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: ENST00000448521
Querying Taster for transcript #2: ENST00000297283
MT speed 0.08 s - this script 2.518737 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
ENST00000297283(MANE Select)	PGAM2	Deleterious	79\|21	simple_aae		No				Single base exchange		Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000448521(MANE Select)	DBNL	Benign	22\|78	3utr		No				Single base exchange		N/A

MutationT@ster 2025

Variant:

7:44065262G>A_2_ENST00000297283

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 79|21 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr7:44065262G>A (GRCh38)

Gene symbol

PGAM2

Gene constraints

LOEUF: 1.42, LOF (oe): 1.00, misssense (oe): 0.96, synonymous (oe): 0.95 ? (gnomAD)

Ensembl transcript ID

ENST00000297283.4

Genbank transcript ID

NM_000290 (exact from MANE)

UniProt / AlphaMissense peptide

PGAM2_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.268C>T
g.306C>T

AA changes

AAE:	R90W	?
Score:	101

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs104894034
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	1	25	26

Protein conservation

Species	Match	AA	Alignment
Human		90	L	P	V	V	R	T	W	R	L	N	E	R	H	Y	G	G	L	T	G	L	N	K	A	E
mutated	not conserved	90	L	P	V	V	R	T	W	R	L	N	E	W	H	Y	G	G	L	T	G	L	N	K	A
Ptroglodytes	all identical	90	L	P	V	V	R	T	W	R	L	N	E	R	H	Y	G	G	L	T	G	L	N	K	A
Mmulatta	all identical	90	L	P	V	V	R	T	W	R	L	N	E	R	H	Y	G	G	L	T	G	L	N	K	A
Fcatus	all identical	90	L	P	V	V	R	T	W	R	L	N	E	R	H	Y	G	G	L	T	G	L	N	K	A
Mmusculus	all identical	90	V	P	V	V	R	T	W	R	L	N	E	R	H	Y	G	G	L	T	G	L	N	K	A
Ggallus	no homologue
Trubripes	all identical	91	L	P	V	I	R	T	W	R	L	N	E	R	H	Y	G	G	L	T	G	L	N	K	A
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	all identical	89	L	P	V	V	R	T	W	R	L	N	E	R	H	Y	G	G	L	T	G	L	N	K	A

Protein features

Start (aa)	End (aa)	Feature	Details
1	253	CHAIN		lost
89	92	BINDING	substrate	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	5.955	1
	2.098	1
(flanking)	1.203	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

7

Strand

-1

Original gDNA sequence snippet

GCACTTGGCGCCTCAATGAGCGGCATTACGGGGGCCTCACA

Altered gDNA sequence snippet

GCACTTGGCGCCTCAATGAGTGGCATTACGGGGGCCTCACA

Original cDNA sequence snippet

GCACTTGGCGCCTCAATGAGCGGCATTACGGGGGCCTCACA

Altered cDNA sequence snippet

GCACTTGGCGCCTCAATGAGTGGCATTACGGGGGCCTCACA

Wildtype AA sequence

MATHRLVMVR HGESTWNQEN RFCGWFDAEL SEKGTEEAKR GAKAIKDAKM EFDICYTSVL
KRAIRTLWAI LDGTDQMWLP VVRTWRLNER HYGGLTGLNK AETAAKHGEE QVKIWRRSFD
IPPPPMDEKH PYYNSISKER RYAGLKPGEL PTCESLKDTI ARALPFWNEE IVPQIKAGKR
VLIAAHGNSL RGIVKHLEGM SDQAIMELNL PTGIPIVYEL NKELKPTKPM QFLGDEETVR
KAMEAVAAQG KAK*

Mutated AA sequence

MATHRLVMVR HGESTWNQEN RFCGWFDAEL SEKGTEEAKR GAKAIKDAKM EFDICYTSVL
KRAIRTLWAI LDGTDQMWLP VVRTWRLNEW HYGGLTGLNK AETAAKHGEE QVKIWRRSFD
IPPPPMDEKH PYYNSISKER RYAGLKPGEL PTCESLKDTI ARALPFWNEE IVPQIKAGKR
VLIAAHGNSL RGIVKHLEGM SDQAIMELNL PTGIPIVYEL NKELKPTKPM QFLGDEETVR
KAMEAVAAQG KAK*

Position of stopcodon in wt / mu CDS

762 / 762

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

254 / 254

Position of stopcodon in wt / mu cDNA

800 / 800

Position of start ATG in wt / mu cDNA

39 / 39

Last intron/exon boundary

633

Theoretical NMD boundary in CDS

544

Length of CDS

762

Coding sequence (CDS) position

268

cDNA position

306

gDNA position

306

Chromosomal position

44065262

Speed

0.04 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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MutationT@ster 2025

Variant:

7:44065262G>A_1_ENST00000448521

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Prediction:

BenignPermalink

Summary:

Model: 3utr
Tree vote: 22|78 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr7:44065262G>A (GRCh38)

Gene symbol

DBNL

Gene constraints

LOEUF: 0.78, LOF (oe): 0.59, misssense (oe): 0.86, synonymous (oe): 0.92 ? (gnomAD)

Ensembl transcript ID

ENST00000448521.6

Genbank transcript ID

NM_001014436 (exact from MANE)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

3'UTR

DNA changes

cDNA.5675G>A
g.20623G>A

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs104894034
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	1	25	26

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	5.955	1
	2.098	1
(flanking)	1.203	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

polyA signal ok

AA sequence altered

N/A

Chromosome

7

Strand

1

Original gDNA sequence snippet

TGTGAGGCCCCCGTAATGCCGCTCATTGAGGCGCCAAGTGC

Altered gDNA sequence snippet

TGTGAGGCCCCCGTAATGCCACTCATTGAGGCGCCAAGTGC

Original cDNA sequence snippet

TGTGAGGCCCCCGTAATGCCGCTCATTGAGGCGCCAAGTGC

Altered cDNA sequence snippet

TGTGAGGCCCCCGTAATGCCACTCATTGAGGCGCCAAGTGC

Wildtype AA sequence

MAANLSRNGP ALQEAYVRVV TEKSPTDWAL FTYEGNSNDI RVAGTGEGGL EEMVEELNSG
KVMYAFCRVK DPNSGLPKFV LINWTGEGVN DVRKGACASH VSTMASFLKG AHVTINARAE
EDVEPECIME KVAKASGANY SFHKESGRFQ DVGPQAPVGS VYQKTNAVSE IKRVGKDSFW
AKAEKEEENR RLEEKRRAEE AQRQLEQERR ERELREAARR EQRYQEQGGE ASPQRTWEQQ
QEVVSRNRNE QESAVHPREI FKQKERAMST TSISSPQPGK LRSPFLQKQL TQPETHFGRE
PAAAISRPRA DLPAEEPAPS TPPCLVQAEE EAVYEEPPEQ ETFYEQPPLV QQQGAGSEHI
DHHIQGQGLS GQGLCARALY DYQAADDTEI SFDPENLITG IEVIDEGWWR GYGPDGHFGM
FPANYVELIE *

Mutated AA sequence

Position of stopcodon in wt / mu CDS

N/A

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

N/A

Position of stopcodon in wt / mu cDNA

N/A

Position of start ATG in wt / mu cDNA

37 / 37

Last intron/exon boundary

1189

Theoretical NMD boundary in CDS

1102

Length of CDS

1293

Coding sequence (CDS) position

N/A

cDNA position

5675

gDNA position

20623

Chromosomal position

44065262

Speed

0.04 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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