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: ENST00000688179
Querying Taster for transcript #2: ENST00000689816
Querying Taster for transcript #3: ENST00000685415
Querying Taster for transcript #4: ENST00000436005
Querying Taster for transcript #5: ENST00000273077
Querying Taster for transcript #6: ENST00000687736
Querying Taster for transcript #7: ENST00000691220
Querying Taster for transcript #8: ENST00000258362
Querying Taster for transcript #9: ENST00000692295
MT speed 0.1 s - this script 2.532962 s

Transcript summary:

Permalink

Transcript	Gene symbol	Prediction	Tree vote	Model	Splice site change	Variant type	Protein length	Features at a glance
ENST00000691220	PNKD	Benign	28\|172	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000689816	PNKD	Benign	42\|158	without_aae	No	Single base exchange	Normal	Homozygous in gnomAD
ENST00000273077(MANE Select)	PNKD	Benign	42\|158	without_aae	No	Single base exchange	Normal	Homozygous in gnomAD
ENST00000688179	PNKD	Benign	43\|157	without_aae	No	Single base exchange	Normal	Homozygous in gnomAD
ENST00000685415	PNKD	Benign	44\|156	without_aae	No	Single base exchange	Normal	Homozygous in gnomAD
ENST00000687736	PNKD	Benign	46\|154	without_aae	No	Single base exchange	Normal	Homozygous in gnomAD
ENST00000692295	PNKD	Benign	46\|154	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000436005	PNKD	Benign	50\|150	without_aae	No	Single base exchange	Normal	Homozygous in gnomAD
ENST00000258362	PNKD	Benign	91\|109	without_aae	No	Single base exchange	Normal	Homozygous in gnomAD

MutationT@ster 2025

Variant:

2:218340748G>A_7_ENST00000691220

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 28|172 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr2:218340748G>A (GRCh38)

Gene symbol

PNKD

Gene constraints

LOEUF: 1.31, LOF (oe): 0.91, misssense (oe): 0.93, synonymous (oe): 0.87 ? (gnomAD)

Ensembl transcript ID

ENST00000691220.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.237-1233G>A
g.71098G>A

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	rs34014804
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	1975	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	7.01	1
	-2.488	0
(flanking)	8.855	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

2

Strand

1

Original gDNA sequence snippet

GCTTCCATTGAAAAGGAAGGGGTCACCTTGGTCGCCATTCT

Altered gDNA sequence snippet

GCTTCCATTGAAAAGGAAGGAGTCACCTTGGTCGCCATTCT

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MAAVVAATAL KGRGARNARV LRGILAGATA NKASHNRTRA LQSHSSPEGK EEPEPLSPEL
EYIPRKRGKN PMKAVGLACP LCHQDVVSVG RLQIRALATP GHTQGHLVYL LDGEPYKGPS
CLFSGDLLFL SGCGRTFEGN AETMLSSLDT VLGLGDDTLL WPGHEYAEEN LGFAGVVEPE
NLARERKMQW VQRQRLERKG TCPSTLGEER SYNPFLRTHC LALQEALGPG PGPTGDDDYS
RAQLLEELRR LKDMHKSK*

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

1 / 1

Last intron/exon boundary

603

Theoretical NMD boundary in CDS

552

Length of CDS

777

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

71098

Chromosomal position

218340748

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:

2:218340748G>A_2_ENST00000689816

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 42|158 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr2:218340748G>A (GRCh38)

Gene symbol

PNKD

Gene constraints

LOEUF: 1.10, LOF (oe): 0.82, misssense (oe): 0.98, synonymous (oe): 0.90 ? (gnomAD)

Ensembl transcript ID

ENST00000689816.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.486G>A
g.71098G>A

AA changes

no AA changes

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs34014804
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	1975	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	7.01	1
	-2.488	0
(flanking)	8.855	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

