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: ENST00000550345
Querying Taster for transcript #2: ENST00000550924
Querying Taster for transcript #3: ENST00000549941
Querying Taster for transcript #4: ENST00000340802
Querying Taster for transcript #5: ENST00000550257
Querying Taster for transcript #6: ENST00000642730
MT speed 0.14 s - this script 2.527268 s

Transcript summary:

Permalink

Transcript	Gene symbol	Prediction	Tree vote	Model	Splice site change	Amino acid changes	Variant type	Protein length	Features at a glance
ENST00000340802	PFKM	Deleterious	9\|1	complex_aae	No	first 11 AA missing	Single base exchange	Delayed start of translation	Amino acid sequence changed Kozak consensus sequence changed Protein features (might be) affected Start ATG shifted
ENST00000642730	PFKM	Deleterious	9\|1	complex_aae	No	first 11 AA missing	Single base exchange	Delayed start of translation	Amino acid sequence changed Kozak consensus sequence changed Start ATG shifted
ENST00000550345	PFKM	Benign	28\|172	without_aae	No		Single base exchange	N/A
ENST00000550924	PFKM	Benign	28\|172	without_aae	No		Single base exchange	N/A
ENST00000549941	PFKM	Benign	40\|160	without_aae	No		Single base exchange	N/A
ENST00000550257	PFKM	Benign	73\|127	without_aae	No		Single base exchange	N/A

MutationT@ster 2025

Variant:

12:48107374A>G_4_ENST00000340802

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Kozak consensus sequence changed
Protein features (might be) affected
Start ATG shifted

Model: complex_aae
Tree vote: 9|1 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr12:48107374A>G (GRCh38)

Gene symbol

PFKM

Gene constraints

LOEUF: 0.83, LOF (oe): 0.67, misssense (oe): 0.66, synonymous (oe): 0.91 ? (gnomAD)

Ensembl transcript ID

ENST00000340802.12

Genbank transcript ID

NM_001166686 (by similarity), NM_001354737 (by similarity), NM_001354739 (by similarity), NM_001354738 (by similarity)

UniProt / AlphaMissense peptide

PFKAM_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS
spans start ATG

DNA changes

c.1A>G
g.2236A>G

AA changes

M1? initiating Methionine lost
possible effect: activation of potential downstream translation initiation site with same reading frame resulting in shortened AA sequence, 11 AA at beginning of AA sequence are missing

AAE:

M1-

H2-

K3-

D4-

E5-

F6-

H7-

L8-

K9-

F10-

F11-

?

Score:

-

Frameshift

No

Length of protein

Delayed start of translation

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs755094329
gnomAD	homozygous (G/G)	heterozygous	allele carriers
	0	8	8

Protein conservation

Species	Match	AA
Human		1	M	H	K	D	E	F	H	L	K	F	F	M	C	V	I	Q	S	R	Q	L	V	R	T
mutated	not conserved	-10												M	C	V	I	Q	S	R	Q	L	V	R	T	P	Q	R	T	A	G	E	A	S
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)	Feature	Details
1	1	INIT_MET	Removed	lost
2	2	MOD_RES	N-acetylthreonine	lost
2	390	REGION	N-terminal	lost
2	780	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.67	0.999
	2.141	1
(flanking)	3.067	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

