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: ENST00000344995
Querying Taster for transcript #2: ENST00000398475
Querying Taster for transcript #3: ENST00000275635
Querying Taster for transcript #4: ENST00000460943
MT speed 0.2 s - this script 2.638808 s

Transcript summary:

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TranscriptGene symbolPredictionTree voteModelPrediction problemSplice site changeKnown ClinVar disease mutationPotential ClinVar disease mutationAmino acid changesVariant typedbSNP IDProtein lengthFeatures at a glance
ENST00000460943(MANE Select)
LAT2Deleterious52|48simple_aaeNoSingle base exchangeNormal
  • Amino acid sequence changed
  • Protein features (might be) affected
LAT2Deleterious55|45simple_aaeNoSingle base exchangeNormal
  • Amino acid sequence changed
  • Protein features (might be) affected
LAT2Deleterious55|45simple_aaeNoSingle base exchangeNormal
  • Amino acid sequence changed
  • Protein features (might be) affected
LAT2Deleterious55|45simple_aaeNoSingle base exchangeNormal
  • Amino acid sequence changed
  • Protein features (might be) affected
Yum, tasty mutations...

MutationT@ster 2025

Variant:

7:74224171A>G_4_ENST00000460943

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Prediction:

DeleteriousPermalink

Summary:

  • Model: simple_aae
  • Tree vote: 52|48 (del | benign) ?
Analysed issue Analysis result
Variant Chr7:74224171A>G (GRCh38)
Gene symbol LAT2
Gene constraints LOEUF: 0.72, LOF (oe): 0.50, misssense (oe): 0.90, synonymous (oe): 1.02 ? (gnomAD)
Ensembl transcript ID ENST00000460943.6
Genbank transcript ID NM_032464 (exact from MANE)
UniProt / AlphaMissense peptide NTAL_HUMAN | AlphaMissense: transcript, gene
Variant type Single base exchange
Gene region CDS
DNA changes c.602A>G
g.24520A>G
AA changes
AAE:Q201R?
Score:43
Frameshift No
Length of protein Normal
Pathogenic variant (ClinVar) Variant not listed in ClinVar as (likely) pathogenic.
Variant DBs
dbSNP IDrs373894850
gnomADhomozygous (G/G)heterozygousallele carriers
01111
Protein conservation
SpeciesMatchGeneAAAlignment
Human      201SEDYQNSASIHQWRESRKVMGQLQ
mutated  all conserved    201SEDYQNSASIHRWRESRKVMGQL
Ptroglodytes  all identical    201SEDYQNSASIHQWRESRKVMGQL
Mmulatta  all identical    200SEDYQNSASIHQWRESRRVMGQL
Fcatus  all identical    198SEDYQNSASIRQWRESRRVVEQG
Mmusculus  all identical    180FEDYQNSVSIHQWRESKRTMG--
Ggallus  not conserved    199AEDYENSTAIEVWK-VQQAKAML
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
Protein features
Start (aa)End (aa)FeatureDetails 
1243CHAINlost
27243TOPO_DOMCytoplasmiclost
174243REGIONlost
Phylogenetic conservation
PhyloPPhastCons
(flanking)0.7970.588
1.4250.935
(flanking)1.8920.998
?
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 GAACTCAGCATCCATCCATCAGTGGCGCGAGTCCAGGAAGG
Altered gDNA sequence snippet GAACTCAGCATCCATCCATCGGTGGCGCGAGTCCAGGAAGG
Original cDNA sequence snippet GAACTCAGCATCCATCCATCAGTGGCGCGAGTCCAGGAAGG
Altered cDNA sequence snippet GAACTCAGCATCCATCCATCGGTGGCGCGAGTCCAGGAAGG
Wildtype AA sequence MSSGTELLWP GAALLVLLGV AASLCVRCSR PGAKRSEKIY QQRSLREDQQ SFTGSRTYSL
VGQAWPGPLA DMAPTRKDKL LQFYPSLEDP ASSRYQNFSK GSRHGSEEAY IDPIAMEYYN
WGRFSKPPED DDANSYENVL ICKQKTTETG AQQEGIGGLC RGDLSLSLAL KTGPTSGLCP
SASPEEDEES EDYQNSASIH QWRESRKVMG QLQREASPGP VGSPDEEDGE PDYVNGEVAA
TEA*
Mutated AA sequence MSSGTELLWP GAALLVLLGV AASLCVRCSR PGAKRSEKIY QQRSLREDQQ SFTGSRTYSL
VGQAWPGPLA DMAPTRKDKL LQFYPSLEDP ASSRYQNFSK GSRHGSEEAY IDPIAMEYYN
WGRFSKPPED DDANSYENVL ICKQKTTETG AQQEGIGGLC RGDLSLSLAL KTGPTSGLCP
SASPEEDEES EDYQNSASIH RWRESRKVMG QLQREASPGP VGSPDEEDGE PDYVNGEVAA
TEA*
Position of stopcodon in wt / mu CDS 732 / 732
Position (AA) of stopcodon in wt / mu AA sequence 244 / 244
Position of stopcodon in wt / mu cDNA 1033 / 1033
Position of start ATG in wt / mu cDNA 302 / 302
Last intron/exon boundary 1051
Theoretical NMD boundary in CDS 699
Length of CDS 732
Coding sequence (CDS) position 602
cDNA position 903
gDNA position 24520
Chromosomal position 74224171
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:

