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: ENST00000541951
Querying Taster for transcript #2: ENST00000536003
Querying Taster for transcript #3: ENST00000376384
Querying Taster for transcript #4: ENST00000544552
Querying Taster for transcript #5: ENST00000310571
Querying Taster for transcript #6: ENST00000535604
Querying Taster for transcript #7: ENST00000544909
MT speed 0.36 s - this script 2.818058 s

Transcript summary:

Permalink

Transcript	Gene symbol	Prediction	Tree vote	Model	Splice site change	Variant type	Protein length	Features at a glance
ENST00000310571(MANE Select)	PAAF1	Deleterious	82\|18	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000541951	PAAF1	Deleterious	88\|12	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000535604	PAAF1	Deleterious	88\|12	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000536003	PAAF1	Deleterious	89\|11	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000376384	PAAF1	Deleterious	89\|11	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000544552	PAAF1	Deleterious	89\|11	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000544909	PAAF1	Deleterious	90\|10	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed

MutationT@ster 2025

Variant:

11:73900359G>C_5_ENST00000310571

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 82|18 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr11:73900359G>C (GRCh38)

Gene symbol

PAAF1

Gene constraints

LOEUF: 1.15, LOF (oe): 0.85, misssense (oe): 0.87, synonymous (oe): 1.02 ? (gnomAD)

Ensembl transcript ID

ENST00000310571.8

Genbank transcript ID

NM_025155 (exact from MANE)

UniProt / AlphaMissense peptide

PAAF1_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.471G>C
g.23661G>C

AA changes

AAE:	Q157H	?
Score:	24

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs182164449
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	1	95	96

Protein conservation

Species	Match	AA	Alignment
Human		157	G	L	V	V	L	S	G	G	M	D	A	Q	L	K	I	W	S	A	E	D	A	S	C	V
mutated	not conserved	157	G	L	V	V	L	S	G	G	M	D	A	H	L	K	I	W	S	A	E	D	A	S	C
Ptroglodytes	all identical	158	G	L	V	V	L	S	G	G	M	D	A	Q	L	K	I	W	S	A	E	D	A	S	C
Mmulatta	all identical	157	G	L	V	V	L	S	G	G	M	D	A	Q	L	K	I	W	S	A	E	D	A	S	C
Fcatus	all identical	157	G	L	V	V	L	S	G	G	M	D	A	Q	L	K	I	W	S	A	E	D	A	S	C
Mmusculus	no homologue
Ggallus	all identical	157	G	L	V	V	L	S	G	G	M	D	A	Q	L	K	I	W	S	A	E	D	A	S	C
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	not conserved	194	G	L	V	V	I	G	G	G	M	D	M	A	I	R	V	W	A	V	D	K	V	P	A
Xtropicalis	all identical	996	G	K	V	V	L	S	G	G	M	D	A	Q	V	K	I	W	S	V	D	D	G	S	C

Protein features

Start (aa)	End (aa)	Feature	Details
2	392	CHAIN		lost
125	163	REPEAT	WD	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	4.994	1
	3.524	1
(flanking)	0.386	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

Yes

Chromosome

11

Strand

1

Original gDNA sequence snippet

AGTGGGGGAATGGATGCCCAGCTGAAGATATGGTCAGCTGA

Altered gDNA sequence snippet

AGTGGGGGAATGGATGCCCACCTGAAGATATGGTCAGCTGA

Original cDNA sequence snippet

AGTGGGGGAATGGATGCCCAGCTGAAGATATGGTCAGCTGA

Altered cDNA sequence snippet

AGTGGGGGAATGGATGCCCACCTGAAGATATGGTCAGCTGA

Wildtype AA sequence

MAAPLRIQSD WAQALRKDEG EAWLSCHPPG KPSLYGSLTC QGIGLDGIPE VTASEGFTVN
EINKKSIHIS CPKENASSKF LAPYTTFSRI HTKSITCLDI SSRGGLGVSS STDGTMKIWQ
ASNGELRRVL EGHVFDVNCC RFFPSGLVVL SGGMDAQLKI WSAEDASCVV TFKGHKGGIL
DTAIVDRGRN VVSASRDGTA RLWDCGRSAC LGVLADCGSS INGVAVGAAD NSINLGSPEQ
MPSEREVGTE AKMLLLARED KKLQCLGLQS RQLVFLFIGS DAFNCCTFLS GFLLLAGTQD
GNIYQLDVRS PRAPVQVIHR SGAPVLSLLS VRDGFIASQG DGSCFIVQQD LDYVTELTGA
DCDPVYKVAT WEKQIYTCCR DGLVRRYQLS DL*

