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: ENST00000373511
Querying Taster for transcript #2: ENST00000373498
Querying Taster for transcript #3: ENST00000350766
Querying Taster for transcript #4: ENST00000373503
Querying Taster for transcript #5: ENST00000394063
Querying Taster for transcript #6: ENST00000265960
MT speed 0.34 s - this script 2.776823 s

Transcript summary:

Permalink

Transcript	Gene symbol	Prediction	Tree vote	Model	Splice site change	Variant type	Protein length	Features at a glance
ENST00000350766	MAPKAP1	Deleterious	91\|9	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000373498	MAPKAP1	Deleterious	92\|8	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000265960(MANE Select)	MAPKAP1	Deleterious	92\|8	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000373511	MAPKAP1	Deleterious	93\|7	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000373503	MAPKAP1	Deleterious	95\|5	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000394063	MAPKAP1	Deleterious	95\|5	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected

MutationT@ster 2025

Variant:

9:125444590T>C_3_ENST00000350766

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 91|9 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr9:125444590T>C (GRCh38)

Gene symbol

MAPKAP1

Gene constraints

LOEUF: 0.36, LOF (oe): 0.22, misssense (oe): 0.59, synonymous (oe): 0.84 ? (gnomAD)

Ensembl transcript ID

ENST00000350766.7

Genbank transcript ID

NM_024117 (by similarity)

UniProt / AlphaMissense peptide

SIN1_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1246A>G
g.262645A>G

AA changes

AAE:	I416V	?
Score:	29

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs752861508
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	0	293	293

Protein conservation

Species	Match	AA	Alignment
Human		416	D	L	A	E	E	K	S	P	S	H	A	I	F	K	L	T	Y	L	S	N	H	D	Y	K
mutated	all conserved	416	D	L	A	E	E	K	S	P	S	H	A	V	F	K	L	T
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	522	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	8.904	1
	5.905	1
(flanking)	0.311	0.997

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

9

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

9

Strand

-1

Original gDNA sequence snippet

CTGTCTCTGCAGGTCACGCAATATTTAAACTCACGTATCTA

Altered gDNA sequence snippet

CTGTCTCTGCAGGTCACGCAGTATTTAAACTCACGTATCTA

Original cDNA sequence snippet

AGAAAAGCCCCAGTCACGCAATATTTAAACTCACGTATCTA

Altered cDNA sequence snippet

AGAAAAGCCCCAGTCACGCAGTATTTAAACTCACGTATCTA

Wildtype AA sequence

MAFLDNPTII LAHIRQSHVT SDDTGMCEMV LIDHDVDLEK IHPPSMPGDS GSEIQGSNGE
TQGYVYAQSV DITSSWDFGI RRRSNTAQRL ERLRKERQNQ IKCKNIQWKE RNSKQSAQEL
KSLFEKKSLK EKPPISGKQS ILSVRLEQCP LQLNNPFNEY SKFDGKGHVG TTATKKIDVY
LPLHSSQDRL LPMTVVTMAS ARVQDLIGLI CWQYTSEGRE PKLNDNVSAY CLHIAEDDGE
VDTDFPPLDS NEPIHKFGFS TLALVEKYSS PGLTSKESLF VRINAAHGFS LIQVDNTKVT
MKEILLKAVK RRKGSQKVSG SRADGVFEED SQIDIATVQD MLSSHHYKSF KVSMIHRLRF
TTDVQLGISG DKVEIDPVTN QKASTKFWIK QKPISIDSDL LCACDLAEEK SPSHAIFKLT
YLSNHDYKHL YFESDAATVN EIVLKVNYIL ESRASTARAD YFAQKQRKLN RRTSFSFQKE
KKSGQQ*

