000542996.7

Genbank transcript ID

NM_001199672 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

3'UTR

DNA changes

cDNA.5231C>T
g.33259C>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

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

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	2.197	1
	1.649	1
(flanking)	1.886	1

?

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

7

Strand

1

Original gDNA sequence snippet

TATTGGGTCCTCAGTTGGGGCCAACTTGGGTAGACGAGACA

Altered gDNA sequence snippet

TATTGGGTCCTCAGTTGGGGTCAACTTGGGTAGACGAGACA

Original cDNA sequence snippet

TATTGGGTCCTCAGTTGGGGCCAACTTGGGTAGACGAGACA

Altered cDNA sequence snippet

TATTGGGTCCTCAGTTGGGGTCAACTTGGGTAGACGAGACA

Wildtype AA sequence

MKETDLIIMD LRQFLMCLSL CTAFALSKPT EKKDRVHHEP QLSDKVHNDA QSFDYDHDAF
LGAEEAKTFD QLTPEESKER LGMIVDKIDA DKDGFVTEGE LKSWIKHAQK KYIYDNVENQ
WQEFDMNQDG LISWDEYRNV TYGTYLDDPD PDDGFNYKQM MVRDERRFKM ADKDGDLIAT
KEEFTAFLHP EEYDYMKDIV VQETMEDIDK NADGFIDLEE YIGDMYSHDG NTDEPEWVKT
EREQFVEFRD KNRDGKMDKE ETKDWILPSD YDHAEAEARH LVYESDQNKD GKLTKEEIVD
KYDLFVGSQA TDFGEALVRH DEF*

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

877 / 877

Last intron/exon boundary

1743

Theoretical NMD boundary in CDS

816

Length of CDS

972

Coding sequence (CDS) position

N/A

cDNA position

5231

gDNA position

33259

Chromosomal position

128772550

Speed

0.10 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