7:74224171A>G_1_ENST00000344995

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

  • Model: simple_aae
  • Tree vote: 55|45 (del | benign) ?
Analysed issue Analysis result
Variant Chr7:74224171A>G (GRCh38)
Gene symbol LAT2
Gene constraints LOEUF: 0.72, LOF (oe): 0.50, misssense (oe): 0.90, synonymous (oe): 1.02 ? (gnomAD)
Ensembl transcript ID ENST00000344995.9
Genbank transcript ID NM_014146 (by similarity)
UniProt / AlphaMissense peptide NTAL_HUMAN | AlphaMissense: transcript, gene
Variant type Single base exchange
Gene region CDS
DNA changes c.602A>G
g.24520A>G
AA changes
AAE:Q201R?
Score:43
Frameshift No
Length of protein Normal
Pathogenic variant (ClinVar) Variant not listed in ClinVar as (likely) pathogenic.
Variant DBs
dbSNP IDrs373894850
gnomADhomozygous (G/G)heterozygousallele carriers
01111
Protein conservation
SpeciesMatchGeneAAAlignment
Human      201SEDYQNSASIHQWRESRKVMGQLQ
mutated  all conserved    201SEDYQNSASIHRWRESRKVMGQL
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)FeatureDetails 
1243CHAINlost
27243TOPO_DOMCytoplasmiclost
174243REGIONlost
Phylogenetic conservation
PhyloPPhastCons
(flanking)0.7970.588
1.4250.935
(flanking)1.8920.998
?
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 GAACTCAGCATCCATCCATCAGTGGCGCGAGTCCAGGAAGG
Altered gDNA sequence snippet GAACTCAGCATCCATCCATCGGTGGCGCGAGTCCAGGAAGG
Original cDNA sequence snippet GAACTCAGCATCCATCCATCAGTGGCGCGAGTCCAGGAAGG
Altered cDNA sequence snippet GAACTCAGCATCCATCCATCGGTGGCGCGAGTCCAGGAAGG
Wildtype AA sequence MSSGTELLWP GAALLVLLGV AASLCVRCSR PGAKRSEKIY QQRSLREDQQ SFTGSRTYSL
VGQAWPGPLA DMAPTRKDKL LQFYPSLEDP ASSRYQNFSK GSRHGSEEAY IDPIAMEYYN
WGRFSKPPED DDANSYENVL ICKQKTTETG AQQEGIGGLC RGDLSLSLAL KTGPTSGLCP
SASPEEDEES EDYQNSASIH QWRESRKVMG QLQREASPGP VGSPDEEDGE PDYVNGEVAA
TEA*
Mutated AA sequence MSSGTELLWP GAALLVLLGV AASLCVRCSR PGAKRSEKIY QQRSLREDQQ SFTGSRTYSL
VGQAWPGPLA DMAPTRKDKL LQFYPSLEDP ASSRYQNFSK GSRHGSEEAY IDPIAMEYYN
WGRFSKPPED DDANSYENVL ICKQKTTETG AQQEGIGGLC RGDLSLSLAL KTGPTSGLCP
SASPEEDEES EDYQNSASIH RWRESRKVMG QLQREASPGP VGSPDEEDGE PDYVNGEVAA
TEA*
Position of stopcodon in wt / mu CDS 732 / 732
Position (AA) of stopcodon in wt / mu AA sequence 244 / 244
Position of stopcodon in wt / mu cDNA 1454 / 1454
Position of start ATG in wt / mu cDNA 723 / 723
Last intron/exon boundary 1472
Theoretical NMD boundary in CDS 699
Length of CDS 732
Coding sequence (CDS) position 602
cDNA position 1324
gDNA position 24520
Chromosomal position 74224171
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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Yum, tasty mutations...

