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: ENST00000369515
Querying Taster for transcript #2: ENST00000369516
MT speed 0.15 s - this script 2.586711 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
ENST00000369516(MANE Select)	TSPAN2	Deleterious	85\|15	simple_aae		Yes				Single base exchange		Normal	Amino acid sequence changed Protein features (might be) affected Splice site changes
ENST00000369515	TSPAN2	Deleterious	93\|7	simple_aae		Yes				Single base exchange		Normal	Amino acid sequence changed Splice site changes

MutationT@ster 2025

Variant:

1:115053380G>T_2_ENST00000369516

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected
Splice site changes

Model: simple_aae
Tree vote: 85|15 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr1:115053380G>T (GRCh38)

Gene symbol

TSPAN2

Gene constraints

LOEUF: 1.20, LOF (oe): 0.85, misssense (oe): 1.03, synonymous (oe): 1.18 ? (gnomAD)

Ensembl transcript ID

ENST00000369516.7

Genbank transcript ID

NM_005725 (exact from MANE)

UniProt / AlphaMissense peptide

TSN2_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.599C>A
g.36124C>A

AA changes

AAE:	T200K	?
Score:	78

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

	Not in dbSNP
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	0	1	1

Protein conservation

Species	Match	AA	Alignment
Human		200	I	G	I	V	G	I	G	I	A	G	L	T	I	F	G	M	I	F	S	M	V	L	C	C
mutated	not conserved	200	I	G	I	V	G	I	G	I	A	G	L	K	I	F	G	M	I	F	S	M	V	L	C
Ptroglodytes	all identical	207	I	G	I	V	G	I	G	I	A	G	L	T	I	F	G
Mmulatta	all identical	253	I	G	I	V	G	I	G	I	A	G	L	T	I	F	G	M	I	F	S	M	V	L	C
Fcatus	all identical	200	I	G	I	V	G	I	G	I	A	G	L	T	I	F	G	M	I	F	S	M	V	L	C
Mmusculus	all identical	200	I	G	I	V	G	I	G	I	A	G	L	T	I	F	G	M	I	F	S	M	V	L	C
Ggallus	all identical	201	V	G	I	V	G	I	A	I	A	G	T	T	I	F	G	M	I	F	S	M	V	L	C
Trubripes	not conserved	408	I	G	Y	V	G	I	G	I	A	G	V	M	I	I	G	M	I	F	S	M	V	L	C
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	all identical	205	V	G	I	L	G	I	A	T	A	G	I	T	I	F	G	M	M	F	S	M	V	L	C

Protein features

Start (aa)	End (aa)	Feature	Details
1	221	CHAIN		lost
189	209	TRANSMEM	Helical	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.824	1
	4.65	1
(flanking)	4.437	1

?

Splice sites

MaxEntScan:

effect	gDNA position	score	sequence	exon-intron border
Donor weakened	36125	wt: 8.94 / mu: 8.68	-	wt: AGGTCTGACG\|gtgagaaagt mu: AGGTCTGAAG\|gtgagaaagt

Distance from splice site

2

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

1

Strand

-1

Original gDNA sequence snippet

TATTGGAATTGCAGGTCTGACGGTGAGAAAGTTCTAGAACT

Altered gDNA sequence snippet

TATTGGAATTGCAGGTCTGAAGGTGAGAAAGTTCTAGAACT

Original cDNA sequence snippet

TATTGGAATTGCAGGTCTGACGATCTTTGGCATGATATTCA

Altered cDNA sequence snippet

TATTGGAATTGCAGGTCTGAAGATCTTTGGCATGATATTCA

Wildtype AA sequence

MGRFRGGLRC IKYLLLGFNL LFWLAGSAVI AFGLWFRFGG AIKELSSEDK SPEYFYVGLY
VLVGAGALMM AVGFFGCCGA MRESQCVLGS FFTCLLVIFA AEVTTGVFAF IGKGVAIRHV
QTMYEEAYND YLKDRGKGNG TLITFHSTFQ CCGKESSEQV QPTCPKELLG HKNCIDEIET
IISVKLQLIG IVGIGIAGLT IFGMIFSMVL CCAIRNSRDV I*

