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: ENST00000309889
Querying Taster for transcript #2: ENST00000578283
MT speed 0.46 s - this script 2.951803 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
ENST00000578283	TCAP	Deleterious	10\|0	complex_aae		No	Yes		E12Rfs*20	Insertion		NMD	Amino acid sequence changed Frameshift Known disease mutation: ClinVar ID 448649 (pathogenic) NMD
ENST00000309889(MANE Select)	TCAP	Deleterious	10\|0	complex_aae		No	Yes		E12Rfs*20	Insertion		Strongly truncated protein, might cause NMD (-137 AA / more than 10% missing)	Amino acid sequence changed Frameshift Known disease mutation: ClinVar ID 448649 (pathogenic) Protein features (might be) affected Truncated protein (might cause NMD)

MutationT@ster 2025

Variant:

17:39665382G>GCGAGGTGT_2_ENST00000578283

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Frameshift
Known disease mutation: ClinVar ID 448649 (pathogenic)
NMD

Model: complex_aae
Tree vote: 10|0 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr17:39665382_39665383insCGAGGTGT (GRCh38)

Gene symbol

TCAP

Gene constraints

LOEUF: 1.32, LOF (oe): 0.84, misssense (oe): 0.94, synonymous (oe): 1.03 ? (gnomAD)

Ensembl transcript ID

ENST00000578283.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Insertion

Gene region

CDS

DNA changes

c.23_24insCGAGGTGT
g.34_35insCGAGGTGT

AA changes

E12Rfs*20

Frameshift

Yes

Length of protein

NMD

Pathogenic variant (ClinVar)

Autosomal recessive limb-girdle muscular dystrophy type 2G
Hypertrophic cardiomyopathy 25
Primary familial hypertrophic cardiomyopathy

pathogenic

ClinVar OMIM

Variant DBs

dbSNP ID	rs778568339
gnomAD	homozygous (CGAGGTGT/CGAGGTGT)	heterozygous	allele carriers
	0	22	22

Protein conservation

Species	Match	AA	Alignment
Human		12	M	A	T	S	E	L	S	C	E	V	S	E	E	N	C	E	R	R	E	A	F	W	A	E
mutated	no alignment	n/a
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	5.792	1
(flanking)	1.083	0.953

?

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

17

Strand

1

Original gDNA sequence snippet

GCTACCTCAGAGCTGAGCTGCGAGGTGTCGGAGGAGAACT

Altered gDNA sequence snippet

GCTACCTCAGAGCTGAGCTGCGAGGTGTCGAGGTGTCGGAGGAGAACT

Original cDNA sequence snippet

GCTACCTCAGAGCTGAGCTGCGAGGTGTCGGAGGAGAACT

Altered cDNA sequence snippet

GCTACCTCAGAGCTGAGCTGCGAGGTGTCGAGGTGTCGGAGGAGAACT

Wildtype AA sequence

MATSELSCEV SEENCERREA FWAEWKDLTL STRPEEGCSL HEEDTQRHET YHQQGQCQLP
YQRVLPLPIF TPAKMGATKE EREDTPIQLQ ELLALETALG GQCVDRQEVA EITKQLPPVV
PVSKPGALRR SLSRSMSQEA QRG*

Mutated AA sequence

MATSELSCEV SRCRRRTVSA GRPSGQNGRI *

Position of stopcodon in wt / mu CDS

432 / 93

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

144 / 31

Position of stopcodon in wt / mu cDNA

443 / 104

Position of start ATG in wt / mu cDNA

12 / 12

Last intron/exon boundary

185

Theoretical NMD boundary in CDS

123

Length of CDS

432

Coding sequence (CDS) position

23 / 24

cDNA position

34 / 35

gDNA position

34 / 35

Chromosomal position

39665382 / 39665383

Speed

0.11 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

MutationT@ster 2025

Variant:

17:39665382G>GCGAGGTGT_1_ENST00000309889

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Frameshift
Known disease mutation: ClinVar ID 448649 (pathogenic)
Protein features (might be) affected
Truncated protein (might cause NMD)