MutationT@ster 2025

Variant:

7:74224171A>G_2_ENST00000398475

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

  • Model: simple_aae
  • Tree vote: 55|45 (del | benign) ?
Analysed issue Analysis result
Variant Chr7:74224171A>G (GRCh38)
Gene symbol LAT2
Gene constraints LOEUF: 0.72, LOF (oe): 0.50, misssense (oe): 0.90, synonymous (oe): 1.02 ? (gnomAD)
Ensembl transcript ID ENST00000398475.5
Genbank transcript ID
UniProt / AlphaMissense peptide NTAL_HUMAN | AlphaMissense: transcript, gene
Variant type Single base exchange
Gene region CDS
DNA changes c.602A>G
g.24520A>G
AA changes
AAE:Q201R?
Score:43
Frameshift No
Length of protein Normal
Pathogenic variant (ClinVar) Variant not listed in ClinVar as (likely) pathogenic.
Variant DBs
dbSNP IDrs373894850
gnomADhomozygous (G/G)heterozygousallele carriers
01111
Protein conservation
SpeciesMatchGeneAAAlignment
Human      201SEDYQNSASIHQWRESRKVMGQLQ
mutated  all conserved    201SEDYQNSASIHRWRESRKVMGQL
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)FeatureDetails 
1243CHAINlost
27243TOPO_DOMCytoplasmiclost
174243REGIONlost
Phylogenetic conservation
PhyloPPhastCons
(flanking)0.7970.588
1.4250.935
(flanking)1.8920.998
?
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 GAACTCAGCATCCATCCATCAGTGGCGCGAGTCCAGGAAGG
Altered gDNA sequence snippet GAACTCAGCATCCATCCATCGGTGGCGCGAGTCCAGGAAGG
Original cDNA sequence snippet GAACTCAGCATCCATCCATCAGTGGCGCGAGTCCAGGAAGG
Altered cDNA sequence snippet GAACTCAGCATCCATCCATCGGTGGCGCGAGTCCAGGAAGG
Wildtype AA sequence MSSGTELLWP GAALLVLLGV AASLCVRCSR PGAKRSEKIY QQRSLREDQQ SFTGSRTYSL
VGQAWPGPLA DMAPTRKDKL LQFYPSLEDP ASSRYQNFSK GSRHGSEEAY IDPIAMEYYN
WGRFSKPPED DDANSYENVL ICKQKTTETG AQQEGIGGLC RGDLSLSLAL KTGPTSGLCP
SASPEEDEES EDYQNSASIH QWRESRKVMG QLQREASPGP VGSPDEEDGE PDYVNGEVAA
TEA*
Mutated AA sequence MSSGTELLWP GAALLVLLGV AASLCVRCSR PGAKRSEKIY QQRSLREDQQ SFTGSRTYSL
VGQAWPGPLA DMAPTRKDKL LQFYPSLEDP ASSRYQNFSK GSRHGSEEAY IDPIAMEYYN
WGRFSKPPED DDANSYENVL ICKQKTTETG AQQEGIGGLC RGDLSLSLAL KTGPTSGLCP
SASPEEDEES EDYQNSASIH RWRESRKVMG QLQREASPGP VGSPDEEDGE PDYVNGEVAA
TEA*
Position of stopcodon in wt / mu CDS 732 / 732
Position (AA) of stopcodon in wt / mu AA sequence 244 / 244
Position of stopcodon in wt / mu cDNA 869 / 869
Position of start ATG in wt / mu cDNA 138 / 138
Last intron/exon boundary 887
Theoretical NMD boundary in CDS 699
Length of CDS 732
Coding sequence (CDS) position 602
cDNA position 739
gDNA position 24520
Chromosomal position 74224171
Speed 0.03 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
Yum, tasty mutations...

