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: ENST00000299698
Querying Taster for transcript #2: ENST00000539547
MT speed 0.13 s - this script 2.563502 s

Transcript summary:

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Transcript	Gene symbol	Prediction	Tree vote	Model	Prediction problem	Splice site change	Known ClinVar disease mutation	Potential ClinVar disease mutation	Amino acid changes	Variant type	dbSNP ID	Protein length	Features at a glance
ENST00000539547	A2ML1	Deleterious	79\|21	simple_aae		No				Single base exchange		Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000299698(MANE Select)	A2ML1	Deleterious	82\|18	simple_aae		No				Single base exchange		Normal	Amino acid sequence changed Protein features (might be) affected

MutationT@ster 2025

Variant:

12:8854244G>A_2_ENST00000539547

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 79|21 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr12:8854244G>A (GRCh38)

Gene symbol

A2ML1

Gene constraints

LOEUF: 0.96, LOF (oe): 0.81, misssense (oe): 0.90, synonymous (oe): 0.88 ? (gnomAD)

Ensembl transcript ID

ENST00000539547.5

Genbank transcript ID

NM_001282424 (by similarity)

UniProt / AlphaMissense peptide

A2ML1_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1234G>A
g.31624G>A

AA changes

AAE:	V412I	?
Score:	29

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs1416944345
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	16	16

Protein conservation

Species	Match	AA	Alignment
Human		412	G	R	S	D	T	L	I	K	P	V	L	V	K	P	E	G	V	L	V	E	K	T	H	S
mutated	all conserved	412	G	R	S	D	T	L	I	K	P	V	L	I	K	P	E	G	V	L	V	E
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
18	1454	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.09	0.996
	5.816	1
(flanking)	6.083	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

6

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

12

Strand

1

Original gDNA sequence snippet

CGCTCATCAAGCCAGTTCTCGTCAAAGTGAGTTTTCTTCAG

Altered gDNA sequence snippet

CGCTCATCAAGCCAGTTCTCATCAAAGTGAGTTTTCTTCAG

Original cDNA sequence snippet

CGCTCATCAAGCCAGTTCTCGTCAAACCTGAGGGAGTCCTG

Altered cDNA sequence snippet

CGCTCATCAAGCCAGTTCTCATCAAACCTGAGGGAGTCCTG

Wildtype AA sequence

MLIGKGSLVM EGQKHLNSKK KGLKASFSLS LTFTSRLAPD PSLVIYAIFP SGGVVADKIQ
FSVEMCFDNQ VSLGFSPSQQ LPGAEVELQL QAAPGSLCAL RAVDESVLLL RPDRELSNRS
VYGMFPFWYG HYPYQVAEYD QCPVSGPWDF PQPLIDPMPQ GHSSQRSIIW RPSFSEGTDL
FSFFRDVGLK ILSNAKIKKP VDCSHRSPEY STAMGAGGGH PEAFESSTPL HQAEDSQVRQ
YFPETWLWDL FPIGNSGKEA VHVTVPDAIT EWKAMSFCTS QSRGFGLSPT VGLTAFKPFF
VDLTLPYSVV RGESFRLTAT IFNYLKDCIR VQTDLAKSHE YQLESWADSQ TSSCLCADDA
KTHHWNITAV KLGHINFTIS TKILDSNEPC GGQKGFVPQK GRSDTLIKPV LVKPEGVLVE
KTHSSLLCPK GKVASESVSL ELPVDIVPDS TKAYVTVLGD IMGTALQNLD GLVQMPSGCG
EQNMVLFAPI IYVLQYLEKA GLLTEEIRSR AVGFLEIGYQ KELMYKHSNG SYSAFGERDG
NGNTWLTAFV TKCFGQAQKF IFIDPKNIQD ALKWMAGNQL PSGCYANVGN LLHTAMKGGV
DDEVSLTAYV TAALLEMGKD VDDPMVSQGL RCLKNSATST TNLYTQALLA YIFSLAGEMD
IRNILLKQLD QQAIISGESI YWSQKPTPSS NASPWSEPAA VDVELTAYAL LAQLTKPSLT
QKEIAKATSI VAWLAKQHNA YGGFSSTQDT VVALQALAKY ATTAYMPSEE INLVVKSTEN
FQRTFNIQSV NRLVFQQDTL PNVPGMYTLE ASGQGCVYVQ TVLRYNILPP TNMKTFSLSV
EIGKARCEQP TSPRSLTLTI HTSYVGSRSS SNMAIVEVKM LSGFSPMEGT NQLLLQQPLV
KKVEFGTDTL NIYLDELIKN TQTYTFTISQ SVLVTNLKPA TIKVYDYYLP DEQATIQYSD
PCE*