Mutated AA sequence

MAFLDNPTII LAHIRQSHVT SDDTGMCEMV LIDHDVDLEK IHPPSMPGDS GSEIQGSNGE
TQGYVYAQSV DITSSWDFGI RRRSNTAQRL ERLRKERQNQ IKCKNIQWKE RNSKQSAQEL
KSLFEKKSLK EKPPISGKQS ILSVRLEQCP LQLNNPFNEY SKFDGKGHVG TTATKKIDVY
LPLHSSQDRL LPMTVVTMAS ARVQDLIGLI CWQYTSEGRE PKLNDNVSAY CLHIAEDDGE
VDTDFPPLDS NEPIHKFGFS TLALVEKYSS PGLTSKESLF VRINAAHGFS LIQVDNTKVT
MKEILLKAVK RRKGSQKVSG SRADGVFEED SQIDIATVQD MLSSHHYKSF KVSMIHRLRF
TTDVQLGISG DKVEIDPVTN QKASTKFWIK QKPISIDSDL LCACDLAEEK SPSHAVFKLT
YLSNHDYKHL YFESDAATVN EIVLKVNYIL ESRASTARAD YFAQKQRKLN RRTSFSFQKE
KKSGQQ*

Position of stopcodon in wt / mu CDS

1461 / 1461

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

487 / 487

Position of stopcodon in wt / mu cDNA

1763 / 1763

Position of start ATG in wt / mu cDNA

303 / 303

Last intron/exon boundary

1637

Theoretical NMD boundary in CDS

1284

Length of CDS

1461

Coding sequence (CDS) position

1246

cDNA position

1548

gDNA position

262645

Chromosomal position

125444590

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:

9:125444590T>C_2_ENST00000373498

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 92|8 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr9:125444590T>C (GRCh38)

Gene symbol

MAPKAP1

Gene constraints

LOEUF: 0.37, LOF (oe): 0.23, misssense (oe): 0.61, synonymous (oe): 0.84 ? (gnomAD)

Ensembl transcript ID

ENST00000373498.5

Genbank transcript ID

UniProt / AlphaMissense peptide

SIN1_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1354A>G
g.262645A>G

AA changes

AAE:	I452V	?
Score:	29

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs752861508
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	0	293	293

Protein conservation

Species	Match	AA	Alignment
Human		452	D	L	A	E	E	K	S	P	S	H	A	I	F	K	L	T	Y	L	S	N	H	D	Y	K
mutated	all conserved	452	D	L	A	E	E	K	S	P	S	H	A	V	F	K	L	T	Y	L	S	N	H	D	Y
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	522	CHAIN		lost
451	459	STRAND		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	8.904	1
	5.905	1
(flanking)	0.311	0.997

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

9

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

9

Strand

-1

Original gDNA sequence snippet

CTGTCTCTGCAGGTCACGCAATATTTAAACTCACGTATCTA

Altered gDNA sequence snippet

CTGTCTCTGCAGGTCACGCAGTATTTAAACTCACGTATCTA

Original cDNA sequence snippet

AGAAAAGCCCCAGTCACGCAATATTTAAACTCACGTATCTA

Altered cDNA sequence snippet

AGAAAAGCCCCAGTCACGCAGTATTTAAACTCACGTATCTA

Wildtype AA sequence

MAFLDNPTII LAHIRQSHVT SDDTGMCEMV LIDHDVDLEK IHPPSMPGDS GSEIQGSNGE
TQGYVYAQSV DITSSWDFGI RRRSNTAQRL ERLRKERQNQ IKCKNIQWKE RNSKQSAQEL
KSLFEKKSLK EKPPISGKQS ILSVRLEQCP LQLNNPFNEY SKFDGKGHVG TTATKKIDVY
LPLHSSQDRL LPMTVVTMAS ARVQDLIGLI CWQYTSEGRE PKLNDNVSAY CLHIAEDDGE
VDTDFPPLDS NEPIHKFGFS TLALVEKYSS PGLTSKESLF VRINAAHGFS LIQVDNTKVT
MKEILLKAVK RRKGSQKVSG PQYRLEKQSE PNVAVDLDST LESQSAWEFC LVRENSSRAD
GVFEEDSQID IATVQDMLSS HHYKSFKVSM IHRLRFTTDV QLGISGDKVE IDPVTNQKAS
TKFWIKQKPI SIDSDLLCAC DLAEEKSPSH AIFKLTYLSN HDYKHLYFES DAATVNEIVL
KVNYILESRA STARADYFAQ KQRKLNRRTS FSFQKEKKSG QQ*

