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: ENST00000392027
MT speed 0.13 s - this script 2.601665 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
ENST00000392027(MANE Select)	ALPP	Benign	44\|56	simple_aae		No				Single base exchange		Normal	Amino acid sequence changed Protein features (might be) affected

MutationT@ster 2025

Variant:

2:232380220G>A_1_ENST00000392027

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Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 44|56 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr2:232380220G>A (GRCh38)

Gene symbol

ALPP

Gene constraints

LOEUF: 1.12, LOF (oe): 0.85, misssense (oe): 0.84, synonymous (oe): 0.86 ? (gnomAD)

Ensembl transcript ID

ENST00000392027.3

Genbank transcript ID

NM_001632 (exact from MANE)

UniProt / AlphaMissense peptide

PPB1_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.692G>A
g.1497G>A

AA changes

AAE:	R231H	?
Score:	29

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs1048988
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	8	8

Protein conservation

Species	Match	AA	Alignment
Human		231	V	I	L	G	G	G	R	K	Y	M	F	R	M	G	T	P	D	P	E	Y	P	D	D	Y
mutated	not conserved	231	V	I	L	G	G	G	R	K	Y	M	F	H	M	G	T	P	D	P	E	Y	P
Ptroglodytes	all identical	230	V	I	L	G	G	G	R	K	Y	M	F	R	M	G	T	P	D	P	E	Y	P
Mmulatta	no homologue
Fcatus	not conserved	229	V	I	L	G	G	G	R	K	Y	M	F	P	K	G	T	P	D	P	E	Y	P	S	D
Mmusculus	not conserved	227	V	I	L	G	G	G	R	K	F	M	F	P	K	G	T	P	D	Q	E	Y	P
Ggallus	not conserved	229	V	I	M	G	G	G	R	V	Y	M	T	P	A	G	T	P	D	P	E	Y	P	E	Y
Trubripes	not conserved	234	V	I	L	G	G	G	R	Q	Y	M	Y	P	K	T	M	Q	D	P	E	Y	P	-	-
Drerio	no homologue
Dmelanogaster	all identical	1266	V	I	M	G	G	G	R	S	Y	-	F	R	-	-	-	-	D	Q	S	Q	H	D	E
Celegans	no homologue
Xtropicalis	no homologue

Protein features

Start (aa)	End (aa)	Feature	Details
23	506	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	4.461	0.964
	2.945	0.956
(flanking)	-0.99	0

?

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

2

Strand

1

Original gDNA sequence snippet

AGGCCGAAAGTACATGTTTCGCATGGGAACCCCAGACCCTG

Altered gDNA sequence snippet

AGGCCGAAAGTACATGTTTCACATGGGAACCCCAGACCCTG

Original cDNA sequence snippet

AGGCCGAAAGTACATGTTTCGCATGGGAACCCCAGACCCTG

Altered cDNA sequence snippet

AGGCCGAAAGTACATGTTTCACATGGGAACCCCAGACCCTG

Wildtype AA sequence

MLGPCMLLLL LLLGLRLQLS LGIIPVEEEN PDFWNREAAE ALGAAKKLQP AQTAAKNLII
FLGDGMGVST VTAARILKGQ KKDKLGPEIP LAMDRFPYVA LSKTYNVDKH VPDSGATATA
YLCGVKGNFQ TIGLSAAARF NQCNTTRGNE VISVMNRAKK AGKSVGVVTT TRVQHASPAG
TYAHTVNRNW YSDADVPASA RQEGCQDIAT QLISNMDIDV ILGGGRKYMF RMGTPDPEYP
DDYSQGGTRL DGKNLVQEWL AKRQGARYVW NRTELMQASL DPSVTHLMGL FEPGDMKYEI
HRDSTLDPSL MEMTEAALRL LSRNPRGFFL FVEGGRIDHG HHESRAYRAL TETIMFDDAI
ERAGQLTSEE DTLSLVTADH SHVFSFGGYP LRGSSIFGLA PGKARDRKAY TVLLYGNGPG
YVLKDGARPD VTESESGSPE YRQQSAVPLD EETHAGEDVA VFARGPQAHL VHGVQEQTFI
AHVMAFAACL EPYTACDLAP PAGTTDAAHP GRSVVPALLP LLAGTLLLLE TATAP*

Mutated AA sequence

MLGPCMLLLL LLLGLRLQLS LGIIPVEEEN PDFWNREAAE ALGAAKKLQP AQTAAKNLII
FLGDGMGVST VTAARILKGQ KKDKLGPEIP LAMDRFPYVA LSKTYNVDKH VPDSGATATA
YLCGVKGNFQ TIGLSAAARF NQCNTTRGNE VISVMNRAKK AGKSVGVVTT TRVQHASPAG
TYAHTVNRNW YSDADVPASA RQEGCQDIAT QLISNMDIDV ILGGGRKYMF HMGTPDPEYP
DDYSQGGTRL DGKNLVQEWL AKRQGARYVW NRTELMQASL DPSVTHLMGL FEPGDMKYEI
HRDSTLDPSL MEMTEAALRL LSRNPRGFFL FVEGGRIDHG HHESRAYRAL TETIMFDDAI
ERAGQLTSEE DTLSLVTADH SHVFSFGGYP LRGSSIFGLA PGKARDRKAY TVLLYGNGPG
YVLKDGARPD VTESESGSPE YRQQSAVPLD EETHAGEDVA VFARGPQAHL VHGVQEQTFI
AHVMAFAACL EPYTACDLAP PAGTTDAAHP GRSVVPALLP LLAGTLLLLE TATAP*

Position of stopcodon in wt / mu CDS

1608 / 1608

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

536 / 536

Position of stopcodon in wt / mu cDNA

1660 / 1660

Position of start ATG in wt / mu cDNA

53 / 53

Last intron/exon boundary

1361

Theoretical NMD boundary in CDS

1258

Length of CDS

1608

Coding sequence (CDS) position

692

cDNA position

744

gDNA position

1497

Chromosomal position

232380220

Speed

0.13 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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