Mutated AA sequence

MLIGKGSLVM EGQKHLNSKK KGLKASFSLS LTFTSRLAPD PSLVIYAIFP SGGVVADKIQ
FSVEMCFDNQ VSLGFSPSQQ LPGAEVELQL QAAPGSLCAL RAVDESVLLL RPDRELSNRS
VYGMFPFWYG HYPYQVAEYD QCPVSGPWDF PQPLIDPMPQ GHSSQRSIIW RPSFSEGTDL
FSFFRDVGLK ILSNAKIKKP VDCSHRSPEY STAMGAGGGH PEAFESSTPL HQAEDSQVRQ
YFPETWLWDL FPIGNSGKEA VHVTVPDAIT EWKAMSFCTS QSRGFGLSPT VGLTAFKPFF
VDLTLPYSVV RGESFRLTAT IFNYLKDCIR VQTDLAKSHE YQLESWADSQ TSSCLCADDA
KTHHWNITAV KLGHINFTIS TKILDSNEPC GGQKGFVPQK GRSDTLIKPV LIKPEGVLVE
KTHSSLLCPK GKVASESVSL ELPVDIVPDS TKAYVTVLGD IMGTALQNLD GLVQMPSGCG
EQNMVLFAPI IYVLQYLEKA GLLTEEIRSR AVGFLEIGYQ KELMYKHSNG SYSAFGERDG
NGNTWLTAFV TKCFGQAQKF IFIDPKNIQD ALKWMAGNQL PSGCYANVGN LLHTAMKGGV
DDEVSLTAYV TAALLEMGKD VDDPMVSQGL RCLKNSATST TNLYTQALLA YIFSLAGEMD
IRNILLKQLD QQAIISGESI YWSQKPTPSS NASPWSEPAA VDVELTAYAL LAQLTKPSLT
QKEIAKATSI VAWLAKQHNA YGGFSSTQDT VVALQALAKY ATTAYMPSEE INLVVKSTEN
FQRTFNIQSV NRLVFQQDTL PNVPGMYTLE ASGQGCVYVQ TVLRYNILPP TNMKTFSLSV
EIGKARCEQP TSPRSLTLTI HTSYVGSRSS SNMAIVEVKM LSGFSPMEGT NQLLLQQPLV
KKVEFGTDTL NIYLDELIKN TQTYTFTISQ SVLVTNLKPA TIKVYDYYLP DEQATIQYSD
PCE*

Position of stopcodon in wt / mu CDS

2892 / 2892

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

964 / 964

Position of stopcodon in wt / mu cDNA

3060 / 3060

Position of start ATG in wt / mu cDNA

169 / 169

Last intron/exon boundary

3061

Theoretical NMD boundary in CDS

2842

Length of CDS

2892

Coding sequence (CDS) position

1234

cDNA position

1402

gDNA position

31624

Chromosomal position

8854244

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:

12:8854244G>A_1_ENST00000299698

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

Chr12:8854244G>A (GRCh38)

Gene symbol

A2ML1

Gene constraints

LOEUF: 0.95, LOF (oe): 0.83, misssense (oe): 0.89, synonymous (oe): 0.93 ? (gnomAD)

Ensembl transcript ID

ENST00000299698.12

Genbank transcript ID

NM_144670 (exact from MANE)

UniProt / AlphaMissense peptide

A2ML1_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.2707G>A
g.31624G>A

AA changes

AAE:	V903I	?
Score:	29

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs1416944345
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	16	16

Protein conservation

Species	Match	AA	Alignment
Human		903	G	R	S	D	T	L	I	K	P	V	L	V	K	P	E	G	V	L	V	E	K	T	H	S
mutated	all conserved	903										V	L	I	K	P	E	G	V	L	V	E	K	T	H
Ptroglodytes	all identical	903										V	L	V	K	P	E	G	V	L	V	E	K	T	H
Mmulatta	all identical	903										V	L	V	K	P	E	G	V	L	V	E	K	T	H
Fcatus	all identical	895						L	I	K	P	V	L	V	K	P	E	G	V	L	V	E	K	T	H
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
18	1454	CHAIN		lost
894	904	STRAND		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.09	0.996
	5.816	1
(flanking)	6.083	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