Mutated AA sequence

MAAPLRIQSD WAQALRKDEG EAWLSCHPPG KPSLYGSLTC QGIGLDGIPE VTASEGFTVN
EINKKSIHIS CPKENASSKF LAPYTTFSRI HTKSITCLDI SSRGGLGVSS STDGTMKIWQ
ASNGELRRVL EGHVFDVNCC RFFPSGLVVL SGGMDAHLKI WSAEDASCVV TFKGHKGGIL
DTAIVDRGRN VVSASRDGTA RLWDCGRSAC LGVLADCGSS INGVAVGAAD NSINLGSPEQ
MPSEREVGTE AKMLLLARED KKLQCLGLQS RQLVFLFIGS DAFNCCTFLS GFLLLAGTQD
GNIYQLDVRS PRAPVQVIHR SGAPVLSLLS VRDGFIASQG DGSCFIVQQD LDYVTELTGA
DCDPVYKVAT WEKQIYTCCR DGLVRRYQLS DL*

Position of stopcodon in wt / mu CDS

1179 / 1179

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

393 / 393

Position of stopcodon in wt / mu cDNA

1202 / 1202

Position of start ATG in wt / mu cDNA

24 / 24

Last intron/exon boundary

1124

Theoretical NMD boundary in CDS

1050

Length of CDS

1179

Coding sequence (CDS) position

471

cDNA position

494

gDNA position

23661

Chromosomal position

73900359

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:

11:73900359G>C_1_ENST00000541951

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 88|12 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr11:73900359G>C (GRCh38)

Gene symbol

PAAF1

Gene constraints

LOEUF: 0.98, LOF (oe): 0.69, misssense (oe): 0.84, synonymous (oe): 0.96 ? (gnomAD)

Ensembl transcript ID

ENST00000541951.5

Genbank transcript ID

NM_001267806 (by similarity)

UniProt / AlphaMissense peptide

PAAF1_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.126G>C
g.23661G>C

AA changes

AAE:	Q42H	?
Score:	24

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs182164449
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	1	95	96

Protein conservation

Species	Match	AA	Alignment
Human		42	G	L	V	V	L	S	G	G	M	D	A	Q	L	K	I	W	S	A	E	D	A	S	C	V
mutated	not conserved	42	G	L	V	V	L	S	G	G	M	D	A	H	L	K	I	W	S	A	E	D	A	S	C
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
2	392	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	4.994	1
	3.524	1
(flanking)	0.386	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

Yes

Chromosome

11

Strand

1

Original gDNA sequence snippet

AGTGGGGGAATGGATGCCCAGCTGAAGATATGGTCAGCTGA

Altered gDNA sequence snippet

AGTGGGGGAATGGATGCCCACCTGAAGATATGGTCAGCTGA

Original cDNA sequence snippet

AGTGGGGGAATGGATGCCCAGCTGAAGATATGGTCAGCTGA

Altered cDNA sequence snippet

AGTGGGGGAATGGATGCCCACCTGAAGATATGGTCAGCTGA

Wildtype AA sequence

MKIWQASNGE LRRVLEGHVF DVNCCRFFPS GLVVLSGGMD AQLKIWSAED ASCVVTFKGH
KGGILDTAIV DRGRNVVSAS RDGTARLWDC GRSACLGVLA DCGSSINGVA VGAADNSINL
GSPEQMPSER EVGTEAKMLL LAREDKKLQC LGLQSRQLVF LFIGSDAFNC CTFLSGFLLL
AGTQDGNIYQ LDVRSPRAPV QVIHRSGAPV LSLLSVRDGF IASQGDGSCF IVQQDLDYVT
ELTGADCDPV YKVATWEKQI YTCCRDGLVR RYQLSDL*