Model: complex_aae
Tree vote: 10|0 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr17:39665382_39665383insCGAGGTGT (GRCh38)

Gene symbol

TCAP

Gene constraints

LOEUF: 1.37, LOF (oe): 0.88, misssense (oe): 0.94, synonymous (oe): 1.03 ? (gnomAD)

Ensembl transcript ID

ENST00000309889.3

Genbank transcript ID

NM_003673 (exact from MANE)

UniProt / AlphaMissense peptide

TELT_HUMAN | AlphaMissense: transcript, gene

Variant type

Insertion

Gene region

CDS

DNA changes

c.23_24insCGAGGTGT
g.34_35insCGAGGTGT

AA changes

E12Rfs*20

Frameshift

Yes

Length of protein

Strongly truncated protein, might cause NMD (-137 AA / more than 10% missing)

Pathogenic variant (ClinVar)

Autosomal recessive limb-girdle muscular dystrophy type 2G
Hypertrophic cardiomyopathy 25
Primary familial hypertrophic cardiomyopathy

pathogenic

ClinVar OMIM

Variant DBs

dbSNP ID	rs778568339
gnomAD	homozygous (CGAGGTGT/CGAGGTGT)	heterozygous	allele carriers
	0	22	22

Protein conservation

Species	Match	AA	Alignment
Human		12	M	A	T	S	E	L	S	C	E	V	S	E	E	N	C	E	R	R	E	A	F	W	A	E	W	K	D	L	T	L	S	T	R	P	E	E	G	C	S	L	H	E	E	D	T	Q	R	H	E	T	Y	H	Q	Q	G	Q	C	Q	V	L	V	Q	R	S	P	W	L	M	M	R	M	G	I	L	G	R	G	L	Q	E	Y	Q	L	P	Y	Q	R	V	L	P	L	P	I	F	T	P	A	K	M	G	A	T	K	E	E	R	E	D	T	P	I	Q	L	Q	E	L	L	A	L	E	T	A	L	G	G	Q	C	V	D	R	Q	E	V	A	E
mutated	no alignment	n/a
Ptroglodytes	all conserved	12	M	A	T	S	E	L	S	C	E	V	S	E	E	N	C	E	R	R	E	A	F	W	A	E	W	K	D	L	T	L	S	T	R	P	E	E	G	C	S	L	H	E	E	D	T	Q	R	H	E	T	Y	H	Q	Q	G	Q	C	Q	V	L	V	Q	R	S	P	W	L	V	M	R	M	G	I	L	G	R	G	L	Q	E	Y	Q	L	P	Y	Q	R	V	L	P	L	P	I	F	T	P	A	K	M	G	A	T	K	E	E	R	E	D	T	P	I	Q	L	Q	E	L	L	A	L	E
Mmulatta	no homologue
Fcatus	partly conserved	12	M	A	T	T	E	L	S	C	Q	V	S	E	E	D	C	E	R	R	E	A	F	W	A	E	W	K	D	L	T	L	S	T	R	P	E	E	G	C	S	L	H	E	E	D	T	Q	R	H	E	T	Y	H	R	Q	G	Q	C	Q	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	L	P	Y	Q	R	V	L	P	L	P	I	F	T	P	A	K	M	G	A	A	K	E	E	R	E	D	T	P	L	Q	L	R	E	L	L	A	L	E
Mmusculus	partly conserved	12	M	A	T	S	E	L	S	C	Q	V	S	E	E	N	Q	E	R	R	E	A	F	W	A	E	W	K	D	L	T	L	S	T	R	P	E	E	G	C	S	L	H	E	E	D	T	Q	R	H	E	T	Y	H	R	Q	G	Q	C	Q	A	V	V	Q	R	S	P	W	L	V	M	R	L	G	I	L	G	R	G	L	Q	E	Y	Q	L	P	Y	Q	R	V	L	P	L	P	I	F	T	P	T	K	V	G	A	S	K	E	E	R	E	E	T	P	I	Q	L	R	E	L	L	A	L	E
Ggallus	partly conserved	25	L	C	N	A	S	L	G	C	R	V	K	E	E	D	T	G	R	R	E	S	F	S	A	E	W	L	D	L	E	L	S	T	R	P	E	E	G	W	C	R	R	E	V	D	Q	Q	R	R	E	S	L	E	Q	R	G	E	T	R	V	L	T	Q	R	S	P	W	G	V	V	R	V	G	V	L	G	Q	P	L	A	Q	H	L	L	P	Y	A	R	T	L	P	L	P	L	F	A	P	S	D	L	R	G	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-
Trubripes	partly conserved	25				A	E	L	T	C	S	L	R	E	E	N	K	A	Q	R	E	S	Y	N	A	E	W	N	C	V	S	L	K	T	Q	P	Q	D	R	Q	T	M	H	L	N	D	V	S	R	R	E	T	L	S	R	Q	W	Q	A	R	S	L	K	Q	Q	T	C	P	S	G	V	F	R	V	G	T	L	E	Q	G	V	R	E	H	Q	L	L	P	K	R	N	T	L	P	L	P	I	F	M	P	T	E	L	G	V	R	L	G	R	G	A	P	H	T	E	Q	D	L	P	P	F	P	I	P	D
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	partly conserved	23				T	E	L	S	C	R	V	Q	E	D	N	T	A	R	R	E	H	F	S	A	E	W	I	D	T	S	M	F	S	R	P	E	E	S	C	N	A	R	D	A	N	V	W	R	R	E	S	F	R	Q	Q	G	Q	T	R	F	L	V	Q	Q	S	P	A	Q	V	M	K	M	G	R	L	G	Q	R	L	T	Q	Y	Q	L	P	Y	Q	R	M	L	P	L	P	I	F	K	P	A	D	L	-	S	T	K	M	E	R	I	A	T	P	P	Q	L	R	G	M	M	E	F	E	R	A	L