10

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

12

Strand

1

Original gDNA sequence snippet

TCTATTTCTAGGAGGCAGCCATGCATAAAGACGAGTTTCAT

Altered gDNA sequence snippet

TCTATTTCTAGGAGGCAGCCGTGCATAAAGACGAGTTTCAT

Original cDNA sequence snippet

AGAGTCGCTAGGAGGCAGCCATGCATAAAGACGAGTTTCAT

Altered cDNA sequence snippet

AGAGTCGCTAGGAGGCAGCCGTGCATAAAGACGAGTTTCAT

Wildtype AA sequence

MHKDEFHLKF FMCVIQSRQL VRTPQRTAGE ASTSSMLIPK PPPKTDILKS LDTMDDPDTV
GSIPVFKTEW IMTHEEHHAA KTLGIGKAIA VLTSGGDAQG MNAAVRAVVR VGIFTGARVF
FVHEGYQGLV DGGDHIKEAT WESVSMMLQL GGTVIGSARC KDFREREGRL RAAYNLVKRG
ITNLCVIGGD GSLTGADTFR SEWSDLLSDL QKAGKITDEE ATKSSYLNIV GLVGSIDNDF
CGTDMTIGTD SALHRIMEIV DAITTTAQSH QRTFVLEVMG RHCGYLALVT SLSCGADWVF
IPECPPDDDW EEHLCRRLSE TRTRGSRLNI IIVAEGAIDK NGKPITSEDI KNLVVKRLGY
DTRVTVLGHV QRGGTPSAFD RILGSRMGVE AVMALLEGTP DTPACVVSLS GNQAVRLPLM
ECVQVTKDVT KAMDEKKFDE ALKLRGRSFM NNWEVYKLLA HVRPPVSKSG SHTVAVMNVG
APAAGMNAAV RSTVRIGLIQ GNRVLVVHDG FEGLAKGQIE EAGWSYVGGW TGQGGSKLGT
KRTLPKKSFE QISANITKFN IQGLVIIGGF EAYTGGLELM EGRKQFDELC IPFVVIPATV
SNNVPGSDFS VGADTALNTI CTTCDRIKQS AAGTKRRVFI IETMGGYCGY LATMAGLAAG
ADAAYIFEEP FTIRDLQANV EHLVQKMKTT VKRGLVLRNE KCNENYTTDF IFNLYSEEGK
GIFDSRKNVL GHMQQGGSPT PFDRNFATKM GAKAMNWMSG KIKESYRNGR IFANTPDSGC
VLGMRKRALV FQPVAELKDQ TDFEHRIPKE QWWLKLRPIL KILAKYEIDL DTSDHAHLEH
ITRKRSGEAA V*

Mutated AA sequence

MCVIQSRQLV RTPQRTAGEA STSSMLIPKP PPKTDILKSL DTMDDPDTVG SIPVFKTEWI
MTHEEHHAAK TLGIGKAIAV LTSGGDAQGM NAAVRAVVRV GIFTGARVFF VHEGYQGLVD
GGDHIKEATW ESVSMMLQLG GTVIGSARCK DFREREGRLR AAYNLVKRGI TNLCVIGGDG
SLTGADTFRS EWSDLLSDLQ KAGKITDEEA TKSSYLNIVG LVGSIDNDFC GTDMTIGTDS
ALHRIMEIVD AITTTAQSHQ RTFVLEVMGR HCGYLALVTS LSCGADWVFI PECPPDDDWE
EHLCRRLSET RTRGSRLNII IVAEGAIDKN GKPITSEDIK NLVVKRLGYD TRVTVLGHVQ
RGGTPSAFDR ILGSRMGVEA VMALLEGTPD TPACVVSLSG NQAVRLPLME CVQVTKDVTK
AMDEKKFDEA LKLRGRSFMN NWEVYKLLAH VRPPVSKSGS HTVAVMNVGA PAAGMNAAVR
STVRIGLIQG NRVLVVHDGF EGLAKGQIEE AGWSYVGGWT GQGGSKLGTK RTLPKKSFEQ
ISANITKFNI QGLVIIGGFE AYTGGLELME GRKQFDELCI PFVVIPATVS NNVPGSDFSV
GADTALNTIC TTCDRIKQSA AGTKRRVFII ETMGGYCGYL ATMAGLAAGA DAAYIFEEPF
TIRDLQANVE HLVQKMKTTV KRGLVLRNEK CNENYTTDFI FNLYSEEGKG IFDSRKNVLG
HMQQGGSPTP FDRNFATKMG AKAMNWMSGK IKESYRNGRI FANTPDSGCV LGMRKRALVF
QPVAELKDQT DFEHRIPKEQ WWLKLRPILK ILAKYEIDLD TSDHAHLEHI TRKRSGEAAV
*