6

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

12

Strand

1

Original gDNA sequence snippet

CGCTCATCAAGCCAGTTCTCGTCAAAGTGAGTTTTCTTCAG

Altered gDNA sequence snippet

CGCTCATCAAGCCAGTTCTCATCAAAGTGAGTTTTCTTCAG

Original cDNA sequence snippet

CGCTCATCAAGCCAGTTCTCGTCAAACCTGAGGGAGTCCTG

Altered cDNA sequence snippet

CGCTCATCAAGCCAGTTCTCATCAAACCTGAGGGAGTCCTG

Wildtype AA sequence

MWAQLLLGML ALSPAIAEEL PNYLVTLPAR LNFPSVQKVC LDLSPGYSDV KFTVTLETKD
KTQKLLEYSG LKKRHLHCIS FLVPPPAGGT EEVATIRVSG VGNNISFEEK KKVLIQRQGN
GTFVQTDKPL YTPGQQVYFR IVTMDSNFVP VNDKYSMVEL QDPNSNRIAQ WLEVVPEQGI
VDLSFQLAPE AMLGTYTVAV AEGKTFGTFS VEEYVLPKFK VEVVEPKELS TVQESFLVKI
CCRYTYGKPM LGAVQVSVCQ KANTYWYREV EREQLPDKCR NLSGQTDKTG CFSAPVDMAT
FDLIGYAYSH QINIVATVVE EGTGVEANAT QNIYISPQMG SMTFEDTSNF YHPNFPFSGK
IRVRGHDDSF LKNHLVFLVI YGTNGTFNQT LVTDNNGLAP FTLETSGWNG TDVSLEGKFQ
MEDLVYNPEQ VPRYYQNAYL HLRPFYSTTR SFLGIHRLNG PLKCGQPQEV LVDYYIDPAD
ASPDQEISFS YYLIGKGSLV MEGQKHLNSK KKGLKASFSL SLTFTSRLAP DPSLVIYAIF
PSGGVVADKI QFSVEMCFDN QVSLGFSPSQ QLPGAEVELQ LQAAPGSLCA LRAVDESVLL
LRPDRELSNR SVYGMFPFWY GHYPYQVAEY DQCPVSGPWD FPQPLIDPMP QGHSSQRSII
WRPSFSEGTD LFSFFRDVGL KILSNAKIKK PVDCSHRSPE YSTAMGAGGG HPEAFESSTP
LHQAEDSQVR QYFPETWLWD LFPIGNSGKE AVHVTVPDAI TEWKAMSFCT SQSRGFGLSP
TVGLTAFKPF FVDLTLPYSV VRGESFRLTA TIFNYLKDCI RVQTDLAKSH EYQLESWADS
QTSSCLCADD AKTHHWNITA VKLGHINFTI STKILDSNEP CGGQKGFVPQ KGRSDTLIKP
VLVKPEGVLV EKTHSSLLCP KGKVASESVS LELPVDIVPD STKAYVTVLG DIMGTALQNL
DGLVQMPSGC GEQNMVLFAP IIYVLQYLEK AGLLTEEIRS RAVGFLEIGY QKELMYKHSN
GSYSAFGERD GNGNTWLTAF VTKCFGQAQK FIFIDPKNIQ DALKWMAGNQ LPSGCYANVG
NLLHTAMKGG VDDEVSLTAY VTAALLEMGK DVDDPMVSQG LRCLKNSATS TTNLYTQALL
AYIFSLAGEM DIRNILLKQL DQQAIISGES IYWSQKPTPS SNASPWSEPA AVDVELTAYA
LLAQLTKPSL TQKEIAKATS IVAWLAKQHN AYGGFSSTQD TVVALQALAK YATTAYMPSE
EINLVVKSTE NFQRTFNIQS VNRLVFQQDT LPNVPGMYTL EASGQGCVYV QTVLRYNILP
PTNMKTFSLS VEIGKARCEQ PTSPRSLTLT IHTSYVGSRS SSNMAIVEVK MLSGFSPMEG
TNQLLLQQPL VKKVEFGTDT LNIYLDELIK NTQTYTFTIS QSVLVTNLKP ATIKVYDYYL
PDEQATIQYS DPCE*

