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: ENST00000297537
MT speed 0.58 s - this script 3.047959 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
ENST00000297537(MANE Select)	GBX1	Deleterious	84\|16	simple_aae		No				Single base exchange		Normal	Amino acid sequence changed Protein features (might be) affected

MutationT@ster 2025

Variant:

7:151148983T>G_1_ENST00000297537

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 84|16 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr7:151148983T>G (GRCh38)

Gene symbol

GBX1

Gene constraints

LOEUF: 0.77, LOF (oe): 0.44, misssense (oe): 1.08, synonymous (oe): 1.04 ? (gnomAD)

Ensembl transcript ID

ENST00000297537.5

Genbank transcript ID

NM_001098834 (exact from MANE)

UniProt / AlphaMissense peptide

GBX1_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.698A>C
g.25763A>C

AA changes

AAE:	K233T	?
Score:	78

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs564806375
gnomAD	homozygous (G/G)	heterozygous	allele carriers
	0	93	93

Protein conservation

Species	Match	AA	Alignment
Human		233	S	A	G	G	P	G	A	L	L	G	P	K	P	K	L	K	G	S	L	G	T	G	A	E
mutated	not conserved	233	S	A	G	G	P	G	A	L	L	G	P	T	P	K	L	K	G	S	L
Ptroglodytes	all identical	233	S	A	G	G	P	G	A	L	L	G	P	K	P	K	L	K	G	S	L
Mmulatta	all identical	232	S	A	G	G	P	G	A	L	L	G	P	K	P	K	L	K	G	S	L
Fcatus	all identical	232	S	A	G	G	P	G	A	L	L	G	P	K	P	K	L	K	G	S	L
Mmusculus	all identical	289	S	A	G	G	P	G	A	L	L	G	P	K	P	K	L	K	G	S	P
Ggallus	all identical	206	A	A	A	-	-	-	A	A	L	G	P	K	G	K	G	K	G	-	-	G	P	A	A
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	all conserved	294	D	S	E	D	C	S	D	D	E	G	A	Q	S	R	H	E	G	-	-	-	-	G	G
Celegans	no homologue
Xtropicalis	all conserved	328	-	V	G	S	P	-	-	-	-	-	P	R	P	R	N	K	G	K	-	-	-	S	A

Protein features

Start (aa)	End (aa)	Feature	Details
1	363	CHAIN		lost
128	265	REGION		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.923	0.417
	2.431	0.739
(flanking)	1.634	0.554

?

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

7

Strand

-1

Original gDNA sequence snippet

AGGGGCTCTTCTGGGACCTAAACCGAAGCTAAAGGGAAGCC

Altered gDNA sequence snippet

AGGGGCTCTTCTGGGACCTACACCGAAGCTAAAGGGAAGCC

Original cDNA sequence snippet

AGGGGCTCTTCTGGGACCTAAACCGAAGCTAAAGGGAAGCC

Altered cDNA sequence snippet

AGGGGCTCTTCTGGGACCTACACCGAAGCTAAAGGGAAGCC

Wildtype AA sequence

MQRAGGGSAP GGNGGGGGGG PGTAFSIDSL IGPPPPRSGH LLYTGYPMFM PYRPLVLPQA
LAPAPLPAGL PPLAPLASFA GRLTNTFCAG LGQAVPSMVA LTTALPSFAE PPDAFYGPQE
LAAAAAAAAA TAARNNPEPG GRRPEGGLEA DELLPAREKV AEPPPPPPPH FSETFPSLPA
EGKVYSSDEE KLEASAGDPA GSEQEEEGSG GDSEDDGFLD SSAGGPGALL GPKPKLKGSL
GTGAEEGAPV TAGVTAPGGK SRRRRTAFTS EQLLELEKEF HCKKYLSLTE RSQIAHALKL
SEVQVKIWFQ NRRAKWKRIK AGNVSSRSGE PVRNPKIVVP IPVHVNRFAV RSQHQQMEQG
ARP*

Mutated AA sequence

MQRAGGGSAP GGNGGGGGGG PGTAFSIDSL IGPPPPRSGH LLYTGYPMFM PYRPLVLPQA
LAPAPLPAGL PPLAPLASFA GRLTNTFCAG LGQAVPSMVA LTTALPSFAE PPDAFYGPQE
LAAAAAAAAA TAARNNPEPG GRRPEGGLEA DELLPAREKV AEPPPPPPPH FSETFPSLPA
EGKVYSSDEE KLEASAGDPA GSEQEEEGSG GDSEDDGFLD SSAGGPGALL GPTPKLKGSL
GTGAEEGAPV TAGVTAPGGK SRRRRTAFTS EQLLELEKEF HCKKYLSLTE RSQIAHALKL
SEVQVKIWFQ NRRAKWKRIK AGNVSSRSGE PVRNPKIVVP IPVHVNRFAV RSQHQQMEQG
ARP*

Position of stopcodon in wt / mu CDS

1092 / 1092

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

364 / 364

Position of stopcodon in wt / mu cDNA

1238 / 1238

Position of start ATG in wt / mu cDNA

147 / 147

Last intron/exon boundary

684

Theoretical NMD boundary in CDS

487

Length of CDS

1092

Coding sequence (CDS) position

698

cDNA position

844

gDNA position

25763

Chromosomal position

151148983

Speed

0.58 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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