Position of stopcodon in wt / mu CDS

2556 / 2523

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

852 / 841

Position of stopcodon in wt / mu cDNA

2780 / 2747

Position of start ATG in wt / mu cDNA

225 / 258

Last intron/exon boundary

2635

Theoretical NMD boundary in CDS

2360

Length of CDS

2556

Coding sequence (CDS) position

1

cDNA position

225

gDNA position

2236

Chromosomal position

48107374

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

MutationT@ster 2025

Variant:

12:48107374A>G_6_ENST00000642730

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Kozak consensus sequence changed
Start ATG shifted

Model: complex_aae
Tree vote: 9|1 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr12:48107374A>G (GRCh38)

Gene symbol

PFKM

Gene constraints

LOEUF: 0.83, LOF (oe): 0.67, misssense (oe): 0.66, synonymous (oe): 0.91 ? (gnomAD)

Ensembl transcript ID

ENST00000642730.1

Genbank transcript ID

NM_001354736 (by similarity), NM_001354735 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS
spans start ATG

DNA changes

c.1A>G
g.2236A>G

AA changes

M1? initiating Methionine lost
possible effect: activation of potential downstream translation initiation site with same reading frame resulting in shortened AA sequence, 11 AA at beginning of AA sequence are missing

AAE:

M1-

H2-

K3-

D4-

E5-

F6-

H7-

L8-

K9-

F10-

F11-

?

Score:

-

Frameshift

No

Length of protein

Delayed start of translation

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs755094329
gnomAD	homozygous (G/G)	heterozygous	allele carriers
	0	8	8

Protein conservation

Species	Match	AA
Human		1	M	H	K	D	E	F	H	L	K	F	F	M	C	V	I	Q	S	R	Q	L	V	R	T
mutated	not conserved	-10												M	C	V	I	Q	S	R	Q	L	V	R	T	P	Q	R	T	A	G	E	A	S
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

	PhyloP	PhastCons
(flanking)	1.67	0.999
	2.141	1
(flanking)	3.067	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

10

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

12

Strand

1

Original gDNA sequence snippet

TCTATTTCTAGGAGGCAGCCATGCATAAAGACGAGTTTCAT

Altered gDNA sequence snippet

TCTATTTCTAGGAGGCAGCCGTGCATAAAGACGAGTTTCAT

Original cDNA sequence snippet

TAAGACTAGTCGAGGCAGCCATGCATAAAGACGAGTTTCAT

Altered cDNA sequence snippet

TAAGACTAGTCGAGGCAGCCGTGCATAAAGACGAGTTTCAT

Wildtype AA sequence

MHKDEFHLKF FMCVIQSRQL VRTPQRTAGE ASTSSMLIPK PPPKTDILKS LDTMDDPDTV
GSIPVFKTEC AEVEIQVSKR KRAVVKARGD PTVETMKQRE EWIMTHEEHH AAKTLGIGKA
IAVLTSGGDA QGMNAAVRAV VRVGIFTGAR VFFVHEGYQG LVDGGDHIKE ATWESVSMML
QLGGTVIGSA RCKDFREREG RLRAAYNLVK RGITNLCVIG GDGSLTGADT FRSEWSDLLS
DLQKAGKITD EEATKSSYLN IVGLVGSIDN DFCGTDMTIG TDSALHRIME IVDAITTTAQ
SHQRTFVLEV MGRHCGYLAL VTSLSCGADW VFIPECPPDD DWEEHLCRRL SETRTRGSRL
NIIIVAEGAI DKNGKPITSE DIKNLVVKRL GYDTRVTVLG HVQRGGTPSA FDRILGSRMG
VEAVMALLEG TPDTPACVVS LSGNQAVRLP LMECVQVTKD VTKAMDEKKF DEALKLRGRS
FMNNWEVYKL LAHVRPPVSK SGSHTVAVMN VGAPAAGMNA AVRSTVRIGL IQGNRVLVVH
DGFEGLAKGQ IEEAGWSYVG GWTGQGGSKL GTKRTLPKKS FEQISANITK FNIQGLVIIG
GFEAYTGGLE LMEGRKQFDE LCIPFVVIPA TVSNNVPGSD FSVGADTALN TICTTCDRIK
QSAAGTKRRV FIIETMGGYC GYLATMAGLA AGADAAYIFE EPFTIRDLQA NVEHLVQKMK
TTVKRGLVLR NEKCNENYTT DFIFNLYSEE GKGIFDSRKN VLGHMQQGGS PTPFDRNFAT
KMGAKAMNWM SGKIKESYRN GRIFANTPDS GCVLGMRKRA LVFQPVAELK DQTDFEHRIP
KEQWWLKLRP ILKILAKYEI DLDTSDHAHL EHITRKRSGE AAV*