Mutated AA sequence

MKIWQASNGE LRRVLEGHVF DVNCCRFFPS GLVVLSGGMD AHLKIWSAED ASCVVTFKGH
KGGILDTAIV DRGRNVVSAS RDGTARLWDC GRSACLGVLA DCGSSINGVA VGAADNSINL
GSPEQMPSER EVGTEAKMLL LAREDKKLQC LGLQSRQLVF LFIGSDAFNC CTFLSGFLLL
AGTQDGNIYQ LDVRSPRAPV QVIHRSGAPV LSLLSVRDGF IASQGDGSCF IVQQDLDYVT
ELTGADCDPV YKVATWEKQI YTCCRDGLVR RYQLSDL*

Position of stopcodon in wt / mu CDS

834 / 834

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

278 / 278

Position of stopcodon in wt / mu cDNA

1175 / 1175

Position of start ATG in wt / mu cDNA

342 / 342

Last intron/exon boundary

1097

Theoretical NMD boundary in CDS

705

Length of CDS

834

Coding sequence (CDS) position

126

cDNA position

467

gDNA position

23661

Chromosomal position

73900359

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

Back to summary table

MutationT@ster 2025

Variant:

11:73900359G>C_6_ENST00000535604

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 88|12 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr11:73900359G>C (GRCh38)

Gene symbol

PAAF1

Gene constraints

LOEUF: 0.98, LOF (oe): 0.69, misssense (oe): 0.84, synonymous (oe): 0.96 ? (gnomAD)

Ensembl transcript ID

ENST00000535604.5

Genbank transcript ID

UniProt / AlphaMissense peptide

PAAF1_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.126G>C
g.23661G>C

AA changes

AAE:	Q42H	?
Score:	24

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs182164449
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	1	95	96

Protein conservation

Species	Match	AA	Alignment
Human		42	G	L	V	V	L	S	G	G	M	D	A	Q	L	K	I	W	S	A	E	D	A	S	C	V
mutated	not conserved	42	G	L	V	V	L	S	G	G	M	D	A	H	L	K	I	W	S	A	E	D	A	S	C
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
2	392	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	4.994	1
	3.524	1
(flanking)	0.386	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

Yes

Chromosome

11

Strand

1

Original gDNA sequence snippet

AGTGGGGGAATGGATGCCCAGCTGAAGATATGGTCAGCTGA

Altered gDNA sequence snippet

AGTGGGGGAATGGATGCCCACCTGAAGATATGGTCAGCTGA

Original cDNA sequence snippet

AGTGGGGGAATGGATGCCCAGCTGAAGATATGGTCAGCTGA

Altered cDNA sequence snippet

AGTGGGGGAATGGATGCCCACCTGAAGATATGGTCAGCTGA

Wildtype AA sequence

MKIWQASNGE LRRVLEGHVF DVNCCRFFPS GLVVLSGGMD AQLKIWSAED ASCVVTFKGH
KGGILDTAIV DRGRNVVSAS RDGTARLWDC GRSACLGVLA DCGSSINGVA VGAADNSINL
GSPEQMPSER EVGTEAKMLL LAREDKKLQC LGLQSRQLVF LFIGSDAFNC CTFLSGFLLL
AGTQDGNIYQ LDVRSPRAPV QVIHRSGAPV LSLLSVRDGF IASQGDGSCF IVQQDLDYVT
ELTGADCDPV YKVATWEKQI YTCCRDGLVR RYQLSDL*

Mutated AA sequence

MKIWQASNGE LRRVLEGHVF DVNCCRFFPS GLVVLSGGMD AHLKIWSAED ASCVVTFKGH
KGGILDTAIV DRGRNVVSAS RDGTARLWDC GRSACLGVLA DCGSSINGVA VGAADNSINL
GSPEQMPSER EVGTEAKMLL LAREDKKLQC LGLQSRQLVF LFIGSDAFNC CTFLSGFLLL
AGTQDGNIYQ LDVRSPRAPV QVIHRSGAPV LSLLSVRDGF IASQGDGSCF IVQQDLDYVT
ELTGADCDPV YKVATWEKQI YTCCRDGLVR RYQLSDL*

