MutationT@ster 2025

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Querying Taster for transcript #1: ENST00000261921
MT speed 0.11 s - this script 2.5624 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
ENST00000261921(MANE Select)	LOXL1	Benign	44\|56	simple_aae		No				Single base exchange		Normal	Amino acid sequence changed Homozygous in gnomAD Protein features (might be) affected

MutationT@ster 2025

Variant:

15:73927241G>A_1_ENST00000261921

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Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Homozygous in gnomAD
Protein features (might be) affected

Model: simple_aae
Tree vote: 44|56 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr15:73927241G>A (GRCh38)

Gene symbol

LOXL1

Gene constraints

LOEUF: 1.06, LOF (oe): 0.76, misssense (oe): 1.14, synonymous (oe): 1.28 ? (gnomAD)

Ensembl transcript ID

ENST00000261921.8

Genbank transcript ID

NM_005576 (exact from MANE)

UniProt / AlphaMissense peptide

LOXL1_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.458G>A
g.1253G>A

AA changes

AAE:	G153D	?
Score:	94

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs3825942
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	25880	>32000	>32000

Protein conservation

Species	Match	AA	Alignment
Human		153	A	R	T	S	V	S	Q	Q	R	H	G	G	S	A	S	S	V	S	A	S	A	F	A	S
mutated	not conserved	153	A	R	T	S	V	S	Q	Q	R	H	G	D	S	A	S	S	V	S	A	S	A	F	A
Ptroglodytes	all identical	153	A	R	T	S	V	S	Q	Q	R	H	G	G	S	A	S	S	V	S	A	S	A	F	A
Mmulatta	all identical	153	A	R	T	S	V	S	Q	Q	R	H	G	G	S	A	S	S	V	S	A	S	A	F	A
Fcatus	all identical	153	V	R	T	S	V	S	Q	Q	R	H	G	G	S	A	S	S	V	S	A	S	A	F	A
Mmusculus	all identical	153	A	R	T	S	V	S	Q	Q	R	H	G	G	S	A	S	SS	V	S	A	S	A	F	A
Ggallus	not conserved	6							R	Q	P	S	S	S	S	A	A	S	A	A	A	S	S	F	A
Trubripes	all identical	142	G	S	S	S	I	P	F	R	P	S	A	G	S	S	S	S	S	S	S	S	S	S	F
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

Start (aa)	End (aa)	Feature	Details
96	574	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.109	0.047
	0.949	0.052
(flanking)	0.144	0.001

?

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

CTCCCAGCAACGGCACGGGGGCTCCGCCTCCTCGGTCTCGG

Altered gDNA sequence snippet

CTCCCAGCAACGGCACGGGGACTCCGCCTCCTCGGTCTCGG

Original cDNA sequence snippet

CTCCCAGCAACGGCACGGGGGCTCCGCCTCCTCGGTCTCGG

Altered cDNA sequence snippet

CTCCCAGCAACGGCACGGGGACTCCGCCTCCTCGGTCTCGG

Wildtype AA sequence

MALARGSRQL GALVWGACLC VLVHGQQAQP GQGSDPARWR QLIQWENNGQ VYSLLNSGSE
YVPAGPQRSE SSSRVLLAGA PQAQQRRSHG SPRRRQAPSL PLPGRVGSDT VRGQARHPFG
FGQVPDNWRE VAVGDSTGMA RARTSVSQQR HGGSASSVSA SAFASTYRQQ PSYPQQFPYP
QAPFVSQYEN YDPASRTYDQ GFVYYRPAGG GVGAGAAAVA SAGVIYPYQP RARYEEYGGG
EELPEYPPQG FYPAPERPYV PPPPPPPDGL DRRYSHSLYS EGTPGFEQAY PDPGPEAAQA
HGGDPRLGWY PPYANPPPEA YGPPRALEPP YLPVRSSDTP PPGGERNGAQ QGRLSVGSVY
RPNQNGRGLP DLVPDPNYVQ ASTYVQRAHL YSLRCAAEEK CLASTAYAPE ATDYDVRVLL
RFPQRVKNQG TADFLPNRPR HTWEWHSCHQ HYHSMDEFSH YDLLDAATGK KVAEGHKASF
CLEDSTCDFG NLKRYACTSH TQGLSPGCYD TYNADIDCQW IDITDVQPGN YILKVHVNPK
YIVLESDFTN NVVRCNIHYT GRYVSATNCK IVQS*

Mutated AA sequence

MALARGSRQL GALVWGACLC VLVHGQQAQP GQGSDPARWR QLIQWENNGQ VYSLLNSGSE
YVPAGPQRSE SSSRVLLAGA PQAQQRRSHG SPRRRQAPSL PLPGRVGSDT VRGQARHPFG
FGQVPDNWRE VAVGDSTGMA RARTSVSQQR HGDSASSVSA SAFASTYRQQ PSYPQQFPYP
QAPFVSQYEN YDPASRTYDQ GFVYYRPAGG GVGAGAAAVA SAGVIYPYQP RARYEEYGGG
EELPEYPPQG FYPAPERPYV PPPPPPPDGL DRRYSHSLYS EGTPGFEQAY PDPGPEAAQA
HGGDPRLGWY PPYANPPPEA YGPPRALEPP YLPVRSSDTP PPGGERNGAQ QGRLSVGSVY
RPNQNGRGLP DLVPDPNYVQ ASTYVQRAHL YSLRCAAEEK CLASTAYAPE ATDYDVRVLL
RFPQRVKNQG TADFLPNRPR HTWEWHSCHQ HYHSMDEFSH YDLLDAATGK KVAEGHKASF
CLEDSTCDFG NLKRYACTSH TQGLSPGCYD TYNADIDCQW IDITDVQPGN YILKVHVNPK
YIVLESDFTN NVVRCNIHYT GRYVSATNCK IVQS*

Position of stopcodon in wt / mu CDS

1725 / 1725

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

575 / 575

Position of stopcodon in wt / mu cDNA

2047 / 2047

Position of start ATG in wt / mu cDNA

323 / 323

Last intron/exon boundary

2040

Theoretical NMD boundary in CDS

1667

Length of CDS

1725

Coding sequence (CDS) position

458

cDNA position

780

gDNA position

1253

Chromosomal position

73927241

Speed

0.11 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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