Mutated AA sequence

MCVIQSRQLV RTPQRTAGEA STSSMLIPKP PPKTDILKSL DTMDDPDTVG SIPVFKTECA
EVEIQVSKRK RAVVKARGDP TVETMKQREE WIMTHEEHHA AKTLGIGKAI AVLTSGGDAQ
GMNAAVRAVV RVGIFTGARV FFVHEGYQGL VDGGDHIKEA TWESVSMMLQ LGGTVIGSAR
CKDFREREGR LRAAYNLVKR GITNLCVIGG DGSLTGADTF RSEWSDLLSD LQKAGKITDE
EATKSSYLNI VGLVGSIDND FCGTDMTIGT DSALHRIMEI VDAITTTAQS HQRTFVLEVM
GRHCGYLALV TSLSCGADWV FIPECPPDDD WEEHLCRRLS ETRTRGSRLN IIIVAEGAID
KNGKPITSED IKNLVVKRLG YDTRVTVLGH VQRGGTPSAF DRILGSRMGV EAVMALLEGT
PDTPACVVSL SGNQAVRLPL MECVQVTKDV TKAMDEKKFD EALKLRGRSF MNNWEVYKLL
AHVRPPVSKS GSHTVAVMNV GAPAAGMNAA VRSTVRIGLI QGNRVLVVHD GFEGLAKGQI
EEAGWSYVGG WTGQGGSKLG TKRTLPKKSF EQISANITKF NIQGLVIIGG FEAYTGGLEL
MEGRKQFDEL CIPFVVIPAT VSNNVPGSDF SVGADTALNT ICTTCDRIKQ SAAGTKRRVF
IIETMGGYCG YLATMAGLAA GADAAYIFEE PFTIRDLQAN VEHLVQKMKT TVKRGLVLRN
EKCNENYTTD FIFNLYSEEG KGIFDSRKNV LGHMQQGGSP TPFDRNFATK MGAKAMNWMS
GKIKESYRNG RIFANTPDSG CVLGMRKRAL VFQPVAELKD QTDFEHRIPK EQWWLKLRPI
LKILAKYEID LDTSDHAHLE HITRKRSGEA AV*

Position of stopcodon in wt / mu CDS

2652 / 2619

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

884 / 873

Position of stopcodon in wt / mu cDNA

2796 / 2763

Position of start ATG in wt / mu cDNA

145 / 178

Last intron/exon boundary

2651

Theoretical NMD boundary in CDS

2456

Length of CDS

2652

Coding sequence (CDS) position

1

cDNA position

145

gDNA position

2236

Chromosomal position

48107374

Speed

0.05 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:

12:48107374A>G_1_ENST00000550345

Back to summary table

Prediction:

BenignPermalink

Summary:

Model: without_aae
Tree vote: 28|172 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr12:48107374A>G (GRCh38)

Gene symbol

PFKM

Gene constraints

LOEUF: 0.77, LOF (oe): 0.61, misssense (oe): 0.64, synonymous (oe): 0.91 ? (gnomAD)

Ensembl transcript ID

ENST00000550345.6

Genbank transcript ID

NM_001354741 (by similarity), NM_001354742 (by similarity), NM_001354747 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.-9+1955A>G
g.2236A>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 ID	rs755094329
gnomAD	homozygous (G/G)	heterozygous	allele carriers
	0	8	8

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.67	0.999
	2.141	1
(flanking)	3.067	1

?