21

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

No

Chromosome

2

Strand

1

Original gDNA sequence snippet

GCTTCCATTGAAAAGGAAGGGGTCACCTTGGTCGCCATTCT

Altered gDNA sequence snippet

GCTTCCATTGAAAAGGAAGGAGTCACCTTGGTCGCCATTCT

Original cDNA sequence snippet

GCTTCCATTGAAAAGGAAGGGGTCACCTTGGTCGCCATTCT

Altered cDNA sequence snippet

GCTTCCATTGAAAAGGAAGGAGTCACCTTGGTCGCCATTCT

Wildtype AA sequence

MAAVVAATAL KGRGARNARV LRGILAGATA NKASHNRTRA LQSHSSPEGK EEPEPLSPEL
EYIPRKRGKN PMKAVGLAWY SLYTRTWLGY LFYRQQLRRA RNRYPKGHSK TQPRLFNGVK
VLPIPVLSDN YSYLIIDTQA QLAVAVDPSD PRAVQASIEK EGVTLVAILC THKHWDHSGG
NRDLSRRHRD CRVYGSPQDG IPYLTHPLCH QDVVSVGRLQ IRALATPGHT QGHLVYLLDG
EPYKGPSCLF SGDLLFLSGC GRTFEGNAET MLSSLDTVLG LGDDTLLWPG VVEPENLARE
RKMQWVQRQR LERKGTCPST LGEERSYNPF LRTHCLALQE ALGPGPGPTG DDDYSRAQLL
EELRRLKDMH KSK*

Mutated AA sequence

MAAVVAATAL KGRGARNARV LRGILAGATA NKASHNRTRA LQSHSSPEGK EEPEPLSPEL
EYIPRKRGKN PMKAVGLAWY SLYTRTWLGY LFYRQQLRRA RNRYPKGHSK TQPRLFNGVK
VLPIPVLSDN YSYLIIDTQA QLAVAVDPSD PRAVQASIEK EGVTLVAILC THKHWDHSGG
NRDLSRRHRD CRVYGSPQDG IPYLTHPLCH QDVVSVGRLQ IRALATPGHT QGHLVYLLDG
EPYKGPSCLF SGDLLFLSGC GRTFEGNAET MLSSLDTVLG LGDDTLLWPG VVEPENLARE
RKMQWVQRQR LERKGTCPST LGEERSYNPF LRTHCLALQE ALGPGPGPTG DDDYSRAQLL
EELRRLKDMH KSK*

Position of stopcodon in wt / mu CDS

1122 / 1122

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

374 / 374

Position of stopcodon in wt / mu cDNA

1144 / 1144

Position of start ATG in wt / mu cDNA

23 / 23

Last intron/exon boundary

970

Theoretical NMD boundary in CDS

897

Length of CDS

1122

Coding sequence (CDS) position

486

cDNA position

508

gDNA position

71098

Chromosomal position

218340748

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:

2:218340748G>A_5_ENST00000273077

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 42|158 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr2:218340748G>A (GRCh38)

Gene symbol

PNKD

Gene constraints

LOEUF: 1.13, LOF (oe): 0.85, misssense (oe): 0.99, synonymous (oe): 0.91 ? (gnomAD)

Ensembl transcript ID

ENST00000273077.9

Genbank transcript ID

NM_015488 (exact from MANE)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.486G>A
g.71098G>A

AA changes

no AA changes

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs34014804
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	1975	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	7.01	1
	-2.488	0
(flanking)	8.855	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

21

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

No

Chromosome

2

Strand

1

Original gDNA sequence snippet

GCTTCCATTGAAAAGGAAGGGGTCACCTTGGTCGCCATTCT

Altered gDNA sequence snippet

GCTTCCATTGAAAAGGAAGGAGTCACCTTGGTCGCCATTCT

Original cDNA sequence snippet

GCTTCCATTGAAAAGGAAGGGGTCACCTTGGTCGCCATTCT

Altered cDNA sequence snippet

GCTTCCATTGAAAAGGAAGGAGTCACCTTGGTCGCCATTCT

Wildtype AA sequence

MAAVVAATAL KGRGARNARV LRGILAGATA NKASHNRTRA LQSHSSPEGK EEPEPLSPEL
EYIPRKRGKN PMKAVGLAWY SLYTRTWLGY LFYRQQLRRA RNRYPKGHSK TQPRLFNGVK
VLPIPVLSDN YSYLIIDTQA QLAVAVDPSD PRAVQASIEK EGVTLVAILC THKHWDHSGG
NRDLSRRHRD CRVYGSPQDG IPYLTHPLCH QDVVSVGRLQ IRALATPGHT QGHLVYLLDG
EPYKGPSCLF SGDLLFLSGC GRTFEGNAET MLSSLDTVLG LGDDTLLWPG HEYAEENLGF
AGVVEPENLA RERKMQWVQR QRLERKGTCP STLGEERSYN PFLRTHCLAL QEALGPGPGP
TGDDDYSRAQ LLEELRRLKD MHKSK*