Mutated AA sequence

MAFLDNPTII LAHIRQSHVT SDDTGMCEMV LIDHDVDLEK IHPPSMPGDS GSEIQGSNGE
TQGYVYAQSV DITSSWDFGI RRRSNTAQRL ERLRKERQNQ IKCKNIQWKE RNSKQSAQEL
KSLFEKKSLK EKPPISGKQS ILSVRLEQCP LQLNNPFNEY SKFDGKGHVG TTATKKIDVY
LPLHSSQDRL LPMTVVTMAS ARVQDLIGLI CWQYTSEGRE PKLNDNVSAY CLHIAEDDGE
VDTDFPPLDS NEPIHKFGFS TLALVEKYSS PGLTSKESLF VRINAAHGFS LIQVDNTKVT
MKEILLKAVK RRKGSQKVSG PQYRLEKQSE PNVAVDLDST LESQSAWEFC LVRENSSRAD
GVFEEDSQID IATVQDMLSS HHYKSFKVSM IHRLRFTTDV QLGISGDKVE IDPVTNQKAS
TKFWIKQKPI SIDSDLLCAC DLAEEKSPSH AVFKLTYLSN HDYKHLYFES DAATVNEIVL
KVNYILESRA STARADYFAQ KQRKLNRRTS FSFQKEKKSG QQ*

Position of stopcodon in wt / mu CDS

1569 / 1569

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

523 / 523

Position of stopcodon in wt / mu cDNA

1638 / 1638

Position of start ATG in wt / mu cDNA

70 / 70

Last intron/exon boundary

1512

Theoretical NMD boundary in CDS

1392

Length of CDS

1569

Coding sequence (CDS) position

1354

cDNA position

1423

gDNA position

262645

Chromosomal position

125444590

Speed

0.07 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:

9:125444590T>C_6_ENST00000265960

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 92|8 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr9:125444590T>C (GRCh38)

Gene symbol

MAPKAP1

Gene constraints

LOEUF: 0.37, LOF (oe): 0.23, misssense (oe): 0.61, synonymous (oe): 0.84 ? (gnomAD)

Ensembl transcript ID

ENST00000265960.8

Genbank transcript ID

NM_001006617 (exact from MANE)

UniProt / AlphaMissense peptide

SIN1_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1354A>G
g.262645A>G

AA changes

AAE:	I452V	?
Score:	29

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs752861508
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	0	293	293

Protein conservation

Species	Match	AA	Alignment
Human		452	D	L	A	E	E	K	S	P	S	H	A	I	F	K	L	T	Y	L	S	N	H	D	Y	K
mutated	all conserved	452	D	L	A	E	E	K	S	P	S	H	A	V	F	K	L	T	Y	L	S	N	H	D	Y
Ptroglodytes	all identical	452	D	L	A	E	E	K	S	P	S	H	A	I	F	K	L	T	Y	L	S	N	H	D	Y
Mmulatta	all identical	452	D	L	A	E	E	K	S	P	S	H	A	I	F	K	L	T	Y	L	S	N	H	D	Y
Fcatus	all identical	505	D	L	A	E	E	K	S	P	S	H	A	I	F	K	L	T	Y	L	S	N	H	D	Y
Mmusculus	all conserved	452	D	L	A	E	E	K	S	P	S	H	A	V	F	K	L	T	Y	L	S	S	H	D	Y
Ggallus	all identical	452	D	L	V	E	E	K	S	P	S	H	A	I	F	K	L	T	Y	L	S	N	H	D	Y
Trubripes	all identical	478	D	L	V	E	E	R	S	P	S	H	A	I	F	K
Drerio	no homologue
Dmelanogaster	not conserved	502						GGIAHSPS	S	P	G	H	S	-	S	G	L	F	S	S	S	N	I	R	F
Celegans	no alignment	n/a
Xtropicalis	all conserved	452	D	L	A	E	E	K	S	P	S	H	A	M	F	K	V	T	Y	L	S	N	H	D	Y

