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: ENST00000495799
Querying Taster for transcript #2: ENST00000466508
Querying Taster for transcript #3: ENST00000055335
MT speed 0.05 s - this script 2.400248 s

Transcript summary:

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Transcript	Gene symbol	Prediction	Tree vote	Model	Splice site change	Variant type	Protein length	Features at a glance
ENST00000466508	PPP1R3F	Benign	0\|200	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000495799	PPP1R3F	Benign	0\|200	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000055335(MANE Select)	PPP1R3F	Benign	0\|200	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD

MutationT@ster 2025

Variant:

23:49274368C>T_2_ENST00000466508

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Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 0|200 (del | benign) ?
Automatic classification due to gnomAD
no values for phylogenetic conservation

Analysed issue

Analysis result

Variant

ChrX:49274368C>T (GRCh38)

Gene symbol

PPP1R3F

Gene constraints

no data

Ensembl transcript ID

ENST00000466508.5

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.-32+3495C>T
g.4576C>T

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 ID	rs5906761
gnomAD	homo-/hemizygous (T/T)	heterozygous	allele carriers
	27799	18908	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

23

Strand

1

Original gDNA sequence snippet

CAATCTGGCCTCCACTGGCTCATAGTCTTAACACCAGTGGT

Altered gDNA sequence snippet

CAATCTGGCCTCCACTGGCTTATAGTCTTAACACCAGTGGT

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MDDNTFAMEH PDVQESVGPL VAPTPLRPWP QMTLQVSDVP MTGNPAEEGD VPRSSPPVAF
TEVLQAPAIR IPPSSPLCGL GGSPRDQASG PDASEGATGP FLEPSQQQAE ATWGVSSENG
GGLEAVSGSE ELLGEDTIDQ ELEQLYLSHL SRLRAAVAAG GAGGGGEGST DGGMSPSHPL
GILTDRDLIL KWPGPERALN SALAEEITLH YARLGRGVEL IKDTEDPDDE GEGEEGLSVT
PSSPEGDSPK ESPPEILSGA RSVVATMGDV WLPWAEGSGC DGPVVLGTEG QFIGDPEKGM
GKDTSSLHMN RVIAGVTESL GEAGTEAQIE VTSEWAGSLD PISGKEPASP VLLQGQNPTL
LSPLGAEVCL SSVARPHVSS QDEKDAGPSL EPPKKSPTLA VPAECVCALP PQLRGPLTQT
LGVLAGLVVV PVALNSGVSL LVLALCLSLA WFS*

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

389 / 389

Last intron/exon boundary

493

Theoretical NMD boundary in CDS

54

Length of CDS

1362

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

4576

Chromosomal position

49274368

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

MutationT@ster 2025

Variant:

23:49274368C>T_1_ENST00000495799

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 0|200 (del | benign) ?
Automatic classification due to gnomAD
no values for phylogenetic conservation

Analysed issue

Analysis result

Variant

ChrX:49274368C>T (GRCh38)

Gene symbol

PPP1R3F

Gene constraints

no data

Ensembl transcript ID

ENST00000495799.5

Genbank transcript ID

NM_001184745 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.-32+4435C>T
g.4576C>T

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 ID	rs5906761
gnomAD	homo-/hemizygous (T/T)	heterozygous	allele carriers
	27799	18908	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

