MutationT@ster 2025

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Querying Taster for transcript #1: ENST00000258888
MT speed 0.06 s - this script 2.516092 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
ENST00000258888(MANE Select)	ALPK3	Deleterious	98\|2	simple_aae		No				Single base exchange		Normal	Amino acid sequence changed Protein features (might be) affected

MutationT@ster 2025

Variant:

15:84858223G>C_1_ENST00000258888

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 98|2 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr15:84858223G>C (GRCh38)

Gene symbol

ALPK3

Gene constraints

LOEUF: 0.87, LOF (oe): 0.74, misssense (oe): 1.01, synonymous (oe): 1.03 ? (gnomAD)

Ensembl transcript ID

ENST00000258888.6

Genbank transcript ID

NM_020778 (exact from MANE)

UniProt / AlphaMissense peptide

ALPK3_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.3485G>C
g.40868G>C

AA changes

AAE:	G1162A	?
Score:	60

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs752749949
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	0	105	105

Protein conservation

Species	Match	AA	Alignment
Human		1162	L	P	A	A	T	P	E	E	L	A	L	G	A	R	R	K	R	F	L	P	K	V	R	A
mutated	not conserved	1162	L	P	A	A	T	P	E	E	L	A	L	A	A	R	R	K	R	F	L	P	K	V	R
Ptroglodytes	all identical	1358	L	P	A	A	T	P	E	E	L	A	L	G	A	R	R	K	R	F	L	P	K	V	R
Mmulatta	all identical	1312	L	P	A	A	T	P	E	E	L	A	L	G	A	R	R	K	R	F	L	P	K	V	R
Fcatus	all identical	1106	L	P	A	A	T	P	E	E	L	A	L	G	A	R	R	K	R	F	L	P	K	V	R
Mmusculus	all identical	1146	L	P	A	A	T	P	E	E	L	A	L	G	A	R	R	K	R	F	L
Ggallus	all identical	798				A	T	P	E	E	L	A	S	G	A	R	R	K	I	Y	L	P	K	T	K
Trubripes	all identical	561	I	R	S	A	T	P	E	E	L	A	S	G	A	R	R	K	I	F	M	P	R	P	K
Drerio	no homologue
Dmelanogaster	no alignment	n/a
Celegans	no alignment	n/a
Xtropicalis	no alignment	n/a

Protein features

Start (aa)	End (aa)	Feature	Details
1	1705	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	6.911	1
	6.822	1
(flanking)	0.762	1

?