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

12

Strand

1

Original gDNA sequence snippet

TCTATTTCTAGGAGGCAGCCATGCATAAAGACGAGTTTCAT

Altered gDNA sequence snippet

TCTATTTCTAGGAGGCAGCCGTGCATAAAGACGAGTTTCAT

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MTHEEHHAAK TLGIGKAIAV LTSGGDAQGM NAAVRAVVRV GIFTGARVFF VHEGYQGLVD
GGDHIKEATW ESVSMMLQLG GTVIGSARCK DFREREGRLR AAYNLVKRGI TNLCVIGGDG
SLTGADTFRS EWSDLLSDLQ KAGKITDEEA TKSSYLNIVG LVGSIDNDFC GTDMTIGTDS
ALHRIMEIVD AITTTAQSHQ RTFVLEVMGR HCGYLALVTS LSCGADWVFI PECPPDDDWE
EHLCRRLSET RTRGSRLNII IVAEGAIDKN GKPITSEDIK NLVVKRLGYD TRVTVLGHVQ
RGGTPSAFDR ILGSRMGVEA VMALLEGTPD TPACVVSLSG NQAVRLPLME CVQVTKDVTK
AMDEKKFDEA LKLRGRSFMN NWEVYKLLAH VRPPVSKSGS HTVAVMNVGA PAAGMNAAVR
STVRIGLIQG NRVLVVHDGF EGLAKGQIEE AGWSYVGGWT GQGGSKLGTK RTLPKKSFEQ
ISANITKFNI QGLVIIGGFE AYTGGLELME GRKQFDELCI PFVVIPATVS NNVPGSDFSV
GADTALNTIC TTCDRIKQSA AGTKRRVFII ETMGGYCGYL ATMAGLAAGA DAAYIFEEPF
TIRDLQANVE HLVQKMKTTV KRGLVLRNEK CNENYTTDFI FNLYSEEGKG IFDSRKNVLG
HMQQGGSPTP FDRNFATKMG AKAMNWMSGK IKESYRNGRI FANTPDSGCV LGMRKRALVF
QPVAELKDQT DFEHRIPKEQ WWLKLRPILK ILAKYEIDLD TSDHAHLEHI TRKRSGEAAV
*

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

290 / 290

Last intron/exon boundary

2487

Theoretical NMD boundary in CDS

2147

Length of CDS

2343

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

2236

Chromosomal position

48107374

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:

12:48107374A>G_2_ENST00000550924

Back to summary table

Prediction:

BenignPermalink

Summary:

Model: without_aae
Tree vote: 28|172 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr12:48107374A>G (GRCh38)

Gene symbol

PFKM

Gene constraints

LOEUF: 0.77, LOF (oe): 0.61, misssense (oe): 0.64, synonymous (oe): 0.91 ? (gnomAD)

Ensembl transcript ID

ENST00000550924.6

Genbank transcript ID

NM_001354743 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.-9+1564A>G
g.2236A>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 ID	rs755094329
gnomAD	homozygous (G/G)	heterozygous	allele carriers
	0	8	8

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.67	0.999
	2.141	1
(flanking)	3.067	1

?