Position of stopcodon in wt / mu CDS

834 / 834

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

278 / 278

Position of stopcodon in wt / mu cDNA

1444 / 1444

Position of start ATG in wt / mu cDNA

611 / 611

Last intron/exon boundary

1366

Theoretical NMD boundary in CDS

705

Length of CDS

834

Coding sequence (CDS) position

126

cDNA position

736

gDNA position

23661

Chromosomal position

73900359

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

Back to summary table

MutationT@ster 2025

Variant:

11:73900359G>C_2_ENST00000536003

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 89|11 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr11:73900359G>C (GRCh38)

Gene symbol

PAAF1

Gene constraints

LOEUF: 0.96, LOF (oe): 0.68, misssense (oe): 0.83, synonymous (oe): 0.98 ? (gnomAD)

Ensembl transcript ID

ENST00000536003.5

Genbank transcript ID

NM_001267803 (by similarity), NM_001267804 (by similarity), NM_001267805 (by similarity)

UniProt / AlphaMissense peptide

PAAF1_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.420G>C
g.23661G>C

AA changes

AAE:	Q140H	?
Score:	24

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs182164449
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	1	95	96

Protein conservation

Species	Match	AA	Alignment
Human		140	G	L	V	V	L	S	G	G	M	D	A	Q	L	K	I	W	S	A	E	D	A	S	C	V
mutated	not conserved	140	G	L	V	V	L	S	G	G	M	D	A	H	L	K	I	W	S	A	E	D	A	S	C
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
2	392	CHAIN		lost
125	163	REPEAT	WD	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	4.994	1
	3.524	1
(flanking)	0.386	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

Yes

Chromosome

11

Strand

1

Original gDNA sequence snippet

AGTGGGGGAATGGATGCCCAGCTGAAGATATGGTCAGCTGA

Altered gDNA sequence snippet

AGTGGGGGAATGGATGCCCACCTGAAGATATGGTCAGCTGA

Original cDNA sequence snippet

AGTGGGGGAATGGATGCCCAGCTGAAGATATGGTCAGCTGA

Altered cDNA sequence snippet

AGTGGGGGAATGGATGCCCACCTGAAGATATGGTCAGCTGA

Wildtype AA sequence

MLVPCFLYSL QNRKPSLYGS LTCQGIGLDG IPEVTASEGF TVNEINKKSI HISCPKENAS
SKFLAPYTTF SRIHTKSITC LDISSRGGLG VSSSTDGTMK IWQASNGELR RVLEGHVFDV
NCCRFFPSGL VVLSGGMDAQ LKIWSAEDAS CVVTFKGHKG GILDTAIVDR GRNVVSASRD
GTARLWDCGR SACLGVLADC GSSINGVAVG AADNSINLGS PEQMPSEREV GTEAKMLLLA
REDKKLQCLG LQSRQLVFLF IGSDAFNCCT FLSGFLLLAG TQDGNIYQLD VRSPRAPVQV
IHRSGAPVLS LLSVRDGFIA SQGDGSCFIV QQDLDYVTEL TGADCDPVYK VATWEKQIYT
CCRDGLVRRY QLSDL*

Mutated AA sequence

MLVPCFLYSL QNRKPSLYGS LTCQGIGLDG IPEVTASEGF TVNEINKKSI HISCPKENAS
SKFLAPYTTF SRIHTKSITC LDISSRGGLG VSSSTDGTMK IWQASNGELR RVLEGHVFDV
NCCRFFPSGL VVLSGGMDAH LKIWSAEDAS CVVTFKGHKG GILDTAIVDR GRNVVSASRD
GTARLWDCGR SACLGVLADC GSSINGVAVG AADNSINLGS PEQMPSEREV GTEAKMLLLA
REDKKLQCLG LQSRQLVFLF IGSDAFNCCT FLSGFLLLAG TQDGNIYQLD VRSPRAPVQV
IHRSGAPVLS LLSVRDGFIA SQGDGSCFIV QQDLDYVTEL TGADCDPVYK VATWEKQIYT
CCRDGLVRRY QLSDL*