Protein features

Start (aa)	End (aa)	Feature	Details
2	522	CHAIN		lost
451	459	STRAND		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	8.904	1
	5.905	1
(flanking)	0.311	0.997

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

9

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

9

Strand

-1

Original gDNA sequence snippet

CTGTCTCTGCAGGTCACGCAATATTTAAACTCACGTATCTA

Altered gDNA sequence snippet

CTGTCTCTGCAGGTCACGCAGTATTTAAACTCACGTATCTA

Original cDNA sequence snippet

AGAAAAGCCCCAGTCACGCAATATTTAAACTCACGTATCTA

Altered cDNA sequence snippet

AGAAAAGCCCCAGTCACGCAGTATTTAAACTCACGTATCTA

Wildtype AA sequence

MAFLDNPTII LAHIRQSHVT SDDTGMCEMV LIDHDVDLEK IHPPSMPGDS GSEIQGSNGE
TQGYVYAQSV DITSSWDFGI RRRSNTAQRL ERLRKERQNQ IKCKNIQWKE RNSKQSAQEL
KSLFEKKSLK EKPPISGKQS ILSVRLEQCP LQLNNPFNEY SKFDGKGHVG TTATKKIDVY
LPLHSSQDRL LPMTVVTMAS ARVQDLIGLI CWQYTSEGRE PKLNDNVSAY CLHIAEDDGE
VDTDFPPLDS NEPIHKFGFS TLALVEKYSS PGLTSKESLF VRINAAHGFS LIQVDNTKVT
MKEILLKAVK RRKGSQKVSG PQYRLEKQSE PNVAVDLDST LESQSAWEFC LVRENSSRAD
GVFEEDSQID IATVQDMLSS HHYKSFKVSM IHRLRFTTDV QLGISGDKVE IDPVTNQKAS
TKFWIKQKPI SIDSDLLCAC DLAEEKSPSH AIFKLTYLSN HDYKHLYFES DAATVNEIVL
KVNYILESRA STARADYFAQ KQRKLNRRTS FSFQKEKKSG QQ*

Mutated AA sequence

MAFLDNPTII LAHIRQSHVT SDDTGMCEMV LIDHDVDLEK IHPPSMPGDS GSEIQGSNGE
TQGYVYAQSV DITSSWDFGI RRRSNTAQRL ERLRKERQNQ IKCKNIQWKE RNSKQSAQEL
KSLFEKKSLK EKPPISGKQS ILSVRLEQCP LQLNNPFNEY SKFDGKGHVG TTATKKIDVY
LPLHSSQDRL LPMTVVTMAS ARVQDLIGLI CWQYTSEGRE PKLNDNVSAY CLHIAEDDGE
VDTDFPPLDS NEPIHKFGFS TLALVEKYSS PGLTSKESLF VRINAAHGFS LIQVDNTKVT
MKEILLKAVK RRKGSQKVSG PQYRLEKQSE PNVAVDLDST LESQSAWEFC LVRENSSRAD
GVFEEDSQID IATVQDMLSS HHYKSFKVSM IHRLRFTTDV QLGISGDKVE IDPVTNQKAS
TKFWIKQKPI SIDSDLLCAC DLAEEKSPSH AVFKLTYLSN HDYKHLYFES DAATVNEIVL
KVNYILESRA STARADYFAQ KQRKLNRRTS FSFQKEKKSG QQ*

Position of stopcodon in wt / mu CDS

1569 / 1569

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

523 / 523

Position of stopcodon in wt / mu cDNA

1876 / 1876

Position of start ATG in wt / mu cDNA

308 / 308

Last intron/exon boundary

1750

Theoretical NMD boundary in CDS

1392

Length of CDS

1569

Coding sequence (CDS) position

1354

cDNA position

1661

gDNA position

262645

Chromosomal position

125444590

Speed

0.07 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:

9:125444590T>C_1_ENST00000373511

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 93|7 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr9:125444590T>C (GRCh38)

Gene symbol

MAPKAP1

Gene constraints

LOEUF: 0.39, LOF (oe): 0.24, misssense (oe): 0.61, synonymous (oe): 0.82 ? (gnomAD)

Ensembl transcript ID

ENST00000373511.6

Genbank transcript ID

NM_001006619 (by similarity)

UniProt / AlphaMissense peptide

SIN1_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1213A>G
g.262645A>G

AA changes

AAE:	I405V	?
Score:	29

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs752861508
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	0	293	293

Protein conservation

Species	Match	AA	Alignment
Human		405	D	L	A	E	E	K	S	P	S	H	A	I	F	K	L	T	Y	L	S	N	H	D	Y	K
mutated	all conserved	405	D	L	A	E	E	K	S	P	S	H	A	V	F	K	L	T	Y	L	S	N	H	D	Y
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	522	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	8.904	1
	5.905	1
(flanking)	0.311	0.997

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

9

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

9

Strand

-1

Original gDNA sequence snippet

CTGTCTCTGCAGGTCACGCAATATTTAAACTCACGTATCTA

Altered gDNA sequence snippet

CTGTCTCTGCAGGTCACGCAGTATTTAAACTCACGTATCTA

Original cDNA sequence snippet

AGAAAAGCCCCAGTCACGCAATATTTAAACTCACGTATCTA

Altered cDNA sequence snippet

AGAAAAGCCCCAGTCACGCAGTATTTAAACTCACGTATCTA

Wildtype AA sequence

MAFLDNPTII LAHIRQSHVT SDDTGMCEMV LIDHDVDLEK IHPPSMPGDS GSEIQGSNGE
TQGYVYAQSV DITSSWDFGI RRRSNTAQRL ERLRKERQNQ IKCKNIQWKE RNSKQSAQEL
KSLFEKKSLK EKPPISGKQS ILSVRLEQCP LQLNNPFNEY SKFDGKGHVG TTATKKIDVY
LPLHSSQDRL LPMTVVTMAS ARVQDLIGLI CWQYTSEGRE PKLNDNVSAY CLHIAEDDGE
VDTDFPPLDS NEPIHKFGFS TLALVEKYSS PGLTSKESLF VRINAAHGFS LIQVDNTKVT
MKEILLKAVK RRKGSQKVSG PQYRLEKQSE PNVAVDLDST LESQSAWEFC LVRENSISGD
KVEIDPVTNQ KASTKFWIKQ KPISIDSDLL CACDLAEEKS PSHAIFKLTY LSNHDYKHLY
FESDAATVNE IVLKVNYILE SRASTARADY FAQKQRKLNR RTSFSFQKEK KSGQQ*

Mutated AA sequence

MAFLDNPTII LAHIRQSHVT SDDTGMCEMV LIDHDVDLEK IHPPSMPGDS GSEIQGSNGE
TQGYVYAQSV DITSSWDFGI RRRSNTAQRL ERLRKERQNQ IKCKNIQWKE RNSKQSAQEL
KSLFEKKSLK EKPPISGKQS ILSVRLEQCP LQLNNPFNEY SKFDGKGHVG TTATKKIDVY
LPLHSSQDRL LPMTVVTMAS ARVQDLIGLI CWQYTSEGRE PKLNDNVSAY CLHIAEDDGE
VDTDFPPLDS NEPIHKFGFS TLALVEKYSS PGLTSKESLF VRINAAHGFS LIQVDNTKVT
MKEILLKAVK RRKGSQKVSG PQYRLEKQSE PNVAVDLDST LESQSAWEFC LVRENSISGD
KVEIDPVTNQ KASTKFWIKQ KPISIDSDLL CACDLAEEKS PSHAVFKLTY LSNHDYKHLY
FESDAATVNE IVLKVNYILE SRASTARADY FAQKQRKLNR RTSFSFQKEK KSGQQ*