23

Strand

1

Original gDNA sequence snippet

CAATCTGGCCTCCACTGGCTCATAGTCTTAACACCAGTGGT

Altered gDNA sequence snippet

CAATCTGGCCTCCACTGGCTTATAGTCTTAACACCAGTGGT

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MDDNTFAMEH PDVQESVGPL VAPTPLRPWP QMTLQVSDVP MTGNPAEEGD VPRSSPPVAF
TEVLQAPAIR IPPSSPLCGL GGSPRDQASG PDASEGATGP FLEPSQQQAE ATWGVSSENG
GGLEAVSGSE ELLGEDTIDQ ELEQLYLSHL SRLRAAVAAG GAGGGGEGST DGGMSPSHPL
GILTDRDLIL KWPGPERALN SALAEEITLH YARLGRGVEL IKDTEDPDDE GEGEEGLSVT
PSSPEGDSPK ESPPEILSGA RSVVATMGDV WLPWAEGSGC DGPVVLGTEG QFIGDPEKGM
GKDTSSLHMN RVIAGVTESL GEAGTEAQIE VTSEWAGSLD PISGKEPASP VLLQGQNPTL
LSPLGAEVCL SSVARPHVSS QDEKDAGPSL EPPKKSPTLA VPAECVCALP PQLRGPLTQT
LGVLAGLVVV PVALNSGVSL LVLALCLSLA WFS*

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

96 / 96

Last intron/exon boundary

200

Theoretical NMD boundary in CDS

54

Length of CDS

1362

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

4576

Chromosomal position

49274368

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

MutationT@ster 2025

Variant:

23:49274368C>T_3_ENST00000055335

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 0|200 (del | benign) ?
Automatic classification due to gnomAD
no values for phylogenetic conservation

Analysed issue

Analysis result

Variant

ChrX:49274368C>T (GRCh38)

Gene symbol

PPP1R3F

Gene constraints

no data

Ensembl transcript ID

ENST00000055335.11

Genbank transcript ID

NM_033215 (exact from MANE)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.1004+3495C>T
g.4576C>T

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 ID	rs5906761
gnomAD	homo-/hemizygous (T/T)	heterozygous	allele carriers
	27799	18908	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

23

Strand

1

Original gDNA sequence snippet

CAATCTGGCCTCCACTGGCTCATAGTCTTAACACCAGTGGT

Altered gDNA sequence snippet

CAATCTGGCCTCCACTGGCTTATAGTCTTAACACCAGTGGT

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MARTAPVEPP LRHSAPPSPA AGEPRTSVEA AVAPRRVLFA DEALGLPLAQ LRRYRPWGGP
GAGKMAAAAG QDGGGGGGAD EDDDGEDGDE GEEEEEACPE PSPLCPVPAG GGFYLVPTFS
LPPAPGRLER LGRVMVELEA LLPPPGAVPG GAGVWVPGGR PPVLRGLVRV LNRSFEKAVH
VRASHDGWAS FCDHPARYVP RSPPWAGAGG TGAGDPILDP GLGLGPGQAS ASSPDDGGRT
DRFAFQLPFA EGAGDGARLD FVVRYETPEG TFWANNHGRN YTVLLRIAPA PTPTDAEGLP
QQQQLPQLEP QPECQGPVEA EARQLKSCMK PVRRRPAEEE LKTKNMDDNT FAMAEHPDVQ
ESVGPLVAPT PLRPWPQMTL QVSDVPMTGN PAEEGDVPRS SPPVAFTEVL QAPAIRIPPS
SPLCGLGGSP RDQASGPDAS EGATGPFLEP SQQQAEATWG VSSENGGGLE AVSGSEELLG
EDTIDQELEQ LYLSHLSRLR AAVAAGGAGG GGEGSTDGGM SPSHPLGILT DRDLILKWPG
PERALNSALA EEITLHYARL GRGVELIKDT EDPDDEGEGE EGLSVTPSSP EGDSPKESPP
EILSGARSVV ATMGDVWLPW AEGSGCDGPV VLGTEGQFIG DPEKGMGKDT SSLHMNRVIA
GVTESLGEAG TEAQIEVTSE WAGSLDPISG KEPASPVLLQ GQNPTLLSPL GAEVCLSSVA
RPHVSSQDEK DAGPSLEPPK KSPTLAVPAE CVCALPPQLR GPLTQTLGVL AGLVVVPVAL
NSGVSLLVLA LCLSLAWFS*

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

78 / 78

Last intron/exon boundary

1220

Theoretical NMD boundary in CDS

1092

Length of CDS

2400

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

4576

Chromosomal position

49274368

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

Back to summary table