Position of stopcodon in wt / mu CDS

1128 / 1128

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

376 / 376

Position of stopcodon in wt / mu cDNA

1273 / 1273

Position of start ATG in wt / mu cDNA

146 / 146

Last intron/exon boundary

1195

Theoretical NMD boundary in CDS

999

Length of CDS

1128

Coding sequence (CDS) position

420

cDNA position

565

gDNA position

23661

Chromosomal position

73900359

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:

11:73900359G>C_3_ENST00000376384

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 89|11 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr11:73900359G>C (GRCh38)

Gene symbol

PAAF1

Gene constraints

LOEUF: 0.96, LOF (oe): 0.68, misssense (oe): 0.83, synonymous (oe): 0.98 ? (gnomAD)

Ensembl transcript ID

ENST00000376384.9

Genbank transcript ID

UniProt / AlphaMissense peptide

PAAF1_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.420G>C
g.23661G>C

AA changes

AAE:	Q140H	?
Score:	24

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs182164449
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	1	95	96

Protein conservation

Species	Match	AA	Alignment
Human		140	G	L	V	V	L	S	G	G	M	D	A	Q	L	K	I	W	S	A	E	D	A	S	C	V
mutated	not conserved	140	G	L	V	V	L	S	G	G	M	D	A	H	L	K	I	W	S	A	E	D	A	S	C
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
2	392	CHAIN		lost
125	163	REPEAT	WD	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	4.994	1
	3.524	1
(flanking)	0.386	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

Yes

Chromosome

11

Strand

1

Original gDNA sequence snippet

AGTGGGGGAATGGATGCCCAGCTGAAGATATGGTCAGCTGA

Altered gDNA sequence snippet

AGTGGGGGAATGGATGCCCACCTGAAGATATGGTCAGCTGA

Original cDNA sequence snippet

AGTGGGGGAATGGATGCCCAGCTGAAGATATGGTCAGCTGA

Altered cDNA sequence snippet

AGTGGGGGAATGGATGCCCACCTGAAGATATGGTCAGCTGA

Wildtype AA sequence

MLVPCFLYSL QNRKPSLYGS LTCQGIGLDG IPEVTASEGF TVNEINKKSI HISCPKENAS
SKFLAPYTTF SRIHTKSITC LDISSRGGLG VSSSTDGTMK IWQASNGELR RVLEGHVFDV
NCCRFFPSGL VVLSGGMDAQ LKIWSAEDAS CVVTFKGHKG GILDTAIVDR GRNVVSASRD
GTARLWDCGR SACLGVLADC GSSINGVAVG AADNSINLGS PEQMPSEREV GTEAKMLLLA
REDKKLQCLG LQSRQLVFLF IGSDAFNCCT FLSGFLLLAG TQDGNIYQLD VRSPRAPVQV
IHRSGAPVLS LLSVRDGFIA SQGDGSCFIV QQDLDYVTEL TGADCDPVYK VATWEKQIYT
CCRDGLVRRY QLSDL*

Mutated AA sequence

MLVPCFLYSL QNRKPSLYGS LTCQGIGLDG IPEVTASEGF TVNEINKKSI HISCPKENAS
SKFLAPYTTF SRIHTKSITC LDISSRGGLG VSSSTDGTMK IWQASNGELR RVLEGHVFDV
NCCRFFPSGL VVLSGGMDAH LKIWSAEDAS CVVTFKGHKG GILDTAIVDR GRNVVSASRD
GTARLWDCGR SACLGVLADC GSSINGVAVG AADNSINLGS PEQMPSEREV GTEAKMLLLA
REDKKLQCLG LQSRQLVFLF IGSDAFNCCT FLSGFLLLAG TQDGNIYQLD VRSPRAPVQV
IHRSGAPVLS LLSVRDGFIA SQGDGSCFIV QQDLDYVTEL TGADCDPVYK VATWEKQIYT
CCRDGLVRRY QLSDL*

