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: ENST00000247005
Querying Taster for transcript #2: ENST00000623882
MT speed 0.1 s - this script 2.485518 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
ENST00000247005(MANE Select)	GDF1	Deleterious	69\|31	simple_aae		No				Single base exchange		Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000623882(MANE Select)	CERS1	Benign	25\|75	3utr		No				Single base exchange		N/A

MutationT@ster 2025

Variant:

19:18868896C>T_1_ENST00000247005

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 69|31 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr19:18868896C>T (GRCh38)

Gene symbol

GDF1

Gene constraints

LOEUF: 1.97, LOF (oe): 2.23, misssense (oe): 1.50, synonymous (oe): 1.67 ? (gnomAD)

Ensembl transcript ID

ENST00000247005.8

Genbank transcript ID

NM_001492 (exact from MANE), NM_001387438 (by similarity)

UniProt / AlphaMissense peptide

GDF1_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.820G>A
g.27263G>A

AA changes

AAE:	V274M	?
Score:	21

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs1349040611
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	0	12	12

Protein conservation

Species	Match	AA	Alignment
Human		274	P	G	G	A	C	R	A	R	R	L	Y	V	S	F	R	E	V	G	W	H	R	W	V	I
mutated	all conserved	274	P	G	G	A	C	R	A	R	R	L	Y	M	S	F	R	E	V	G	W	H	R	W	V
Ptroglodytes	all identical	274	P	G	G	A	C	R	A	R	R	L	Y	V	S	F	R	E	V	G	W	H	R	W	V
Mmulatta	all identical	272	P	G	G	A	C	R	A	R	R	L	Y	V	S	F	R	E	V	G	W	H	R	W	V
Fcatus	no homologue
Mmusculus	all identical	258	P	V	G	T	C	R	T	R	R	L	H	V	S	F	R	E	V	G	W	H	R	W	V
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

Start (aa)	End (aa)	Feature	Details
254	372	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	3.918	0.999
	0.53	0.994
(flanking)	0.777	0.996

?

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

19

Strand

-1

Original gDNA sequence snippet

GTCGCGCGCGGCGGCTGTACGTGAGCTTCCGCGAGGTGGGC

Altered gDNA sequence snippet

GTCGCGCGCGGCGGCTGTACATGAGCTTCCGCGAGGTGGGC

Original cDNA sequence snippet

GTCGCGCGCGGCGGCTGTACGTGAGCTTCCGCGAGGTGGGC

Altered cDNA sequence snippet

GTCGCGCGCGGCGGCTGTACATGAGCTTCCGCGAGGTGGGC

Wildtype AA sequence

MPPPQQGPCG HHLLLLLALL LPSLPLTRAP VPPGPAAALL QALGLRDEPQ GAPRLRPVPP
VMWRLFRRRD PQETRSGSRR TSPGVTLQPC HVEELGVAGN IVRHIPDRGA PTRASEPASA
AGHCPEWTVV FDLSAVEPAE RPSRARLELR FAAAAAAAPE GGWELSVAQA GQGAGADPGP
VLLRQLVPAL GPPVRAELLG AAWARNASWP RSLRLALALR PRAPAACARL AEASLLLVTL
DPRLCHPLAR PRRDAEPVLG GGPGGACRAR RLYVSFREVG WHRWVIAPRG FLANYCQGQC
ALPVALSGSG GPPALNHAVL RALMHAAAPG AADLPCCVPA RLSPISVLFF DNSDNVVLRQ
YEDMVVDECG CR*

Mutated AA sequence

MPPPQQGPCG HHLLLLLALL LPSLPLTRAP VPPGPAAALL QALGLRDEPQ GAPRLRPVPP
VMWRLFRRRD PQETRSGSRR TSPGVTLQPC HVEELGVAGN IVRHIPDRGA PTRASEPASA
AGHCPEWTVV FDLSAVEPAE RPSRARLELR FAAAAAAAPE GGWELSVAQA GQGAGADPGP
VLLRQLVPAL GPPVRAELLG AAWARNASWP RSLRLALALR PRAPAACARL AEASLLLVTL
DPRLCHPLAR PRRDAEPVLG GGPGGACRAR RLYMSFREVG WHRWVIAPRG FLANYCQGQC
ALPVALSGSG GPPALNHAVL RALMHAAAPG AADLPCCVPA RLSPISVLFF DNSDNVVLRQ
YEDMVVDECG CR*

Position of stopcodon in wt / mu CDS

1119 / 1119

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

373 / 373

Position of stopcodon in wt / mu cDNA

2527 / 2527

Position of start ATG in wt / mu cDNA

1409 / 1409

Last intron/exon boundary

1733

Theoretical NMD boundary in CDS

274

Length of CDS

1119

Coding sequence (CDS) position

820

cDNA position

2228

gDNA position

27263

Chromosomal position

18868896

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

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MutationT@ster 2025

Variant:

19:18868896C>T_2_ENST00000623882

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Prediction:

BenignPermalink

Summary:

Model: 3utr
Tree vote: 25|75 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr19:18868896C>T (GRCh38)

Gene symbol

CERS1

Gene constraints

LOEUF: 0.68, LOF (oe): 0.43, misssense (oe): 1.07, synonymous (oe): 1.33 ? (gnomAD)

Ensembl transcript ID

ENST00000623882.4

Genbank transcript ID

NM_021267 (exact from MANE), NM_001387440 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

3'UTR

DNA changes

cDNA.2228G>A
g.27832G>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	rs1349040611
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	0	12	12

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	3.918	0.999
	0.53	0.994
(flanking)	0.777	0.996

?

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

19

Strand

-1

Original gDNA sequence snippet

GTCGCGCGCGGCGGCTGTACGTGAGCTTCCGCGAGGTGGGC

Altered gDNA sequence snippet

GTCGCGCGCGGCGGCTGTACATGAGCTTCCGCGAGGTGGGC

Original cDNA sequence snippet

GTCGCGCGCGGCGGCTGTACGTGAGCTTCCGCGAGGTGGGC

Altered cDNA sequence snippet

GTCGCGCGCGGCGGCTGTACATGAGCTTCCGCGAGGTGGGC

Wildtype AA sequence

MAAAGPAAGP TGPEPMPSYA QLVQRGWGSA LAAARGCTDC GWGLARRGLA EHAHLAPPEL
LLLALGALGW TALRSAATAR LFRPLAKRCC LQPRDAAKMP ESAWKFLFYL GSWSYSAYLL
FGTDYPFFHD PPSVFYDWTP GMAVPRDIAA AYLLQGSFYG HSIYATLYMD TWRKDSVVML
LHHVVTLILI VSSYAFRYHN VGILVLFLHD ISDVQLEFTK LNIYFKSRGG SYHRLHALAA
DLGCLSFGFS WFWFRLYWFP LKVLYATSHC SLRTVPDIPF YFFFNALLLL LTLMNLYWFL
YIVAFAAKVL TGQVHELKDL REYDTAEAQS LKPSKAEKPL RNGLVKDKRF *

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

87 / 87

Last intron/exon boundary

1733

Theoretical NMD boundary in CDS

1596

Length of CDS

1053

Coding sequence (CDS) position

N/A

cDNA position

2228

gDNA position

27832

Chromosomal position

18868896

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

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