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: ENST00000696032
Querying Taster for transcript #2: ENST00000367425
Querying Taster for transcript #3: ENST00000391985
Querying Taster for transcript #4: ENST00000471440
MT speed 0.03 s - this script 2.368927 s

Transcript summary:

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Some transcripts had annotation problems and are not shown

Yum, tasty mutations...

MutationT@ster 2025

Variant:

1:196774952A>G_2_ENST00000367425

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Prediction:

BenignPermalink

Summary:

  • Model: without_aae
  • Tree vote: 0|200 (del | benign) ?
Analysed issue Analysis result
Variant Chr1:196774952A>G (GRCh38)
Gene symbol CFHR3
Gene constraints LOEUF: 1.30, LOF (oe): 0.90, misssense (oe): 0.76, synonymous (oe): 0.84 ? (gnomAD)
Ensembl transcript ID ENST00000367425.9
Genbank transcript ID NM_021023 (exact from MANE)
UniProt / AlphaMissense peptide N/A
Variant type Single base exchange
Gene region intron
DNA changes c.58+8A>G
g.140A>G
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 IDrs191734103
gnomADhomozygous (G/G)heterozygousallele carriers
6194200
Protein conservation N/A
Protein features N/A
Phylogenetic conservation
PhyloPPhastCons
(flanking)-0.2320.077
-0.6770.031
(flanking)1.2730.077
?
Splice sites No abrogation of potential splice sites predicted by MaxEntScan.
Distance from splice site 8
Kozak consensus sequence altered? N/A
poly(A) signal N/A
AA sequence altered N/A
Chromosome 1
Strand 1
Original gDNA sequence snippet GCTAATGGACAAGGTAAGTTAAAAGAGATCTAAACACTCAG
Altered gDNA sequence snippet GCTAATGGACAAGGTAAGTTGAAAGAGATCTAAACACTCAG
Original cDNA sequence snippet N/A
Altered cDNA sequence snippet N/A
Wildtype AA sequence MLLLINVILT LWVSCANGQV KPCDFPDIKH GGLFHENMRR PYFPVAVGKY YSYYCDEHFE
TPSGSYWDYI HCTQNGWSPA VPCLRKCYFP YLENGYNQNY GRKFVQGNST EVACHPGYGL
PKAQTTVTCT EKGWSPTPRC IRVRTCSKSD IEIENGFISE SSSIYILNKE IQYKCKPGYA
TADGNSSGSI TCLQNGWSAQ PICINSSEKC GPPPPISNGD TTSFLLKVYV PQSRVEYQCQ
PYYELQGSNY VTCSNGEWSE PPRCIHPCII TEENMNKNNI KLKGRSDRKY YAKTGDTIEF
MCKLGYNANT SILSFQAVCR EGIVEYPRCE *
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 48 / 48
Last intron/exon boundary 843
Theoretical NMD boundary in CDS 745
Length of CDS 993
Coding sequence (CDS) position N/A
cDNA position N/A
gDNA position 140
Chromosomal position 196774952
Speed 0.01 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:

1:196774952A>G_3_ENST00000391985

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Prediction:

BenignPermalink

Summary:

  • Model: without_aae
  • Tree vote: 0|200 (del | benign) ?
Analysed issue Analysis result
Variant Chr1:196774952A>G (GRCh38)
Gene symbol CFHR3
Gene constraints LOEUF: 1.44, LOF (oe): 0.96, misssense (oe): 0.76, synonymous (oe): 0.86 ? (gnomAD)
Ensembl transcript ID ENST00000391985.7
Genbank transcript ID NM_001166624 (by similarity)
UniProt / AlphaMissense peptide N/A
Variant type Single base exchange
Gene region intron
DNA changes c.58+8A>G
g.140A>G
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 IDrs191734103
gnomADhomozygous (G/G)heterozygousallele carriers
6194200
Protein conservation N/A
Protein features N/A
Phylogenetic conservation
PhyloPPhastCons
(flanking)-0.2320.077
-0.6770.031
(flanking)1.2730.077
?
Splice sites No abrogation of potential splice sites predicted by MaxEntScan.
Distance from splice site 8
Kozak consensus sequence altered? N/A
poly(A) signal N/A
AA sequence altered N/A
Chromosome 1
Strand 1
Original gDNA sequence snippet GCTAATGGACAAGGTAAGTTAAAAGAGATCTAAACACTCAG
Altered gDNA sequence snippet GCTAATGGACAAGGTAAGTTGAAAGAGATCTAAACACTCAG
Original cDNA sequence snippet N/A
Altered cDNA sequence snippet N/A
Wildtype AA sequence MLLLINVILT LWVSCANGQV KPCDFPDIKH GGLFHENMRR PYFPVAVGKY YSYYCDEHFE
TPSGSYWDYI HCTQNGWSPA VPCLRKCYFP YLENGYNQNY GRKFVQGNST EVACHPGYGL
PKAQTTVTCT EKGWSPTPRC IRVNSSEKCG PPPPISNGDT TSFLLKVYVP QSRVEYQCQP
YYELQGSNYV TCSNGEWSEP PRCIHPCIIT EENMNKNNIK LKGRSDRKYY AKTGDTIEFM
CKLGYNANTS ILSFQAVCRE GIVEYPRCE*
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 72 / 72
Last intron/exon boundary 684
Theoretical NMD boundary in CDS 562
Length of CDS 810
Coding sequence (CDS) position N/A
cDNA position N/A
gDNA position 140
Chromosomal position 196774952
Speed 0.01 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:

1:196774952A>G_4_ENST00000471440

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Prediction:

BenignPermalink

Summary:

  • Model: without_aae
  • Tree vote: 0|200 (del | benign) ?
Analysed issue Analysis result
Variant Chr1:196774952A>G (GRCh38)
Gene symbol CFHR3
Gene constraints LOEUF: 1.63, LOF (oe): 1.13, misssense (oe): 0.74, synonymous (oe): 0.81 ? (gnomAD)
Ensembl transcript ID ENST00000471440.6
Genbank transcript ID
UniProt / AlphaMissense peptide N/A
Variant type Single base exchange
Gene region intron
DNA changes c.58+8A>G
g.140A>G
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 IDrs191734103
gnomADhomozygous (G/G)heterozygousallele carriers
6194200
Protein conservation N/A
Protein features N/A
Phylogenetic conservation
PhyloPPhastCons
(flanking)-0.2320.077
-0.6770.031
(flanking)1.2730.077
?
Splice sites No abrogation of potential splice sites predicted by MaxEntScan.
Distance from splice site 8
Kozak consensus sequence altered? N/A
poly(A) signal N/A
AA sequence altered N/A
Chromosome 1
Strand 1
Original gDNA sequence snippet GCTAATGGACAAGGTAAGTTAAAAGAGATCTAAACACTCAG
Altered gDNA sequence snippet GCTAATGGACAAGGTAAGTTGAAAGAGATCTAAACACTCAG
Original cDNA sequence snippet N/A
Altered cDNA sequence snippet N/A
Wildtype AA sequence MLLLINVILT LWVSCANGQV KPCDFPDIKH GGLFHENMRR PYFPVAVGKY YSYYCDEHFE
TPSGSYWDYI HCTQNGWSPA VPCLRKCYFP YLENGYNQNY GRKFVQGNST EVACHPGYGL
PKAQTTVTCT EKGWSPTPRC IRVRTCSKSD IEIENGFISE SSSIYILNKE IQYKCKPGYA
TADGNSSGSI TCLQNGWSAQ PICITACIAF RAHAQKSCTC RGRNECLILN FC*
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 75 / 75
Last intron/exon boundary 687
Theoretical NMD boundary in CDS 562
Length of CDS 699
Coding sequence (CDS) position N/A
cDNA position N/A
gDNA position 140
Chromosomal position 196774952
Speed 0.01 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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Problem:

1

Yum, tasty mutations...

MutationT@ster 2025

Data problem



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