Mutated AA sequence

MAAVVAATAL KGRGARNARV LRGILAGATA NKASHNRTRA LQSHSSPEGK EEPEPLSPEL
EYIPRKRGKN PMKAVGLAWY SLYTRTWLGY LFYRQQLRRA RNRYPKGHSK TQPRLFNGVK
VLPIPVLSDN YSYLIIDTQA QLAVAVDPSD PRAVQASIEK EGVTLVAILC THKHWDHSGG
NRDLSRRHRD CRVYGSPQDG IPYLTHPLCH QDVVSVGRLQ IRALATPGHT QGHLVYLLDG
EPYKGPSCLF SGDLLFLSGC GRTFEGNAET MLSSLDTVLG LGDDTLLWPG HEYAEENLGF
AGVVEPENLA RERKMQWVQR QRLERKGTCP STLGEERSYN PFLRTHCLAL QEALGPGPGP
TGDDDYSRAQ LLEELRRLKD MHKSK*

Position of stopcodon in wt / mu CDS

1158 / 1158

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

386 / 386

Position of stopcodon in wt / mu cDNA

1175 / 1175

Position of start ATG in wt / mu cDNA

18 / 18

Last intron/exon boundary

1001

Theoretical NMD boundary in CDS

933

Length of CDS

1158

Coding sequence (CDS) position

486

cDNA position

503

gDNA position

71098

Chromosomal position

218340748

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:

2:218340748G>A_1_ENST00000688179

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 43|157 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr2:218340748G>A (GRCh38)

Gene symbol

PNKD

Gene constraints

LOEUF: 1.20, LOF (oe): 0.89, misssense (oe): 0.99, synonymous (oe): 0.89 ? (gnomAD)

Ensembl transcript ID

ENST00000688179.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.486G>A
g.71098G>A

AA changes

no AA changes

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs34014804
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	1975	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	7.01	1
	-2.488	0
(flanking)	8.855	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

21

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

No

Chromosome

2

Strand

1

Original gDNA sequence snippet

GCTTCCATTGAAAAGGAAGGGGTCACCTTGGTCGCCATTCT

Altered gDNA sequence snippet

GCTTCCATTGAAAAGGAAGGAGTCACCTTGGTCGCCATTCT

Original cDNA sequence snippet

GCTTCCATTGAAAAGGAAGGGGTCACCTTGGTCGCCATTCT

Altered cDNA sequence snippet

GCTTCCATTGAAAAGGAAGGAGTCACCTTGGTCGCCATTCT

Wildtype AA sequence

MAAVVAATAL KGRGARNARV LRGILAGATA NKASHNRTRA LQSHSSPEGK EEPEPLSPEL
EYIPRKRGKN PMKAVGLAWY SLYTRTWLGY LFYRQQLRRA RNRYPKGHSK TQPRLFNGVK
VLPIPVLSDN YSYLIIDTQA QLAVAVDPSD PRAVQASIEK EGVTLVAILC THKHWDHSGG
NRDLSRRHRD CRVYGSPQDG IPYLTHPLCH QDVVSVGRLQ IRALATPGHT QGHLVYLLDG
EPYKGPSCLF SGDLLFLSGC GVVEPENLAR ERKMQWVQRQ RLERKGTCPS TLGEERSYNP
FLRTHCLALQ EALGPGPGPT GDDDYSRAQL LEELRRLKDM HKSK*

