MutationT@ster 2025

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Querying Taster for transcript #1: ENST00000379044
MT speed 0.09 s - this script 2.534618 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
ENST00000379044(MANE Select)	ARX	Benign	3\|7	complex_aae		No				Deletion		Deletion of more than 2 AA	Amino acid sequence changed Homozygous in gnomAD Protein features (might be) affected

MutationT@ster 2025

Variant:

23:25013530GGCCGCGGCGGCCGCGGCCGCGGCT>G_1_ENST00000379044

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Prediction:

BenignPermalink

Summary:

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

Model: complex_aae
Tree vote: 3|7 (del | benign) ?
Automatic classification due to gnomAD
no values for phylogenetic conservation

Analysed issue

Analysis result

Variant

ChrX:25013531_25013554delGCCGCGGCGGCCGCGGCCGCGGCT (GRCh38)

Gene symbol

ARX

Gene constraints

no data

Ensembl transcript ID

ENST00000379044.5

Genbank transcript ID

NM_139058 (exact from MANE)

UniProt / AlphaMissense peptide

ARX_HUMAN | AlphaMissense: transcript, gene

Variant type

Deletion

Gene region

CDS

DNA changes

c.441_464delAGCCGCGGCCGCGGCCGCCGCGGC
g.2867_2890delAGCCGCGGCCGCGGCCGCCGCGGC

AA changes

deletion of more than 2 AA

AAE:	A144-	A145-	A146-	A147-	A148-	A149-	A150-	A151-	?
Score:	-	-	-	-	-	-	-	-

Frameshift

No

Length of protein

Deletion of more than 2 AA

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs398124510
gnomAD	homo-/hemizygous (-/-)	heterozygous	allele carriers
	126	306	432

Protein conservation

Species	Match	AA	Alignment
Human		144	A	R	P	G	E	R	P	D	G	A	G	A	A	A	A	A	A	A	A	A	A	A	A	W	D	T	L	K	I	S	Q
mutated	partly conserved	144	A	R	P	G	E	R	P	D	G	A	G	A	A	A	A	-	-	-	-	-	-	-	-	W	D	T	L	K	I	S
Ptroglodytes	partly conserved	144	G	T	A	G	R	R	R	G	R	R	G	R	P	L	P	A	W	F	P	A	A	-	-	W	D	T	L	K	I	S
Mmulatta	all identical	144	A	R	P	G	E	R	P	D	G	A	G	A	A	A	A	A	A	A	A	A	A	A	A	W	D	T	L	K	I	S
Fcatus	all identical	144	A	R	P	G	E	R	P	D	G	A	G	A	A	A	A	A	A	A	A	A	A	A	A	W	D	T	L	K	I	S
Mmusculus	partly conserved	145	A	R	P	G	E	R	Q	D	S	A	G	A	V	A	A	A	A	A	A	A	A	-	-	W	D	T	L	K	I	S
Ggallus	partly conserved	124	-	R	P	E	G	R	P	E	G	G	A	G	A	G	A	T	A	G	A	G	AGP	A	P	W	D	T	L	K	I	S
Trubripes	not conserved	117	-	-	-	-	-	-	-	D	H	K	E	T	L	D	R	E	R	L	L	M	E	Q	A	S	E	S	L	K	I	S
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	partly conserved	125	-	-	-	-	-	R	S	E	K	T	D	R	I	L	L	L	G	G	A	G	E	N	T	W	DNH	S	L	K	I	S

Protein features

Start (aa)	End (aa)	Feature	Details
1	562	CHAIN		lost
118	255	REGION		lost

Phylogenetic conservation

	PhyloP	PhastCons

?

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

23

Strand

-1

Original gDNA sequence snippet

GGCGCAGGGGCCGCCGCGGCAGCCGCGGCCGCGGCCGCCGCGGCCTGGGACACGCTCAAGATCA

Altered gDNA sequence snippet

GGCGCAGGGGCCGCCGCGGCCTGGGACACGCTCAAGATCA

Original cDNA sequence snippet

GGCGCAGGGGCCGCCGCGGCAGCCGCGGCCGCGGCCGCCGCGGCCTGGGACACGCTCAAGATCA

Altered cDNA sequence snippet

GGCGCAGGGGCCGCCGCGGCCTGGGACACGCTCAAGATCA

Wildtype AA sequence

MSNQYQEEGC SERPECKSKS PTLLSSYCID SILGRRSPCK MRLLGAAQSL PAPLTSRADP
EKAVQGSPKS SSAPFEAELH LPPKLRRLYG PGGGRLLQGA AAAAAAAAAA AAAAATATAG
PRGEAPPPPP PTARPGERPD GAGAAAAAAA AAAAAWDTLK ISQAPQVSIS RSKSYRENGA
PFVPPPPALD ELGGPGGVTH PEERLGVAGG PGSAPAAGGG TGTEDDEEEL LEDEEDEDEE
EELLEDDEEE LLEDDARALL KEPRRCPVAA TGAVAAAAAA AVATEGGELS PKEELLLHPE
DAEGKDGEDS VCLSAGSDSE EGLLKRKQRR YRTTFTSYQL EELERAFQKT HYPDVFTREE
LAMRLDLTEA RVQVWFQNRR AKWRKREKAG AQTHPPGLPF PGPLSATHPL SPYLDASPFP
PHHPALDSAW TAAAAAAAAA FPSLPPPPGS ASLPPSGAPL GLSTFLGAAV FRHPAFISPA
FGRLFSTMAP LTSASTAAAL LRQPTPAVEG AVASGALADP ATAAADRRAS SIAALRLKAK
EHAAQLTQLN ILPGTSTGKE VC*

Mutated AA sequence

MSNQYQEEGC SERPECKSKS PTLLSSYCID SILGRRSPCK MRLLGAAQSL PAPLTSRADP
EKAVQGSPKS SSAPFEAELH LPPKLRRLYG PGGGRLLQGA AAAAAAAAAA AAAAATATAG
PRGEAPPPPP PTARPGERPD GAGAAAAWDT LKISQAPQVS ISRSKSYREN GAPFVPPPPA
LDELGGPGGV THPEERLGVA GGPGSAPAAG GGTGTEDDEE ELLEDEEDED EEEELLEDDE
EELLEDDARA LLKEPRRCPV AATGAVAAAA AAAVATEGGE LSPKEELLLH PEDAEGKDGE
DSVCLSAGSD SEEGLLKRKQ RRYRTTFTSY QLEELERAFQ KTHYPDVFTR EELAMRLDLT
EARVQVWFQN RRAKWRKREK AGAQTHPPGL PFPGPLSATH PLSPYLDASP FPPHHPALDS
AWTAAAAAAA AAFPSLPPPP GSASLPPSGA PLGLSTFLGA AVFRHPAFIS PAFGRLFSTM
APLTSASTAA ALLRQPTPAV EGAVASGALA DPATAAADRR ASSIAALRLK AKEHAAQLTQ
LNILPGTSTG KEVC*

Position of stopcodon in wt / mu CDS

1689 / 1665

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

563 / 555

Position of stopcodon in wt / mu cDNA

1917 / 1893

Position of start ATG in wt / mu cDNA

229 / 229

Last intron/exon boundary

1676

Theoretical NMD boundary in CDS

1397

Length of CDS

1689

Coding sequence (CDS) position

440 / 465

cDNA position

668 / 693

gDNA position

2866 / 2891

Chromosomal position

25013530 / 25013555

Speed

0.09 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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