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

12

Strand

1

Original gDNA sequence snippet

TCTATTTCTAGGAGGCAGCCATGCATAAAGACGAGTTTCAT

Altered gDNA sequence snippet

TCTATTTCTAGGAGGCAGCCGTGCATAAAGACGAGTTTCAT

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MTHEEHHAAK TLGIGKAIAV LTSGGDAQGM NAAVRAVVRV GIFTGARVFF VHEGYQGLVD
GGDHIKEATW ESVSMMLQLG GTVIGSARCK DFREREGRLR AAYNLVKRGI TNLCVIGGDG
SLTGADTFRS EWSDLLSDLQ KAGKITDEEA TKSSYLNIVG LVGSIDNDFC GTDMTIGTDS
ALHRIMEIVD AITTTAQSHQ RTFVLEVMGR HCGYLALVTS LSCGADWVFI PECPPDDDWE
EHLCRRLSET RTRGSRLNII IVAEGAIDKN GKPITSEDIK NLVVKRLGYD TRVTVLGHVQ
RGGTPSAFDR ILGSRMGVEA VMALLEGTPD TPACVVSLSG NQAVRLPLME CVQVTKDVTK
AMDEKKFDEA LKLRGRSFMN NWEVYKLLAH VRPPVSKSGS HTVAVMNVGA PAAGMNAAVR
STVRIGLIQG NRVLVVHDGF EGLAKGQIEE AGWSYVGGWT GQGGSKLGTK RTLPKKSFEQ
ISANITKFNI QGLVIIGGFE AYTGGLELME GRKQFDELCI PFVVIPATVS NNVPGSDFSV
GADTALNTIC TTCDRIKQSA AGTKRRVFII ETMGGYCGYL ATMAGLAAGA DAAYIFEEPF
TIRDLQANVE HLVQKMKTTV KRGLVLRNEK CNENYTTDFI FNLYSEEGKG IFDSRKNVLG
HMQQGGSPTP FDRNFATKMG AKAMNWMSGK IKESYRNGRI FANTPDSGCV LGMRKRALVF
QPVAELKDQT DFEHRIPKEQ WWLKLRPILK ILAKYEIDLD TSDHAHLEHI TRKRSGEAAV
*

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

199 / 199

Last intron/exon boundary

2396

Theoretical NMD boundary in CDS

2147

Length of CDS

2343

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

2236

Chromosomal position

48107374

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

MutationT@ster 2025

Variant:

12:48107374A>G_3_ENST00000549941

Back to summary table

Prediction:

BenignPermalink

Summary:

Model: without_aae
Tree vote: 40|160 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr12:48107374A>G (GRCh38)

Gene symbol

PFKM

Gene constraints

LOEUF: 0.83, LOF (oe): 0.65, misssense (oe): 0.65, synonymous (oe): 0.92 ? (gnomAD)

Ensembl transcript ID

ENST00000549941.7

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.-9+1237A>G
g.2236A>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 ID	rs755094329
gnomAD	homozygous (G/G)	heterozygous	allele carriers
	0	8	8

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.67	0.999
	2.141	1
(flanking)	3.067	1

?

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

12

Strand

1

Original gDNA sequence snippet

TCTATTTCTAGGAGGCAGCCATGCATAAAGACGAGTTTCAT

Altered gDNA sequence snippet

TCTATTTCTAGGAGGCAGCCGTGCATAAAGACGAGTTTCAT

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MTHEEHHAAK TLGIGKAIAV LTSGGDAQGM NAAVRAVVRV GIFTGARVFF VHEGYQGLVD
GGDHIKEATW ESVSMMLQLG GTVIGSARCK DFREREGRLR AAYNLVKRGI TNLCVIGGDG
SLTGADTFRS EWSDLLSDLQ KAGKITDEEA TKSSYLNIVG LVGSIDNDFC GTDMTIGTDS
ALHRIMEIVD AITTTAQSHQ RTFVLEVMGR HCGYLALVTS LSCGADWVFI PECPPDDDWE
EHLCRRLSET RTRGSRLNII IVAEGAIDKN GKPITSEDIK NGSRMGVEAV MALLEGTPDT
PACVVSLSGN QAVRLPLMEC VQVTKDVTKA MDEKKFDEAL KLRGRSFMNN WEVYKLLAHV
RPPVSKSGSH TVAVMNVGAP AAGMNAAVRS TVRIGLIQGN RVLVVHDGFE GLAKGQIEEA
GWSYVGGWTG QGGSKLGTKR TLPKKSFEQI SANITKFNIQ GLVIIGGFEA YTGGLELMEG
RKQFDELCIP FVVIPATVSN NVPGSDFSVG ADTALNTICT ANVEHLVQKM KTTVKRGLVL
RNEKCNENYT TDFIFNLYSE EGKGIFDSRK NVLGHMQQGG SPTPFDRNFA TKMGAKAMNW
MSGKIKESYR NGRIFANTPD SGCVLGMRKR ALVFQPVAEL KDQTDFEHRI PKEQWWLKLR
PILKILAKYE IDLDTSDHAH LEHITRKRSG EAAV*