Mutated AA sequence

MAAVVAATAL KGRGARNARV LRGILAGATA NKASHNRTRA LQSHSSPEGK EEPEPLSPEL
EYIPRKRGKN PMKAVGLAWY SLYTRTWLGY LFYRQQLRRA RNRYPKGHSK TQPRLFNGVK
VLPIPVLSDN YSYLIIDTQA QLAVAVDPSD PRAVQASIEK EGVTLVAILC THKHWDHSGG
NRDLSRRHRD CRVYGSPQDG IPYLTHPLCH QDVVSVGRLQ IRALATPGHT QGHLVYLLDG
EPYKGPSCLF SGDLLFLSGC GVVEPENLAR ERKMQWVQRQ RLERKGTCPS TLGEERSYNP
FLRTHCLALQ EALGPGPGPT GDDDYSRAQL LEELRRLKDM HKSK*

Position of stopcodon in wt / mu CDS

1035 / 1035

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

345 / 345

Position of stopcodon in wt / mu cDNA

1057 / 1057

Position of start ATG in wt / mu cDNA

23 / 23

Last intron/exon boundary

883

Theoretical NMD boundary in CDS

810

Length of CDS

1035

Coding sequence (CDS) position

486

cDNA position

508

gDNA position

71098

Chromosomal position

218340748

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:

2:218340748G>A_3_ENST00000685415

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 44|156 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr2:218340748G>A (GRCh38)

Gene symbol

PNKD

Gene constraints

LOEUF: 1.11, LOF (oe): 0.84, misssense (oe): 0.99, synonymous (oe): 0.89 ? (gnomAD)

Ensembl transcript ID

ENST00000685415.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.603G>A
g.71098G>A

AA changes

no AA changes

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs34014804
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	1975	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	7.01	1
	-2.488	0
(flanking)	8.855	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

21

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

No

Chromosome

2

Strand

1

Original gDNA sequence snippet

GCTTCCATTGAAAAGGAAGGGGTCACCTTGGTCGCCATTCT

Altered gDNA sequence snippet

GCTTCCATTGAAAAGGAAGGAGTCACCTTGGTCGCCATTCT

Original cDNA sequence snippet

GCTTCCATTGAAAAGGAAGGGGTCACCTTGGTCGCCATTCT

Altered cDNA sequence snippet

GCTTCCATTGAAAAGGAAGGAGTCACCTTGGTCGCCATTCT

Wildtype AA sequence

MAAVVAATAL KGRGARNARV LRGILAGATA NKASHNRTRA LQSHSSPEGK EEPEPLSPEL
EYIPRKRGKN PMKAVGLAWA IGFPCGILLF ILTKREVDKD RVKQMKARQN MRLSNTGEYS
LYTRTWLGYL FYRQQLRRAR NRYPKGHSKT QPRLFNGVKV LPIPVLSDNY SYLIIDTQAQ
LAVAVDPSDP RAVQASIEKE GVTLVAILCT HKHWDHSGGN RDLSRRHRDC RVYGSPQDGI
PYLTHPLCHQ DVVSVGRLQI RALATPGHTQ GHLVYLLDGE PYKGPSCLFS GDLLFLSGCG
RTFEGNAETM LSSLDTVLGL GDDTLLWPGH EYAEENLGFA GVVEPENLAR ERKMQWVQRQ
RLERKGTCPS TLGEERSYNP FLRTHCLALQ EALGPGPGPT GDDDYSRAQL LEELRRLKDM
HKSK*

Mutated AA sequence

MAAVVAATAL KGRGARNARV LRGILAGATA NKASHNRTRA LQSHSSPEGK EEPEPLSPEL
EYIPRKRGKN PMKAVGLAWA IGFPCGILLF ILTKREVDKD RVKQMKARQN MRLSNTGEYS
LYTRTWLGYL FYRQQLRRAR NRYPKGHSKT QPRLFNGVKV LPIPVLSDNY SYLIIDTQAQ
LAVAVDPSDP RAVQASIEKE GVTLVAILCT HKHWDHSGGN RDLSRRHRDC RVYGSPQDGI
PYLTHPLCHQ DVVSVGRLQI RALATPGHTQ GHLVYLLDGE PYKGPSCLFS GDLLFLSGCG
RTFEGNAETM LSSLDTVLGL GDDTLLWPGH EYAEENLGFA GVVEPENLAR ERKMQWVQRQ
RLERKGTCPS TLGEERSYNP FLRTHCLALQ EALGPGPGPT GDDDYSRAQL LEELRRLKDM
HKSK*