Mutated AA sequence

MGRFRGGLRC IKYLLLGFNL LFWLAGSAVI AFGLWFRFGG AIKELSSEDK SPEYFYVGLY
VLVGAGALMM AVGFFGCCGA MRESQCVLGS FFTCLLVIFA AEVTTGVFAF IGKGVAIRHV
QTMYEEAYND YLKDRGKGNG TLITFHSTFQ CCGKESSEQV QPTCPKELLG HKNCIDEIET
IISVKLQLIG IVGIGIAGLK IFGMIFSMVL CCAIRNSRDV I*

Position of stopcodon in wt / mu CDS

666 / 666

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

222 / 222

Position of stopcodon in wt / mu cDNA

737 / 737

Position of start ATG in wt / mu cDNA

72 / 72

Last intron/exon boundary

671

Theoretical NMD boundary in CDS

549

Length of CDS

666

Coding sequence (CDS) position

599

cDNA position

670

gDNA position

36124

Chromosomal position

115053380

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

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MutationT@ster 2025

Variant:

1:115053380G>T_1_ENST00000369515

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Splice site changes

Model: simple_aae
Tree vote: 93|7 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr1:115053380G>T (GRCh38)

Gene symbol

TSPAN2

Gene constraints

LOEUF: 1.21, LOF (oe): 0.86, misssense (oe): 1.07, synonymous (oe): 1.17 ? (gnomAD)

Ensembl transcript ID

ENST00000369515.6

Genbank transcript ID

NM_001308315 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.524C>A
g.36124C>A

AA changes

AAE:	T175K	?
Score:	78

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

	Not in dbSNP
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	0	1	1

Protein conservation

Species	Match	AA	Alignment
Human		175	I	G	I	V	G	I	G	I	A	G	L	T	I	F	G	M	I	F	S	M	V	L	C	C
mutated	not conserved	175	I	G	I	V	G	I	G	I	A	G	L	K	I	F	G	M	I
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)	1.824	1
	4.65	1
(flanking)	4.437	1

?

Splice sites

MaxEntScan:

effect	gDNA position	score	sequence	exon-intron border
Donor weakened	36125	wt: 8.94 / mu: 8.68	-	wt: AGGTCTGACG\|gtgagaaagt mu: AGGTCTGAAG\|gtgagaaagt

Distance from splice site

2

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

1

Strand

-1

Original gDNA sequence snippet

TATTGGAATTGCAGGTCTGACGGTGAGAAAGTTCTAGAACT

Altered gDNA sequence snippet

TATTGGAATTGCAGGTCTGAAGGTGAGAAAGTTCTAGAACT

Original cDNA sequence snippet

TATTGGAATTGCAGGTCTGACGATCTTTGGCATGATATTCA

Altered cDNA sequence snippet

TATTGGAATTGCAGGTCTGAAGATCTTTGGCATGATATTCA

Wildtype AA sequence

MGRFRGGLRC IKYLLLGFNL LFWLAGSAVI AFGLWFRFGG AIKELSSEDK SPEYFYVGLY
VLVGAGALMM AVGFFGCCGA MRESQCVLGS AIRHVQTMYE EAYNDYLKDR GKGNGTLITF
HSTFQCCGKE SSEQVQPTCP KELLGHKNCI DEIETIISVK LQLIGIVGIG IAGLTIFGMI
FSMVLCCAIR NSRDVI*

Mutated AA sequence

MGRFRGGLRC IKYLLLGFNL LFWLAGSAVI AFGLWFRFGG AIKELSSEDK SPEYFYVGLY
VLVGAGALMM AVGFFGCCGA MRESQCVLGS AIRHVQTMYE EAYNDYLKDR GKGNGTLITF
HSTFQCCGKE SSEQVQPTCP KELLGHKNCI DEIETIISVK LQLIGIVGIG IAGLKIFGMI
FSMVLCCAIR NSRDVI*

Position of stopcodon in wt / mu CDS

591 / 591

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

197 / 197

Position of stopcodon in wt / mu cDNA

659 / 659

Position of start ATG in wt / mu cDNA

69 / 69

Last intron/exon boundary

593

Theoretical NMD boundary in CDS

474

Length of CDS

591

Coding sequence (CDS) position

524

cDNA position

592

gDNA position

36124

Chromosomal position

115053380

Speed

0.08 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