Mutated AA sequence

MWAQLLLGML ALSPAIAEEL PNYLVTLPAR LNFPSVQKVC LDLSPGYSDV KFTVTLETKD
KTQKLLEYSG LKKRHLHCIS FLVPPPAGGT EEVATIRVSG VGNNISFEEK KKVLIQRQGN
GTFVQTDKPL YTPGQQVYFR IVTMDSNFVP VNDKYSMVEL QDPNSNRIAQ WLEVVPEQGI
VDLSFQLAPE AMLGTYTVAV AEGKTFGTFS VEEYVLPKFK VEVVEPKELS TVQESFLVKI
CCRYTYGKPM LGAVQVSVCQ KANTYWYREV EREQLPDKCR NLSGQTDKTG CFSAPVDMAT
FDLIGYAYSH QINIVATVVE EGTGVEANAT QNIYISPQMG SMTFEDTSNF YHPNFPFSGK
IRVRGHDDSF LKNHLVFLVI YGTNGTFNQT LVTDNNGLAP FTLETSGWNG TDVSLEGKFQ
MEDLVYNPEQ VPRYYQNAYL HLRPFYSTTR SFLGIHRLNG PLKCGQPQEV LVDYYIDPAD
ASPDQEISFS YYLIGKGSLV MEGQKHLNSK KKGLKASFSL SLTFTSRLAP DPSLVIYAIF
PSGGVVADKI QFSVEMCFDN QVSLGFSPSQ QLPGAEVELQ LQAAPGSLCA LRAVDESVLL
LRPDRELSNR SVYGMFPFWY GHYPYQVAEY DQCPVSGPWD FPQPLIDPMP QGHSSQRSII
WRPSFSEGTD LFSFFRDVGL KILSNAKIKK PVDCSHRSPE YSTAMGAGGG HPEAFESSTP
LHQAEDSQVR QYFPETWLWD LFPIGNSGKE AVHVTVPDAI TEWKAMSFCT SQSRGFGLSP
TVGLTAFKPF FVDLTLPYSV VRGESFRLTA TIFNYLKDCI RVQTDLAKSH EYQLESWADS
QTSSCLCADD AKTHHWNITA VKLGHINFTI STKILDSNEP CGGQKGFVPQ KGRSDTLIKP
VLIKPEGVLV EKTHSSLLCP KGKVASESVS LELPVDIVPD STKAYVTVLG DIMGTALQNL
DGLVQMPSGC GEQNMVLFAP IIYVLQYLEK AGLLTEEIRS RAVGFLEIGY QKELMYKHSN
GSYSAFGERD GNGNTWLTAF VTKCFGQAQK FIFIDPKNIQ DALKWMAGNQ LPSGCYANVG
NLLHTAMKGG VDDEVSLTAY VTAALLEMGK DVDDPMVSQG LRCLKNSATS TTNLYTQALL
AYIFSLAGEM DIRNILLKQL DQQAIISGES IYWSQKPTPS SNASPWSEPA AVDVELTAYA
LLAQLTKPSL TQKEIAKATS IVAWLAKQHN AYGGFSSTQD TVVALQALAK YATTAYMPSE
EINLVVKSTE NFQRTFNIQS VNRLVFQQDT LPNVPGMYTL EASGQGCVYV QTVLRYNILP
PTNMKTFSLS VEIGKARCEQ PTSPRSLTLT IHTSYVGSRS SSNMAIVEVK MLSGFSPMEG
TNQLLLQQPL VKKVEFGTDT LNIYLDELIK NTQTYTFTIS QSVLVTNLKP ATIKVYDYYL
PDEQATIQYS DPCE*

Position of stopcodon in wt / mu CDS

4365 / 4365

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

1455 / 1455

Position of stopcodon in wt / mu cDNA

4396 / 4396

Position of start ATG in wt / mu cDNA

32 / 32

Last intron/exon boundary

4397

Theoretical NMD boundary in CDS

4315

Length of CDS

4365

Coding sequence (CDS) position

2707

cDNA position

2738

gDNA position

31624

Chromosomal position

8854244

Speed

0.08 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