Position of stopcodon in wt / mu CDS

1428 / 1428

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

476 / 476

Position of stopcodon in wt / mu cDNA

1758 / 1758

Position of start ATG in wt / mu cDNA

331 / 331

Last intron/exon boundary

1632

Theoretical NMD boundary in CDS

1251

Length of CDS

1428

Coding sequence (CDS) position

1213

cDNA position

1543

gDNA position

262645

Chromosomal position

125444590

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:

9:125444590T>C_4_ENST00000373503

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 95|5 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr9:125444590T>C (GRCh38)

Gene symbol

MAPKAP1

Gene constraints

LOEUF: 0.41, LOF (oe): 0.23, misssense (oe): 0.58, synonymous (oe): 0.84 ? (gnomAD)

Ensembl transcript ID

ENST00000373503.7

Genbank transcript ID

NM_001006620 (by similarity)

UniProt / AlphaMissense peptide

SIN1_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.778A>G
g.262645A>G

AA changes

AAE:	I260V	?
Score:	29

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs752861508
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	0	293	293

Protein conservation

Species	Match	AA	Alignment
Human		260	D	L	A	E	E	K	S	P	S	H	A	I	F	K	L	T	Y	L	S	N	H	D	Y	K
mutated	all conserved	260	D	L	A	E	E	K	S	P	S	H	A	V	F	K	L	T	Y	L	S	N	H	D	Y
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	267	REGION	Interaction with NBN	lost
2	522	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	8.904	1
	5.905	1
(flanking)	0.311	0.997

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

9

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

9

Strand

-1

Original gDNA sequence snippet

CTGTCTCTGCAGGTCACGCAATATTTAAACTCACGTATCTA

Altered gDNA sequence snippet

CTGTCTCTGCAGGTCACGCAGTATTTAAACTCACGTATCTA

Original cDNA sequence snippet

AGAAAAGCCCCAGTCACGCAATATTTAAACTCACGTATCTA

Altered cDNA sequence snippet

AGAAAAGCCCCAGTCACGCAGTATTTAAACTCACGTATCTA

Wildtype AA sequence

MTVVTMASAR VQDLIGLICW QYTSEGREPK LNDNVSAYCL HIAEDDGEVD TDFPPLDSNE
PIHKFGFSTL ALVEKYSSPG LTSKESLFVR INAAHGFSLI QVDNTKVTMK EILLKAVKRR
KGSQKVSGPQ YRLEKQSEPN VAVDLDSTLE SQSAWEFCLV RENSSRADGV FEEDSQIDIA
TVQDMLSSHH YKSFKVSMIH RLRFTTDVQL GISGDKVEID PVTNQKASTK FWIKQKPISI
DSDLLCACDL AEEKSPSHAI FKLTYLSNHD YKHLYFESDA ATVNEIVLKV NYILESRAST
ARADYFAQKQ RKLNRRTSFS FQKEKKSGQQ *

Mutated AA sequence

MTVVTMASAR VQDLIGLICW QYTSEGREPK LNDNVSAYCL HIAEDDGEVD TDFPPLDSNE
PIHKFGFSTL ALVEKYSSPG LTSKESLFVR INAAHGFSLI QVDNTKVTMK EILLKAVKRR
KGSQKVSGPQ YRLEKQSEPN VAVDLDSTLE SQSAWEFCLV RENSSRADGV FEEDSQIDIA
TVQDMLSSHH YKSFKVSMIH RLRFTTDVQL GISGDKVEID PVTNQKASTK FWIKQKPISI
DSDLLCACDL AEEKSPSHAV FKLTYLSNHD YKHLYFESDA ATVNEIVLKV NYILESRAST
ARADYFAQKQ RKLNRRTSFS FQKEKKSGQQ *