MutationT@ster 2025

Variant:

7:74224171A>G_3_ENST00000275635

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

  • Model: simple_aae
  • Tree vote: 55|45 (del | benign) ?
Analysed issue Analysis result
Variant Chr7:74224171A>G (GRCh38)
Gene symbol LAT2
Gene constraints LOEUF: 0.72, LOF (oe): 0.50, misssense (oe): 0.90, synonymous (oe): 1.02 ? (gnomAD)
Ensembl transcript ID ENST00000275635.11
Genbank transcript ID NM_032463 (by similarity)
UniProt / AlphaMissense peptide NTAL_HUMAN | AlphaMissense: transcript, gene
Variant type Single base exchange
Gene region CDS
DNA changes c.602A>G
g.24520A>G
AA changes
AAE:Q201R?
Score:43
Frameshift No
Length of protein Normal
Pathogenic variant (ClinVar) Variant not listed in ClinVar as (likely) pathogenic.
Variant DBs
dbSNP IDrs373894850
gnomADhomozygous (G/G)heterozygousallele carriers
01111
Protein conservation
SpeciesMatchGeneAAAlignment
Human      201SEDYQNSASIHQWRESRKVMGQLQ
mutated  all conserved    201SEDYQNSASIHRWRESRKVMGQL
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)FeatureDetails 
1243CHAINlost
27243TOPO_DOMCytoplasmiclost
174243REGIONlost
Phylogenetic conservation
PhyloPPhastCons
(flanking)0.7970.588
1.4250.935
(flanking)1.8920.998
?
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 GAACTCAGCATCCATCCATCAGTGGCGCGAGTCCAGGAAGG
Altered gDNA sequence snippet GAACTCAGCATCCATCCATCGGTGGCGCGAGTCCAGGAAGG
Original cDNA sequence snippet GAACTCAGCATCCATCCATCAGTGGCGCGAGTCCAGGAAGG
Altered cDNA sequence snippet GAACTCAGCATCCATCCATCGGTGGCGCGAGTCCAGGAAGG
Wildtype AA sequence MSSGTELLWP GAALLVLLGV AASLCVRCSR PGAKRSEKIY QQRSLREDQQ SFTGSRTYSL
VGQAWPGPLA DMAPTRKDKL LQFYPSLEDP ASSRYQNFSK GSRHGSEEAY IDPIAMEYYN
WGRFSKPPED DDANSYENVL ICKQKTTETG AQQEGIGGLC RGDLSLSLAL KTGPTSGLCP
SASPEEDEES EDYQNSASIH QWRESRKVMG QLQREASPGP VGSPDEEDGE PDYVNGEVAA
TEA*
Mutated AA sequence MSSGTELLWP GAALLVLLGV AASLCVRCSR PGAKRSEKIY QQRSLREDQQ SFTGSRTYSL
VGQAWPGPLA DMAPTRKDKL LQFYPSLEDP ASSRYQNFSK GSRHGSEEAY IDPIAMEYYN
WGRFSKPPED DDANSYENVL ICKQKTTETG AQQEGIGGLC RGDLSLSLAL KTGPTSGLCP
SASPEEDEES EDYQNSASIH RWRESRKVMG QLQREASPGP VGSPDEEDGE PDYVNGEVAA
TEA*
Position of stopcodon in wt / mu CDS 732 / 732
Position (AA) of stopcodon in wt / mu AA sequence 244 / 244
Position of stopcodon in wt / mu cDNA 963 / 963
Position of start ATG in wt / mu cDNA 232 / 232
Last intron/exon boundary 981
Theoretical NMD boundary in CDS 699
Length of CDS 732
Coding sequence (CDS) position 602
cDNA position 833
gDNA position 24520
Chromosomal position 74224171
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

Back to summary table