Yum, tasty mutations...

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 0.13 s - this script 2.566572 s

Transcript summary:

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Yum, tasty mutations...

MutationT@ster 2025

Variant:

1:115053380G>C_2_ENST00000369516

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Prediction:

DeleteriousPermalink

Summary:

  • Model: simple_aae
  • Tree vote: 86|14 (del | benign) ?
Analysed issue Analysis result
Variant Chr1:115053380G>C (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>G
g.36124C>G
AA changes
AAE:T200R?
Score:71
Frameshift No
Length of protein Normal
Pathogenic variant (ClinVar) Variant not listed in ClinVar as (likely) pathogenic.
Variant DBs
Not in dbSNP
gnomADhomozygous (C/C)heterozygousallele carriers
011
Protein conservation
SpeciesMatchGeneAAAlignment
Human      200IGIVGIGIAGLTIFGMIFSMVLCC
mutated  not conserved    200IGIVGIGIAGLRIFGMIFSMVLC
Ptroglodytes  all identical    207IGIVGIGIAGLTIFG
Mmulatta  all identical    253IGIVGIGIAGLTIFGMIFSMVLC
Fcatus  all identical    200IGIVGIGIAGLTIFGMIFSMVLC
Mmusculus  all identical    200IGIVGIGIAGLTIFGMIFSMVLC
Ggallus  all identical    201VGIVGIAIAGTTIFGMIFSMVLC
Trubripes  not conserved    408IGYVGIGIAGVMIIGMIFSMVLC
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical    205VGILGIATAGITIFGMMFSMVLC
Protein features
Start (aa)End (aa)FeatureDetails 
1221CHAINlost
189209TRANSMEMHelicallost
Phylogenetic conservation
PhyloPPhastCons
(flanking)1.8241
4.651
(flanking)4.4371
?
Splice sites MaxEntScan:
effectgDNA positionscoresequence exon-intron border
Donor weakened36125wt: 8.94 / mu: 6.65- wt: AGGTCTGACG|gtgagaaagt
 mu: AGGTCTGAGG|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 TATTGGAATTGCAGGTCTGAGGGTGAGAAAGTTCTAGAACT
Original cDNA sequence snippet TATTGGAATTGCAGGTCTGACGATCTTTGGCATGATATTCA
Altered cDNA sequence snippet TATTGGAATTGCAGGTCTGAGGATCTTTGGCATGATATTCA
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 IVGIGIAGLR 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 0.06 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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Yum, tasty mutations...

MutationT@ster 2025

Variant:

1:115053380G>C_1_ENST00000369515

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

  • Model: simple_aae
  • Tree vote: 93|7 (del | benign) ?
Analysed issue Analysis result
Variant Chr1:115053380G>C (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>G
g.36124C>G
AA changes
AAE:T175R?
Score:71
Frameshift No
Length of protein Normal
Pathogenic variant (ClinVar) Variant not listed in ClinVar as (likely) pathogenic.
Variant DBs
Not in dbSNP
gnomADhomozygous (C/C)heterozygousallele carriers
011
Protein conservation
SpeciesMatchGeneAAAlignment
Human      175IGIVGIGIAGLTIFGMIFSMVLCC
mutated  not conserved    175IGIVGIGIAGLRIFGMI
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
PhyloPPhastCons
(flanking)1.8241
4.651
(flanking)4.4371
?
Splice sites MaxEntScan:
effectgDNA positionscoresequence exon-intron border
Donor weakened36125wt: 8.94 / mu: 6.65- wt: AGGTCTGACG|gtgagaaagt
 mu: AGGTCTGAGG|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 TATTGGAATTGCAGGTCTGAGGGTGAGAAAGTTCTAGAACT
Original cDNA sequence snippet TATTGGAATTGCAGGTCTGACGATCTTTGGCATGATATTCA
Altered cDNA sequence snippet TATTGGAATTGCAGGTCTGAGGATCTTTGGCATGATATTCA
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 IAGLRIFGMI
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 0.07 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