Protein features

Start (aa)	End (aa)	Feature	Details
1	167	CHAIN		lost
4	14	STRAND		lost
15	18	TURN		lost
19	33	STRAND		lost
35	37	HELIX		lost
38	44	STRAND		lost
39	39	MOD_RES	Phosphoserine	lost
45	48	TURN		lost
49	55	STRAND		lost
57	62	STRAND		lost
67	73	STRAND		lost
78	84	STRAND		lost
144	167	REGION		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	5.792	1
(flanking)	1.083	0.953

?

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

17

Strand

1

Original gDNA sequence snippet

GCTACCTCAGAGCTGAGCTGCGAGGTGTCGGAGGAGAACT

Altered gDNA sequence snippet

GCTACCTCAGAGCTGAGCTGCGAGGTGTCGAGGTGTCGGAGGAGAACT

Original cDNA sequence snippet

GCTACCTCAGAGCTGAGCTGCGAGGTGTCGGAGGAGAACT

Altered cDNA sequence snippet

GCTACCTCAGAGCTGAGCTGCGAGGTGTCGAGGTGTCGGAGGAGAACT

Wildtype AA sequence

MATSELSCEV SEENCERREA FWAEWKDLTL STRPEEGCSL HEEDTQRHET YHQQGQCQVL
VQRSPWLMMR MGILGRGLQE YQLPYQRVLP LPIFTPAKMG ATKEEREDTP IQLQELLALE
TALGGQCVDR QEVAEITKQL PPVVPVSKPG ALRRSLSRSM SQEAQRG*

Mutated AA sequence

MATSELSCEV SRCRRRTVSA GRPSGQNGRI *

Position of stopcodon in wt / mu CDS

504 / 93

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

168 / 31

Position of stopcodon in wt / mu cDNA

515 / 104

Position of start ATG in wt / mu cDNA

12 / 12

Last intron/exon boundary

121

Theoretical NMD boundary in CDS

59

Length of CDS

504

Coding sequence (CDS) position

23 / 24

cDNA position

34 / 35

gDNA position

34 / 35

Chromosomal position

39665382 / 39665383

Speed

0.35 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