Position of stopcodon in wt / mu CDS

1128 / 1128

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

376 / 376

Position of stopcodon in wt / mu cDNA

1128 / 1128

Position of start ATG in wt / mu cDNA

1 / 1

Last intron/exon boundary

1050

Theoretical NMD boundary in CDS

999

Length of CDS

1128

Coding sequence (CDS) position

420

cDNA position

420

gDNA position

23661

Chromosomal position

73900359

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

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MutationT@ster 2025

Variant:

11:73900359G>C_4_ENST00000544552

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 89|11 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr11:73900359G>C (GRCh38)

Gene symbol

PAAF1

Gene constraints

LOEUF: 0.96, LOF (oe): 0.68, misssense (oe): 0.83, synonymous (oe): 0.98 ? (gnomAD)

Ensembl transcript ID

ENST00000544552.5

Genbank transcript ID

UniProt / AlphaMissense peptide

PAAF1_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.420G>C
g.23661G>C

AA changes

AAE:	Q140H	?
Score:	24

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs182164449
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	1	95	96

Protein conservation

Species	Match	AA	Alignment
Human		140	G	L	V	V	L	S	G	G	M	D	A	Q	L	K	I	W	S	A	E	D	A	S	C	V
mutated	not conserved	140	G	L	V	V	L	S	G	G	M	D	A	H	L	K	I	W	S	A	E	D	A	S	C
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
2	392	CHAIN		lost
125	163	REPEAT	WD	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	4.994	1
	3.524	1
(flanking)	0.386	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

Yes

Chromosome

11

Strand

1

Original gDNA sequence snippet

AGTGGGGGAATGGATGCCCAGCTGAAGATATGGTCAGCTGA

Altered gDNA sequence snippet

AGTGGGGGAATGGATGCCCACCTGAAGATATGGTCAGCTGA

Original cDNA sequence snippet

AGTGGGGGAATGGATGCCCAGCTGAAGATATGGTCAGCTGA

Altered cDNA sequence snippet

AGTGGGGGAATGGATGCCCACCTGAAGATATGGTCAGCTGA

Wildtype AA sequence

MLVPCFLYSL QNRKPSLYGS LTCQGIGLDG IPEVTASEGF TVNEINKKSI HISCPKENAS
SKFLAPYTTF SRIHTKSITC LDISSRGGLG VSSSTDGTMK IWQASNGELR RVLEGHVFDV
NCCRFFPSGL VVLSGGMDAQ LKIWSAEDAS CVVTFKGHKG GILDTAIVDR GRNVVSASRD
GTARLWDCGR SACLGVLADC GSSINGVAVG AADNSINLGS PEQMPSEREV GTEAKMLLLA
REDKKLQCLG LQSRQLVFLF IGSDAFNCCT FLSGFLLLAG TQDGNIYQLD VRSPRAPVQV
IHRSGAPVLS LLSVRDGFIA SQGDGSCFIV QQDLDYVTEL TGADCDPVYK VATWEKQIYT
CCRDGLVRRY QLSDL*

Mutated AA sequence

MLVPCFLYSL QNRKPSLYGS LTCQGIGLDG IPEVTASEGF TVNEINKKSI HISCPKENAS
SKFLAPYTTF SRIHTKSITC LDISSRGGLG VSSSTDGTMK IWQASNGELR RVLEGHVFDV
NCCRFFPSGL VVLSGGMDAH LKIWSAEDAS CVVTFKGHKG GILDTAIVDR GRNVVSASRD
GTARLWDCGR SACLGVLADC GSSINGVAVG AADNSINLGS PEQMPSEREV GTEAKMLLLA
REDKKLQCLG LQSRQLVFLF IGSDAFNCCT FLSGFLLLAG TQDGNIYQLD VRSPRAPVQV
IHRSGAPVLS LLSVRDGFIA SQGDGSCFIV QQDLDYVTEL TGADCDPVYK VATWEKQIYT
CCRDGLVRRY QLSDL*

Position of stopcodon in wt / mu CDS

1128 / 1128

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

376 / 376

Position of stopcodon in wt / mu cDNA

1229 / 1229

Position of start ATG in wt / mu cDNA

102 / 102

Last intron/exon boundary

1151

Theoretical NMD boundary in CDS

999

Length of CDS

1128

Coding sequence (CDS) position

420

cDNA position

521

gDNA position

23661

Chromosomal position

73900359

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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MutationT@ster 2025