Position of stopcodon in wt / mu CDS

993 / 993

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

331 / 331

Position of stopcodon in wt / mu cDNA

1552 / 1552

Position of start ATG in wt / mu cDNA

560 / 560

Last intron/exon boundary

1426

Theoretical NMD boundary in CDS

816

Length of CDS

993

Coding sequence (CDS) position

778

cDNA position

1337

gDNA position

262645

Chromosomal position

125444590

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:

9:125444590T>C_5_ENST00000394063

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 95|5 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr9:125444590T>C (GRCh38)

Gene symbol

MAPKAP1

Gene constraints

LOEUF: 0.41, LOF (oe): 0.23, misssense (oe): 0.58, synonymous (oe): 0.84 ? (gnomAD)

Ensembl transcript ID

ENST00000394063.5

Genbank transcript ID

NM_001006621 (by similarity)

UniProt / AlphaMissense peptide

SIN1_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.778A>G
g.262645A>G

AA changes

AAE:	I260V	?
Score:	29

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs752861508
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	0	293	293

Protein conservation

Species	Match	AA	Alignment
Human		260	D	L	A	E	E	K	S	P	S	H	A	I	F	K	L	T	Y	L	S	N	H	D	Y	K
mutated	all conserved	260	D	L	A	E	E	K	S	P	S	H	A	V	F	K	L	T	Y	L	S	N	H	D	Y
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	267	REGION	Interaction with NBN	lost
2	522	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	8.904	1
	5.905	1
(flanking)	0.311	0.997

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

9

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

9

Strand

-1

Original gDNA sequence snippet

CTGTCTCTGCAGGTCACGCAATATTTAAACTCACGTATCTA

Altered gDNA sequence snippet

CTGTCTCTGCAGGTCACGCAGTATTTAAACTCACGTATCTA

Original cDNA sequence snippet

AGAAAAGCCCCAGTCACGCAATATTTAAACTCACGTATCTA

Altered cDNA sequence snippet

AGAAAAGCCCCAGTCACGCAGTATTTAAACTCACGTATCTA

Wildtype AA sequence

MTVVTMASAR VQDLIGLICW QYTSEGREPK LNDNVSAYCL HIAEDDGEVD TDFPPLDSNE
PIHKFGFSTL ALVEKYSSPG LTSKESLFVR INAAHGFSLI QVDNTKVTMK EILLKAVKRR
KGSQKVSGPQ YRLEKQSEPN VAVDLDSTLE SQSAWEFCLV RENSSRADGV FEEDSQIDIA
TVQDMLSSHH YKSFKVSMIH RLRFTTDVQL GISGDKVEID PVTNQKASTK FWIKQKPISI
DSDLLCACDL AEEKSPSHAI FKLTYLSNHD YKHLYFESDA ATVNEIVLKV NYILESRAST
ARADYFAQKQ RKLNRRTSFS FQKEKKSGQQ *

Mutated AA sequence

MTVVTMASAR VQDLIGLICW QYTSEGREPK LNDNVSAYCL HIAEDDGEVD TDFPPLDSNE
PIHKFGFSTL ALVEKYSSPG LTSKESLFVR INAAHGFSLI QVDNTKVTMK EILLKAVKRR
KGSQKVSGPQ YRLEKQSEPN VAVDLDSTLE SQSAWEFCLV RENSSRADGV FEEDSQIDIA
TVQDMLSSHH YKSFKVSMIH RLRFTTDVQL GISGDKVEID PVTNQKASTK FWIKQKPISI
DSDLLCACDL AEEKSPSHAV FKLTYLSNHD YKHLYFESDA ATVNEIVLKV NYILESRAST
ARADYFAQKQ RKLNRRTSFS FQKEKKSGQQ *

Position of stopcodon in wt / mu CDS

993 / 993

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

331 / 331

Position of stopcodon in wt / mu cDNA

1484 / 1484

Position of start ATG in wt / mu cDNA

492 / 492

Last intron/exon boundary

1358

Theoretical NMD boundary in CDS

816

Length of CDS

993

Coding sequence (CDS) position

778

cDNA position

1269

gDNA position

262645

Chromosomal position

125444590

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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