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: ENST00000376751
Querying Taster for transcript #2: ENST00000244360
MT speed 0.03 s - this script 2.355169 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
ENST00000244360(MANE Select)	RNF39	Benign	96\|104	without_aae		No				Single base exchange		Normal
ENST00000376751	RNF39	Benign	99\|101	without_aae		No				Single base exchange		Normal

MutationT@ster 2025

Variant:

6:30071573G>A_2_ENST00000244360

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Prediction:

BenignPermalink

Summary:

Model: without_aae
Tree vote: 96|104 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr6:30071573G>A (GRCh38)

Gene symbol

RNF39

Gene constraints

LOEUF: 1.83, LOF (oe): 1.33, misssense (oe): 1.42, synonymous (oe): 1.43 ? (gnomAD)

Ensembl transcript ID

ENST00000244360.8

Genbank transcript ID

NM_025236 (exact from MANE)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.597C>T
g.4277C>T

AA changes

no AA changes

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

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

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.733	0
	-0.161	0.001
(flanking)	6.878	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

No

Chromosome

6

Strand

-1

Original gDNA sequence snippet

CCTGACGGCCCCAAGCGCTTCGATCAGCTCCCAGCTGTGCT

Altered gDNA sequence snippet

CCTGACGGCCCCAAGCGCTTTGATCAGCTCCCAGCTGTGCT

Original cDNA sequence snippet

CCTGACGGCCCCAAGCGCTTCGATCAGCTCCCAGCTGTGCT

Altered cDNA sequence snippet

CCTGACGGCCCCAAGCGCTTTGATCAGCTCCCAGCTGTGCT

Wildtype AA sequence

MDAPELGPGL VERLEQLATC PLCGGSFEDP VLLACEHSFC RACLARRWGT PPATGTEASP
TACPCCGLPC PRRSLRSNVR LAVEVRISRE LREKLAEPGA RAGRRRGGRI PTMGCLDLPG
EDMRKTWRRF EVPTSKSSNS EDDLPEDYPV VKKMLHRLTA DLTLDPGTAH RRLLISADRR
SVQLAPPGTP APPDGPKRFD QLPAVLGAQG FGAGRHCWEV ETADAASCRD SSGEDADDEE
SHYAVGAAGE SVQRKGCVRL CPAGAVWAVE GRGGRLWALT APEPTLLGGV EPPPRRIRVD
LDWERGRVAF YDGRSLDLLY AFQAPGPLGE RIFPLFCTCD PRAPLRIVPA ES*

Mutated AA sequence

MDAPELGPGL VERLEQLATC PLCGGSFEDP VLLACEHSFC RACLARRWGT PPATGTEASP
TACPCCGLPC PRRSLRSNVR LAVEVRISRE LREKLAEPGA RAGRRRGGRI PTMGCLDLPG
EDMRKTWRRF EVPTSKSSNS EDDLPEDYPV VKKMLHRLTA DLTLDPGTAH RRLLISADRR
SVQLAPPGTP APPDGPKRFD QLPAVLGAQG FGAGRHCWEV ETADAASCRD SSGEDADDEE
SHYAVGAAGE SVQRKGCVRL CPAGAVWAVE GRGGRLWALT APEPTLLGGV EPPPRRIRVD
LDWERGRVAF YDGRSLDLLY AFQAPGPLGE RIFPLFCTCD PRAPLRIVPA ES*

Position of stopcodon in wt / mu CDS

1059 / 1059

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

353 / 353

Position of stopcodon in wt / mu cDNA

1243 / 1243

Position of start ATG in wt / mu cDNA

185 / 185

Last intron/exon boundary

662

Theoretical NMD boundary in CDS

427

Length of CDS

1059

Coding sequence (CDS) position

597

cDNA position

781

gDNA position

4277

Chromosomal position

30071573

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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MutationT@ster 2025

Variant:

6:30071573G>A_1_ENST00000376751

Back to summary table

Prediction:

BenignPermalink

Summary:

Model: without_aae
Tree vote: 99|101 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr6:30071573G>A (GRCh38)

Gene symbol

RNF39

Gene constraints

LOEUF: 1.84, LOF (oe): 1.35, misssense (oe): 1.45, synonymous (oe): 1.45 ? (gnomAD)

Ensembl transcript ID

ENST00000376751.8

Genbank transcript ID

NM_170769 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.597C>T
g.4277C>T

AA changes

no AA changes

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

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

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.733	0
	-0.161	0.001
(flanking)	6.878	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

No

Chromosome

6

Strand

-1

Original gDNA sequence snippet

CCTGACGGCCCCAAGCGCTTCGATCAGCTCCCAGCTGTGCT

Altered gDNA sequence snippet

CCTGACGGCCCCAAGCGCTTTGATCAGCTCCCAGCTGTGCT

Original cDNA sequence snippet

CCTGACGGCCCCAAGCGCTTCGATCAGCTCCCAGCTGTGCT

Altered cDNA sequence snippet

CCTGACGGCCCCAAGCGCTTTGATCAGCTCCCAGCTGTGCT

Wildtype AA sequence

MDAPELGPGL VERLEQLATC PLCGGSFEDP VLLACEHSFC RACLARRWGT PPATGTEASP
TACPCCGLPC PRRSLRSNVR LAVEVRISRE LREKLAEPGA RAGRRRGGRI PTMGCLDLPG
EDMRKTWRRF EVPTSKSSNS EDDLPEDYPV VKKMLHRLTA DLTLDPGTAH RRLLISADRR
SVQLAPPGTP APPDGPKRFD QLPAVLGAQG FGAGRHCWEV ETADAASCRD SSGEDADDEE
SHYAVGAAGE SVQRKGCAPG PLGERIFPLF CTCDPRAPLR IVPAES*

Mutated AA sequence

MDAPELGPGL VERLEQLATC PLCGGSFEDP VLLACEHSFC RACLARRWGT PPATGTEASP
TACPCCGLPC PRRSLRSNVR LAVEVRISRE LREKLAEPGA RAGRRRGGRI PTMGCLDLPG
EDMRKTWRRF EVPTSKSSNS EDDLPEDYPV VKKMLHRLTA DLTLDPGTAH RRLLISADRR
SVQLAPPGTP APPDGPKRFD QLPAVLGAQG FGAGRHCWEV ETADAASCRD SSGEDADDEE
SHYAVGAAGE SVQRKGCAPG PLGERIFPLF CTCDPRAPLR IVPAES*

Position of stopcodon in wt / mu CDS

861 / 861

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

287 / 287

Position of stopcodon in wt / mu cDNA

1125 / 1125

Position of start ATG in wt / mu cDNA

265 / 265

Last intron/exon boundary

1035

Theoretical NMD boundary in CDS

720

Length of CDS

861

Coding sequence (CDS) position

597

cDNA position

861

gDNA position

4277

Chromosomal position

30071573

Speed

0.02 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