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

236 / 236

Last intron/exon boundary

2175

Theoretical NMD boundary in CDS

1889

Length of CDS

2085

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

2236

Chromosomal position

48107374

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:

12:48107374A>G_5_ENST00000550257

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Prediction:

BenignPermalink

Summary:

Model: without_aae
Tree vote: 73|127 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr12:48107374A>G (GRCh38)

Gene symbol

PFKM

Gene constraints

LOEUF: 1.72, LOF (oe): 1.03, misssense (oe): 0.80, synonymous (oe): 0.96 ? (gnomAD)

Ensembl transcript ID

ENST00000550257.7

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.92-698A>G
g.2236A>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 ID	rs755094329
gnomAD	homozygous (G/G)	heterozygous	allele carriers
	0	8	8

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.67	0.999
	2.141	1
(flanking)	3.067	1

?

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

12

Strand

1

Original gDNA sequence snippet

TCTATTTCTAGGAGGCAGCCATGCATAAAGACGAGTTTCAT

Altered gDNA sequence snippet

TCTATTTCTAGGAGGCAGCCGTGCATAAAGACGAGTTTCAT

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MRRGFRPGAE RKTREPPRTG TAFTAPEESL AGEASTSSML IPKPPPKTDI LKSLDTMDDP
DTVGSIPVFK TEWIMTHEEH HAAKTLGIGK AIAVLTSGGD AQGMNAAVRA VVRVGIFTGA
RVFFVHEGYQ GLVDGGDHIK EATWESVSMM LQLGGTVIGS ARCKDFRERE GRLRAAYNLV
KRGITNLCVI GGDGSLTGAD TFRSEWSDLL SDLQKAGKIT DEEATKSSYL NIVGLVGSID
NDFCGTDMTI GTDSALHRIM EIVDAITTTA QSHQRTFVLE VMGRHCGYLA LVTSLSCGAD
WVFIPECPPD DDWEEHLCRR LSETRTRGSR LNIIIVAEGA IDKNGKPITS EDIKNLVVKR
LGYDTRVTVL GHVQRGGTPS AFDRILGSRM GVEAVMALLE GTPDTPACVV SLSGNQAVRL
PLMECVQVTK DVTKAMDEKK FDEALKLRGR SFMNNWEVYK LLAHVRPPVS KSGSHTVAVM
NVGAPAAGMN AAVRSTVRIG LIQGNRVLVV HDGFEGLAKG QIEEAGWSYV GGWTGQGGSK
LGTKRTLPKK SFEQISANIT KFNIQGLVII GGFEAYTGGL ELMEGRKQFD ELCIPFVVIP
ATVSNNVPGS DFSVGADTAL NTICTTCDRI KQSAAGTKRR VFIIETMGGY CGYLATMAGL
AAGADAAYIF EEPFTIRDLQ ANVEHLVQKM KTTVKRGLVL RNEKCNENYT TDFIFNLYSE
EGKGIFDSRK NVLGHMQQGG SPTPFDRNFA TKMGAKAMNW MSGKIKESYR NGRIFANTPD
SGCVLGMRKR ALVFQPVAEL KDQTDFEHRI PKEQWWLKLR PILKILAKYE IDLDTSDHAH
LEHITRKRSG EAAV*

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

125 / 125

Last intron/exon boundary

2544

Theoretical NMD boundary in CDS

2369

Length of CDS

2565

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

2236

Chromosomal position

48107374

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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