Position of stopcodon in wt / mu CDS

1275 / 1275

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

425 / 425

Position of stopcodon in wt / mu cDNA

1297 / 1297

Position of start ATG in wt / mu cDNA

23 / 23

Last intron/exon boundary

1123

Theoretical NMD boundary in CDS

1050

Length of CDS

1275

Coding sequence (CDS) position

603

cDNA position

625

gDNA position

71098

Chromosomal position

218340748

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:

2:218340748G>A_6_ENST00000687736

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 46|154 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr2:218340748G>A (GRCh38)

Gene symbol

PNKD

Gene constraints

LOEUF: 1.32, LOF (oe): 0.98, misssense (oe): 0.97, synonymous (oe): 0.85 ? (gnomAD)

Ensembl transcript ID

ENST00000687736.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.486G>A
g.71098G>A

AA changes

no AA changes

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs34014804
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	1975	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	7.01	1
	-2.488	0
(flanking)	8.855	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

21

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

No

Chromosome

2

Strand

1

Original gDNA sequence snippet

GCTTCCATTGAAAAGGAAGGGGTCACCTTGGTCGCCATTCT

Altered gDNA sequence snippet

GCTTCCATTGAAAAGGAAGGAGTCACCTTGGTCGCCATTCT

Original cDNA sequence snippet

GCTTCCATTGAAAAGGAAGGGGTCACCTTGGTCGCCATTCT

Altered cDNA sequence snippet

GCTTCCATTGAAAAGGAAGGAGTCACCTTGGTCGCCATTCT

Wildtype AA sequence

MAAVVAATAL KGRGARNARV LRGILAGATA NKASHNRTRA LQSHSSPEGK EEPEPLSPEL
EYIPRKRGKN PMKAVGLAWY SLYTRTWLGY LFYRQQLRRA RNRYPKGHSK TQPRLFNGVK
VLPIPVLSDN YSYLIIDTQA QLAVAVDPSD PRAVQASIEK EGVTLVAILC THKHCPLCHQ
DVVSVGRLQI RALATPGHTQ GHLVYLLDGE PYKGPSCLFS GDLLFLSGCG HEYAEENLGF
AGVVEPENLA RERKMQWVQR QRLERKGTCP STLGEERSYN PFLRTHCLAL QEALGPGPGP
TGDDDYSRAQ LLEELRRLKD MHKSK*

Mutated AA sequence

MAAVVAATAL KGRGARNARV LRGILAGATA NKASHNRTRA LQSHSSPEGK EEPEPLSPEL
EYIPRKRGKN PMKAVGLAWY SLYTRTWLGY LFYRQQLRRA RNRYPKGHSK TQPRLFNGVK
VLPIPVLSDN YSYLIIDTQA QLAVAVDPSD PRAVQASIEK EGVTLVAILC THKHCPLCHQ
DVVSVGRLQI RALATPGHTQ GHLVYLLDGE PYKGPSCLFS GDLLFLSGCG HEYAEENLGF
AGVVEPENLA RERKMQWVQR QRLERKGTCP STLGEERSYN PFLRTHCLAL QEALGPGPGP
TGDDDYSRAQ LLEELRRLKD MHKSK*

Position of stopcodon in wt / mu CDS

978 / 978

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

326 / 326

Position of stopcodon in wt / mu cDNA

978 / 978

Position of start ATG in wt / mu cDNA

1 / 1

Last intron/exon boundary

804

Theoretical NMD boundary in CDS

753

Length of CDS

978

Coding sequence (CDS) position

486

cDNA position

486

gDNA position

71098

Chromosomal position

218340748

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:

2:218340748G>A_9_ENST00000692295

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Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 46|154 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr2:218340748G>A (GRCh38)

Gene symbol

PNKD

Gene constraints

LOEUF: 1.58, LOF (oe): 1.16, misssense (oe): 1.12, synonymous (oe): 1.10 ? (gnomAD)

