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: ENST00000644715
Querying Taster for transcript #2: ENST00000460874
Querying Taster for transcript #3: ENST00000580900
MT speed 0.06 s - this script 2.412101 s

Transcript summary:

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Transcript	Gene symbol	Prediction	Tree vote	Model	Splice site change	Variant type	Protein length	Features at a glance
ENST00000644715(MANE Select)	MTAP	Benign	0\|200	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000580900	MTAP	Benign	0\|200	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000460874	MTAP	Benign	1\|199	without_aae	No	Single base exchange	Normal	Homozygous in gnomAD

MutationT@ster 2025

Variant:

9:21802923C>G_1_ENST00000644715

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Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 0|200 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr9:21802923C>G (GRCh38)

Gene symbol

MTAP

Gene constraints

LOEUF: 1.49, LOF (oe): 1.10, misssense (oe): 1.00, synonymous (oe): 1.12 ? (gnomAD)

Ensembl transcript ID

ENST00000644715.2

Genbank transcript ID

NM_002451 (exact from MANE), NM_001396043 (by similarity), NM_001396042 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.33+142C>G
g.288C>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	rs117769854
gnomAD	homozygous (G/G)	heterozygous	allele carriers
	1054	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.712	0
	0.011	0
(flanking)	0.413	0.003

?

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

9

Strand

1

Original gDNA sequence snippet

AGGGACTGGGGCGCGGCACTCGGGACTCACTTGCCGCGCGA

Altered gDNA sequence snippet

AGGGACTGGGGCGCGGCACTGGGGACTCACTTGCCGCGCGA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MASGTTTTAV KIGIIGGTGL DDPEILEGRT EKYVDTPFGK PSDALILGKI KNVDCVLLAR
HGRQHTIMPS KVNYQANIWA LKEEGCTHVI VTTACGSLRE EIQPGDIVII DQFIDRTTMR
PQSFYDGSHS CARGVCHIPM AEPFCPKTRE VLIETAKKLG LRCHSKGTMV TIEGPRFSSR
AESFMFRTWG ADVINMTTVP EVVLAKEAGI CYASIAMATD YDCWKEHEEA VSVDRVLKTL
KENANKAKSL LLTTIPQIGS TEWSETLHNL KNMAQFSVLL PRH*

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

114 / 114

Last intron/exon boundary

926

Theoretical NMD boundary in CDS

762

Length of CDS

852

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

288

Chromosomal position

21802923

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

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MutationT@ster 2025

Variant:

9:21802923C>G_3_ENST00000580900

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 0|200 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr9:21802923C>G (GRCh38)

Gene symbol

MTAP

Gene constraints

LOEUF: 1.52, LOF (oe): 1.12, misssense (oe): 1.00, synonymous (oe): 1.11 ? (gnomAD)

Ensembl transcript ID

ENST00000580900.5

Genbank transcript ID

NM_001396044 (by similarity), NM_001396045 (by similarity), NM_001396041 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.33+142C>G
g.288C>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	rs117769854
gnomAD	homozygous (G/G)	heterozygous	allele carriers
	1054	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.712	0
	0.011	0
(flanking)	0.413	0.003

?

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

9

Strand

1

Original gDNA sequence snippet

AGGGACTGGGGCGCGGCACTCGGGACTCACTTGCCGCGCGA

Altered gDNA sequence snippet

AGGGACTGGGGCGCGGCACTGGGGACTCACTTGCCGCGCGA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MASGTTTTAV KIGIIGGTGL DDPEILEGRT EKYVDTPFGK PSDALILGKI KNVDCVLLAR
HGRQHTIMPS KVNYQANIWA LKEEGCTHVI VTTACGSLRE EIQPGDIVII DQFIDRTTMR
PQSFYDGSHS CARGVCHIPM AEPFCPKTRE VLIETAKKLG LRCHSKGTMV TIEGPRFSSR
AESFMFRTWG ADVINMTTVP EVVLAKEAGI CYASIAMATD YDCWKEHEEA VSVDRVLKTL
KENANKAKSL LLTTIPQIGS TEWSETLHNL KMIKFQMILS EGYHPFNIQE SPFYRGLLDF
PSVGHGRGEI LPLSPLDLAG YCFQQPMQPP CPDS*

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

101 / 101

Last intron/exon boundary

913

Theoretical NMD boundary in CDS

762

Length of CDS

1005

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

288

Chromosomal position

21802923

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:

9:21802923C>G_2_ENST00000460874

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 1|199 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr9:21802923C>G (GRCh38)

Gene symbol

MTAP

Gene constraints

LOEUF: 1.50, LOF (oe): 1.11, misssense (oe): 1.08, synonymous (oe): 1.21 ? (gnomAD)

Ensembl transcript ID

ENST00000460874.6

Genbank transcript ID

NM_001396040 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.57C>G
g.288C>G

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	rs117769854
gnomAD	homozygous (G/G)	heterozygous	allele carriers
	1054	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.712	0
	0.011	0
(flanking)	0.413	0.003

?

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

No

Chromosome

9

Strand

1

Original gDNA sequence snippet

AGGGACTGGGGCGCGGCACTCGGGACTCACTTGCCGCGCGA

Altered gDNA sequence snippet

AGGGACTGGGGCGCGGCACTGGGGACTCACTTGCCGCGCGA

Original cDNA sequence snippet

AGGGACTGGGGCGCGGCACTCGGGACTCACTTGCCGCGCGA

Altered cDNA sequence snippet

AGGGACTGGGGCGCGGCACTGGGGACTCACTTGCCGCGCGA

Wildtype AA sequence

MRPARASLAA AGRDWGAALG THLPREERIG IIGGTGLDDP EILEGRTEKY VDTPFGKPSD
ALILGKIKNV DCVLLARHGR QHTIMPSKVN YQANIWALKE EGCTHVIVTT ACGSLREEIQ
PGDIVIIDQF IDRTTMRPQS FYDGSHSCAR GVCHIPMAEP FCPKTREVLI ETAKKLGLRC
HSKGTMVTIE GPRFSSRAES FMFRTWGADV INMTTVPEVV LAKEAGICYA SIAMATDYDC
WKEHEEAVSV DRVLKTLKEN ANKAKSLLLT TIPQIGSTEW SETLHNLKNM AQFSVLLPRH
*

Mutated AA sequence

MRPARASLAA AGRDWGAALG THLPREERIG IIGGTGLDDP EILEGRTEKY VDTPFGKPSD
ALILGKIKNV DCVLLARHGR QHTIMPSKVN YQANIWALKE EGCTHVIVTT ACGSLREEIQ
PGDIVIIDQF IDRTTMRPQS FYDGSHSCAR GVCHIPMAEP FCPKTREVLI ETAKKLGLRC
HSKGTMVTIE GPRFSSRAES FMFRTWGADV INMTTVPEVV LAKEAGICYA SIAMATDYDC
WKEHEEAVSV DRVLKTLKEN ANKAKSLLLT TIPQIGSTEW SETLHNLKNM AQFSVLLPRH
*

Position of stopcodon in wt / mu CDS

903 / 903

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

301 / 301

Position of stopcodon in wt / mu cDNA

1128 / 1128

Position of start ATG in wt / mu cDNA

226 / 226

Last intron/exon boundary

1089

Theoretical NMD boundary in CDS

813

Length of CDS

903

Coding sequence (CDS) position

57

cDNA position

282

gDNA position

288

Chromosomal position

21802923

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