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

15

Strand

1

Original gDNA sequence snippet

ACCTGAGGAACTGGCTCTAGGGGCCCGGAGGAAGAGATTTC

Altered gDNA sequence snippet

ACCTGAGGAACTGGCTCTAGCGGCCCGGAGGAAGAGATTTC

Original cDNA sequence snippet

ACCTGAGGAACTGGCTCTAGGGGCCCGGAGGAAGAGATTTC

Altered cDNA sequence snippet

ACCTGAGGAACTGGCTCTAGCGGCCCGGAGGAAGAGATTTC

Wildtype AA sequence

MGSRRAPSRG WGAGGRSGAG GDGEDDGPVW IPSPASRSYL LSVRPETSLS SNRLSHPSSG
RSTFCSIIAQ LTEETQPLFE TTLKSRSVSE DSDVRFTCIV TGYPEPEVTW YKDDTELDRY
CGLPKYEITH QGNRHTLQLY RCREEDAAIY QASAQNSKGI VSCSGVLEVG TMTEYKIHQR
WFAKLKRKAA AKLREIEQSW KHEKAVPGEV DTLRKLSPDR FQRKRRLSGA QAPGPSVPTR
EPEGGTLAAW QEGETETAQH SGLGLINSFA SGEVTTNGEA APENGEDGEH GLLTYICDAM
ELGPQRALKE ESGAKKKKKD EESKQGLRKP ELEKAAQSRR SSENCIPSSD EPDSCGTQGP
VGVEQVQTQP RGRAARGPGS SGTDSTRKPA SAVGTPDKAQ KAPGPGPGQE VYFSLKDMYL
ENTQAVRPLG EEGPQTLSVR APGESPKGKA PLRARSEGVP GAPGQPTHSL TPQPTRPFNR
KRFAPPKPKG EATTDSKPIS SLSQAPECGA QSLGKAPPQA SVQVPTPPAR RRHGTRDSTL
QGQAGHRTPG EVLECQTTTA PTMSASSSSD VASIGVSTSG SQGIIEPMDM ETQEDGRTSA
NQRTGSKKNV QADGKIQVDG RTRGDGTQTA QRTRADRKTQ VDAGTQESKR PQSDRSAQKG
MMTQGRAETQ LETTQAGEKI QEDRKAQADK GTQEDRRMQG EKGMQGEKGT QSEGSAPTAM
EGQSEQEVAT SLGPPSRTPK LPPTAGPRAP LNIECFVQTP EGSCFPKKPG CLPRSEEAVV
TASRNHEQTV LGPLSGNLML PAQPPHEGSV EQVGGERCRG PQSSGPVEAK QEDSPFQCPK
EERPGGVPCM DQGGCPLAGL SQEVPTMPSL PGTGLTASPK AGPCSTPTSQ HGSTATFLPS
EDQVLMSSAP TLHLGLGTPT QSHPPETMAT SSEGACAQVP DVEGRTPGPR SCDPGLIDSL
KNYLLLLLKL SSTETSGAGG ESQVGAATGG LVPSATLTPT VEVAGLSPRT SRRILERVEN
NHLVQSAQTL LLSPCTSRRL TGLLDREVQA GRQALAAARG SWGPGPSSLT VPAIVVDEED
PGLASEGASE GEGEVSPEGP GLLGASQESS MAGRLGEAGG QAAPGQGPSA ESIAQEPSQE
EKFPGEALTG LPAATPEELA LGARRKRFLP KVRAAGDGEA TTPEERESPT VSPRGPRKSL
VPGSPGTPGR ERRSPTQGRK ASMLEVPRAE EELAAGDLGP SPKAGGLDTE VALDEGKQET
LAKPRKAKDL LKAPQVIRKI RVEQFPDASG SLKLWCQFFN ILSDSVLTWA KDQRPVGEVG
RSAGDEGPAA LAIVQASPVD CGVYRCTIHN EHGSASTDFC LSPEVLSGFI SREEGEVGEE
IEMTPMVFAK GLADSGCWGD KLFGRLVSEE LRGGGYGCGL RKASQAKVIY GLEPIFESGR
TCIIKVSSLL VFGPSSETSL VGRNYDVTIQ GCKIQNMSRE YCKIFAAEAR AAPGFGEVPE
IIPLYLIYRP ANNIPYATLE EDLGKPLESY CSREWGCAEA PTASGSSEAM QKCQTFQHWL
YQWTNGSFLV TDLAGVDWKM TDVQIATKLR GYQGLKESCF PALLDRFASS HQCNAYCELL
GLTPLKGPEA AHPQAKAKGS KSPSAGRKGS QLSPQPQKKG LPSPQGTRKS APSSKATPQA
SEPVTTQLLG QPPTQEEGSK AQGMR*