Ensembl transcript ID

ENST00000692295.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.165-786G>A
g.71098G>A

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	rs34014804
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	1975	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	7.01	1
	-2.488	0
(flanking)	8.855	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

2

Strand

1

Original gDNA sequence snippet

GCTTCCATTGAAAAGGAAGGGGTCACCTTGGTCGCCATTCT

Altered gDNA sequence snippet

GCTTCCATTGAAAAGGAAGGAGTCACCTTGGTCGCCATTCT

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MAWQGWPAAW QWVAGCWLLL VLVLVLLVSP RGCRARRGLR GLLMAHSQRL LFRIGDHSGG
NRDLSRRHRD CRVYGSPQDG IPYLTHPLCH QDVVSVGRLQ IRALATPGHT QGHLVYLLDG
EPYKGPSCLF SGDLLFLSGC GRTFEGNAET MLSSLDTVLG LGDDTLLWPG HEYAEENLGF
AGVVEPENLA RERKMQWVQR QRLERKGTCP STLGEERSYN PFLRTHCLAL QEALGPGPGP
TGDDDYSRAQ LLEELRRLKD MHKSK*

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

1 / 1

Last intron/exon boundary

624

Theoretical NMD boundary in CDS

573

Length of CDS

798

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

71098

Chromosomal position

218340748

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:

2:218340748G>A_4_ENST00000436005

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Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 50|150 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr2:218340748G>A (GRCh38)

Gene symbol

PNKD

Gene constraints

LOEUF: 1.22, LOF (oe): 0.92, misssense (oe): 0.98, synonymous (oe): 0.91 ? (gnomAD)

Ensembl transcript ID

ENST00000436005.3

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.486G>A
g.71098G>A

AA changes

no AA changes

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs34014804
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	1975	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	7.01	1
	-2.488	0
(flanking)	8.855	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

21

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

No

Chromosome

2

Strand

1

Original gDNA sequence snippet

GCTTCCATTGAAAAGGAAGGGGTCACCTTGGTCGCCATTCT

Altered gDNA sequence snippet

GCTTCCATTGAAAAGGAAGGAGTCACCTTGGTCGCCATTCT

Original cDNA sequence snippet

GCTTCCATTGAAAAGGAAGGGGTCACCTTGGTCGCCATTCT

Altered cDNA sequence snippet

GCTTCCATTGAAAAGGAAGGAGTCACCTTGGTCGCCATTCT

Wildtype AA sequence

MAAVVAATAL KGRGARNARV LRGILAGATA NKASHNRTRA LQSHSSPEGK EEPEPLSPEL
EYIPRKRGKN PMKAVGLAWY SLYTRTWLGY LFYRQQLRRA RNRYPKGHSK TQPRLFNGVK
VLPIPVLSDN YSYLIIDTQA QLAVAVDPSD PRAVQASIEK EGVTLVAILC THKHCGGNRD
LSRRHRDCRV YGSPQDGIPY LTHPLCHQDV VSVGRLQIRA LATPGHTQGH LVYLLDGEPY
KGPSCLFSGD LLFLSGCGRT FEGNAETMLS SLDTVLGLGD DTLLWPGHEY AEENLGFAGV
VEPENLARER KMQWVQRQRL ERKGTCPSTL GEERSYNPFL RTHCLALQEA LGPGPGPTGD
DDYSRAQLLE ELRRLKDMHK SK*

Mutated AA sequence

MAAVVAATAL KGRGARNARV LRGILAGATA NKASHNRTRA LQSHSSPEGK EEPEPLSPEL
EYIPRKRGKN PMKAVGLAWY SLYTRTWLGY LFYRQQLRRA RNRYPKGHSK TQPRLFNGVK
VLPIPVLSDN YSYLIIDTQA QLAVAVDPSD PRAVQASIEK EGVTLVAILC THKHCGGNRD
LSRRHRDCRV YGSPQDGIPY LTHPLCHQDV VSVGRLQIRA LATPGHTQGH LVYLLDGEPY
KGPSCLFSGD LLFLSGCGRT FEGNAETMLS SLDTVLGLGD DTLLWPGHEY AEENLGFAGV
VEPENLARER KMQWVQRQRL ERKGTCPSTL GEERSYNPFL RTHCLALQEA LGPGPGPTGD
DDYSRAQLLE ELRRLKDMHK SK*

