MutationT@ster 2025

NEVER press reload or F5 - unless you want to start from the very beginning.
Input seems to be ok - now mapping the variant to the different transcripts...
Querying Taster for transcript #1: ENST00000372808
MT speed 0.05 s - this script 2.506823 s

Transcript summary:

Permalink

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
ENST00000372808(MANE Select)	GNMT	Deleterious	87\|13	simple_aae		No				Single base exchange		Normal	Amino acid sequence changed Heterozygous in gnomAD Protein features (might be) affected

MutationT@ster 2025

Variant:

6:42963149C>A_1_ENST00000372808

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

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

Model: simple_aae
Tree vote: 87|13 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr6:42963149C>A (GRCh38)

Gene symbol

GNMT

Gene constraints

LOEUF: 1.33, LOF (oe): 0.96, misssense (oe): 0.96, synonymous (oe): 1.07 ? (gnomAD)

Ensembl transcript ID

ENST00000372808.4

Genbank transcript ID

NM_018960 (exact from MANE), NM_001318865 (by similarity), NM_001318856 (by similarity)

UniProt / AlphaMissense peptide

GNMT_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.529C>A
g.2396C>A

AA changes

AAE:	H177N	?
Score:	68

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs121907889
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	1	1227	1228

Protein conservation

Species	Match	AA	Alignment
Human		177	M	V	R	A	G	G	L	L	V	I	D	H	R	N	Y	D	H	I	L	S	T	G	C	A
mutated	all conserved	177	M	V	R	A	G	G	L	L	V	I	D	N	R	N	Y
Ptroglodytes	all identical	177	M	V	R	A	G	G	L	L	V	I	D	H	R	N	Y
Mmulatta	all identical	177	M	V	R	A	G	G	L	L	V	I	D	H	R	N	Y
Fcatus	all identical	177	M	V	R	S	G	G	L	L	V	I	D	H	R	N	Y
Mmusculus	all identical	177	M	V	R	P	G	G	L	L	V	I	D	H	R	N	Y
Ggallus	all identical	177	M	V	R	P	G	G	V	L	V	I	D	H	R	N	Y
Trubripes	all identical	178	M	V	R	P	G	G	I	L	I	I	D	H	R	N	Y	D
Drerio	no homologue
Dmelanogaster	all identical	180	C	L	K	P	G	G	V	L	L	I	D	H	R	N	Y	D	N
Celegans	no homologue
Xtropicalis	all identical	177	M	V	R	P	G	G	I	L	I	I	D	H	R	N	Y

Protein features

Start (aa)	End (aa)	Feature	Details
2	295	CHAIN		lost
167	178	STRAND		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.161	0.568
	5.505	1
(flanking)	6.743	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

6

Strand

1

Original gDNA sequence snippet

GGGGCCTACTGGTCATTGATCATCGCAACTACGACCACATC

Altered gDNA sequence snippet

GGGGCCTACTGGTCATTGATAATCGCAACTACGACCACATC

Original cDNA sequence snippet

GGGGCCTACTGGTCATTGATCATCGCAACTACGACCACATC

Altered cDNA sequence snippet

GGGGCCTACTGGTCATTGATAATCGCAACTACGACCACATC

Wildtype AA sequence

MVDSVYRTRS LGVAAEGLPD QYADGEAARV WQLYIGDTRS RTAEYKAWLL GLLRQHGCQR
VLDVACGTGV DSIMLVEEGF SVTSVDASDK MLKYALKERW NRRHEPAFDK WVIEEANWMT
LDKDVPQSAE GGFDAVICLG NSFAHLPDCK GDQSEHRLAL KNIASMVRAG GLLVIDHRNY
DHILSTGCAP PGKNIYYKSD LTKDVTTSVL IVNNKAHMVT LDYTVQVPGA GQDGSPGLSK
FRLSYYPHCL ASFTELLQAA FGGKCQHSVL GDFKPYKPGQ TYIPCYFIHV LKRTD*

Mutated AA sequence

MVDSVYRTRS LGVAAEGLPD QYADGEAARV WQLYIGDTRS RTAEYKAWLL GLLRQHGCQR
VLDVACGTGV DSIMLVEEGF SVTSVDASDK MLKYALKERW NRRHEPAFDK WVIEEANWMT
LDKDVPQSAE GGFDAVICLG NSFAHLPDCK GDQSEHRLAL KNIASMVRAG GLLVIDNRNY
DHILSTGCAP PGKNIYYKSD LTKDVTTSVL IVNNKAHMVT LDYTVQVPGA GQDGSPGLSK
FRLSYYPHCL ASFTELLQAA FGGKCQHSVL GDFKPYKPGQ TYIPCYFIHV LKRTD*

Position of stopcodon in wt / mu CDS

888 / 888

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

296 / 296

Position of stopcodon in wt / mu cDNA

902 / 902

Position of start ATG in wt / mu cDNA

15 / 15

Last intron/exon boundary

730

Theoretical NMD boundary in CDS

665

Length of CDS

888

Coding sequence (CDS) position

529

cDNA position

543

gDNA position

2396

Chromosomal position

42963149

Speed

0.05 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

Back to summary table