Mutated AA sequence

MGSRRAPSRG WGAGGRSGAG GDGEDDGPVW IPSPASRSYL LSVRPETSLS SNRLSHPSSG
RSTFCSIIAQ LTEETQPLFE TTLKSRSVSE DSDVRFTCIV TGYPEPEVTW YKDDTELDRY
CGLPKYEITH QGNRHTLQLY RCREEDAAIY QASAQNSKGI VSCSGVLEVG TMTEYKIHQR
WFAKLKRKAA AKLREIEQSW KHEKAVPGEV DTLRKLSPDR FQRKRRLSGA QAPGPSVPTR
EPEGGTLAAW QEGETETAQH SGLGLINSFA SGEVTTNGEA APENGEDGEH GLLTYICDAM
ELGPQRALKE ESGAKKKKKD EESKQGLRKP ELEKAAQSRR SSENCIPSSD EPDSCGTQGP
VGVEQVQTQP RGRAARGPGS SGTDSTRKPA SAVGTPDKAQ KAPGPGPGQE VYFSLKDMYL
ENTQAVRPLG EEGPQTLSVR APGESPKGKA PLRARSEGVP GAPGQPTHSL TPQPTRPFNR
KRFAPPKPKG EATTDSKPIS SLSQAPECGA QSLGKAPPQA SVQVPTPPAR RRHGTRDSTL
QGQAGHRTPG EVLECQTTTA PTMSASSSSD VASIGVSTSG SQGIIEPMDM ETQEDGRTSA
NQRTGSKKNV QADGKIQVDG RTRGDGTQTA QRTRADRKTQ VDAGTQESKR PQSDRSAQKG
MMTQGRAETQ LETTQAGEKI QEDRKAQADK GTQEDRRMQG EKGMQGEKGT QSEGSAPTAM
EGQSEQEVAT SLGPPSRTPK LPPTAGPRAP LNIECFVQTP EGSCFPKKPG CLPRSEEAVV
TASRNHEQTV LGPLSGNLML PAQPPHEGSV EQVGGERCRG PQSSGPVEAK QEDSPFQCPK
EERPGGVPCM DQGGCPLAGL SQEVPTMPSL PGTGLTASPK AGPCSTPTSQ HGSTATFLPS
EDQVLMSSAP TLHLGLGTPT QSHPPETMAT SSEGACAQVP DVEGRTPGPR SCDPGLIDSL
KNYLLLLLKL SSTETSGAGG ESQVGAATGG LVPSATLTPT VEVAGLSPRT SRRILERVEN
NHLVQSAQTL LLSPCTSRRL TGLLDREVQA GRQALAAARG SWGPGPSSLT VPAIVVDEED
PGLASEGASE GEGEVSPEGP GLLGASQESS MAGRLGEAGG QAAPGQGPSA ESIAQEPSQE
EKFPGEALTG LPAATPEELA LAARRKRFLP KVRAAGDGEA TTPEERESPT VSPRGPRKSL
VPGSPGTPGR ERRSPTQGRK ASMLEVPRAE EELAAGDLGP SPKAGGLDTE VALDEGKQET
LAKPRKAKDL LKAPQVIRKI RVEQFPDASG SLKLWCQFFN ILSDSVLTWA KDQRPVGEVG
RSAGDEGPAA LAIVQASPVD CGVYRCTIHN EHGSASTDFC LSPEVLSGFI SREEGEVGEE
IEMTPMVFAK GLADSGCWGD KLFGRLVSEE LRGGGYGCGL RKASQAKVIY GLEPIFESGR
TCIIKVSSLL VFGPSSETSL VGRNYDVTIQ GCKIQNMSRE YCKIFAAEAR AAPGFGEVPE
IIPLYLIYRP ANNIPYATLE EDLGKPLESY CSREWGCAEA PTASGSSEAM QKCQTFQHWL
YQWTNGSFLV TDLAGVDWKM TDVQIATKLR GYQGLKESCF PALLDRFASS HQCNAYCELL
GLTPLKGPEA AHPQAKAKGS KSPSAGRKGS QLSPQPQKKG LPSPQGTRKS APSSKATPQA
SEPVTTQLLG QPPTQEEGSK AQGMR*

Position of stopcodon in wt / mu CDS

5118 / 5118

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

1706 / 1706

Position of stopcodon in wt / mu cDNA

5215 / 5215

Position of start ATG in wt / mu cDNA

98 / 98

Last intron/exon boundary

4869

Theoretical NMD boundary in CDS

4721

Length of CDS

5118

Coding sequence (CDS) position

3485

cDNA position

3582

gDNA position

40868

Chromosomal position

84858223

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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