Position of stopcodon in wt / mu CDS

1149 / 1149

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

383 / 383

Position of stopcodon in wt / mu cDNA

1171 / 1171

Position of start ATG in wt / mu cDNA

23 / 23

Last intron/exon boundary

997

Theoretical NMD boundary in CDS

924

Length of CDS

1149

Coding sequence (CDS) position

486

cDNA position

508

gDNA position

71098

Chromosomal position

218340748

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:

2:218340748G>A_8_ENST00000258362

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Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 91|109 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr2:218340748G>A (GRCh38)

Gene symbol

PNKD

Gene constraints

LOEUF: 1.36, LOF (oe): 1.04, misssense (oe): 1.10, synonymous (oe): 1.03 ? (gnomAD)

Ensembl transcript ID

ENST00000258362.7

Genbank transcript ID

NM_022572 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.414G>A
g.71098G>A

AA changes

no AA changes

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs34014804
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	1975	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	7.01	1
	-2.488	0
(flanking)	8.855	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

21

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

No

Chromosome

2

Strand

1

Original gDNA sequence snippet

GCTTCCATTGAAAAGGAAGGGGTCACCTTGGTCGCCATTCT

Altered gDNA sequence snippet

GCTTCCATTGAAAAGGAAGGAGTCACCTTGGTCGCCATTCT

Original cDNA sequence snippet

GCTTCCATTGAAAAGGAAGGGGTCACCTTGGTCGCCATTCT

Altered cDNA sequence snippet

GCTTCCATTGAAAAGGAAGGAGTCACCTTGGTCGCCATTCT

Wildtype AA sequence

MAWQGWPAAW QWVAGCWLLL VLVLVLLVSP RGCRARRGLR GLLMAHSQRL LFRIGYSLYT
RTWLGYLFYR QQLRRARNRY PKGHSKTQPR LFNGVKVLPI PVLSDNYSYL IIDTQAQLAV
AVDPSDPRAV QASIEKEGVT LVAILCTHKH WDHSGGNRDL SRRHRDCRVY GSPQDGIPYL
THPLCHQDVV SVGRLQIRAL ATPGHTQGHL VYLLDGEPYK GPSCLFSGDL LFLSGCGRTF
EGNAETMLSS LDTVLGLGDD TLLWPGHEYA EENLGFAGVV EPENLARERK MQWVQRQRLE
RKGTCPSTLG EERSYNPFLR THCLALQEAL GPGPGPTGDD DYSRAQLLEE LRRLKDMHKS
K*

Mutated AA sequence

MAWQGWPAAW QWVAGCWLLL VLVLVLLVSP RGCRARRGLR GLLMAHSQRL LFRIGYSLYT
RTWLGYLFYR QQLRRARNRY PKGHSKTQPR LFNGVKVLPI PVLSDNYSYL IIDTQAQLAV
AVDPSDPRAV QASIEKEGVT LVAILCTHKH WDHSGGNRDL SRRHRDCRVY GSPQDGIPYL
THPLCHQDVV SVGRLQIRAL ATPGHTQGHL VYLLDGEPYK GPSCLFSGDL LFLSGCGRTF
EGNAETMLSS LDTVLGLGDD TLLWPGHEYA EENLGFAGVV EPENLARERK MQWVQRQRLE
RKGTCPSTLG EERSYNPFLR THCLALQEAL GPGPGPTGDD DYSRAQLLEE LRRLKDMHKS
K*

Position of stopcodon in wt / mu CDS

1086 / 1086

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

362 / 362

Position of stopcodon in wt / mu cDNA

1181 / 1181

Position of start ATG in wt / mu cDNA

96 / 96

Last intron/exon boundary

1007

Theoretical NMD boundary in CDS

861

Length of CDS

1086

Coding sequence (CDS) position

414

cDNA position

509

gDNA position

71098

Chromosomal position

218340748

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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