Variant:

11:73900359G>C_7_ENST00000544909

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed

Model: simple_aae
Tree vote: 90|10 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr11:73900359G>C (GRCh38)

Gene symbol

PAAF1

Gene constraints

LOEUF: 0.96, LOF (oe): 0.68, misssense (oe): 0.83, synonymous (oe): 0.98 ? (gnomAD)

Ensembl transcript ID

ENST00000544909.5

Genbank transcript ID

NM_001363556 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.474G>C
g.23661G>C

AA changes

AAE:	Q158H	?
Score:	24

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs182164449
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	1	95	96

Protein conservation

Species	Match	AA	Alignment
Human		158	G	L	V	V	L	S	G	G	M	D	A	Q	L	K	I	W	S	A	E	D	A	S	C	V
mutated	not conserved	158	G	L	V	V	L	S	G	G	M	D	A	H	L	K	I	W	S	A	E	D	A	S	C
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)	4.994	1
	3.524	1
(flanking)	0.386	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

Yes

Chromosome

11

Strand

1

Original gDNA sequence snippet

AGTGGGGGAATGGATGCCCAGCTGAAGATATGGTCAGCTGA

Altered gDNA sequence snippet

AGTGGGGGAATGGATGCCCACCTGAAGATATGGTCAGCTGA

Original cDNA sequence snippet

AGTGGGGGAATGGATGCCCAGCTGAAGATATGGTCAGCTGA

Altered cDNA sequence snippet

AGTGGGGGAATGGATGCCCACCTGAAGATATGGTCAGCTGA

Wildtype AA sequence

MLELKPSSVD SKFSTTMQAY VFPRCFGTAW VLTSFFPSYS DLDTVFITSN MIANFCCEPA
EWVQTKSIHI SCPKENASSK FLAPYTTFSR IHTKSITCLD ISSRGGLGVS SSTDGTMKIW
QASNGELRRV LEGHVFDVNC CRFFPSGLVV LSGGMDAQLK IWSAEDASCV VTFKGHKGGI
LDTAIVDRGR NVVSASRDGT ARLWDCGRSA CLGVLADCGS SINGVAVGAA DNSINLGSPE
QMPSEREVGT EAKMLLLARE DKKLQCLGLQ SRQLVFLFIG SDAFNCCTFL SGFLLLAGTQ
DGNIYQLDVR SPRAPVQVIH RSGAPVLSLL SVRDGFIASQ GDGSCFIVQQ DLDYVTELTG
ADCDPVYKVA TWEKQIYTCC RDGLVRRYQL SDL*

Mutated AA sequence

MLELKPSSVD SKFSTTMQAY VFPRCFGTAW VLTSFFPSYS DLDTVFITSN MIANFCCEPA
EWVQTKSIHI SCPKENASSK FLAPYTTFSR IHTKSITCLD ISSRGGLGVS SSTDGTMKIW
QASNGELRRV LEGHVFDVNC CRFFPSGLVV LSGGMDAHLK IWSAEDASCV VTFKGHKGGI
LDTAIVDRGR NVVSASRDGT ARLWDCGRSA CLGVLADCGS SINGVAVGAA DNSINLGSPE
QMPSEREVGT EAKMLLLARE DKKLQCLGLQ SRQLVFLFIG SDAFNCCTFL SGFLLLAGTQ
DGNIYQLDVR SPRAPVQVIH RSGAPVLSLL SVRDGFIASQ GDGSCFIVQQ DLDYVTELTG
ADCDPVYKVA TWEKQIYTCC RDGLVRRYQL SDL*

Position of stopcodon in wt / mu CDS

1182 / 1182

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

394 / 394

Position of stopcodon in wt / mu cDNA

1439 / 1439

Position of start ATG in wt / mu cDNA

258 / 258

Last intron/exon boundary

1361

Theoretical NMD boundary in CDS

1053

Length of CDS

1182

Coding sequence (CDS) position

474

cDNA position

731

gDNA position

23661

Chromosomal position

73900359

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

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