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: ENST00000366683
Querying Taster for transcript #2: ENST00000366684
Querying Taster for transcript #3: ENST00000684723
MT speed 0.57 s - this script 2.990759 s

Transcript summary:

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Transcript	Gene symbol	Prediction	Tree vote	Model	Splice site change	Known ClinVar disease mutation	Variant type	Protein length	Features at a glance
ENST00000366683	ACTA1	Deleterious	100\|0	simple_aae	No	Yes	Single base exchange	Normal	Amino acid sequence changed Known disease mutation: ClinVar ID 801630 (pathogenic)
ENST00000366684(MANE Select)	ACTA1	Deleterious	100\|0	simple_aae	No	Yes	Single base exchange	Normal	Amino acid sequence changed Known disease mutation: ClinVar ID 801630 (pathogenic) Protein features (might be) affected
ENST00000684723	ACTA1	Deleterious	100\|0	simple_aae	No	Yes	Single base exchange	Normal	Amino acid sequence changed Known disease mutation: ClinVar ID 801630 (pathogenic)

MutationT@ster 2025

Variant:

1:229431506C>A_1_ENST00000366683

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 801630 (pathogenic)

Model: simple_aae
Tree vote: 100|0 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr1:229431506C>A (GRCh38)

Gene symbol

ACTA1

Gene constraints

LOEUF: 1.03, LOF (oe): 0.74, misssense (oe): 0.31, synonymous (oe): 0.92 ? (gnomAD)

Ensembl transcript ID

ENST00000366683.4

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1049G>T
g.2599G>T

AA changes

AAE:	C350F	?
Score:	205

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Actin accumulation myopathy

pathogenic

ClinVar OMIM

Variant DBs

	Not in dbSNP
	Allele 'A' was not found in gnomAD

Protein conservation

Species	Match	AA	Alignment
Human		350	D	E	A	G	P	S	I	V	H	R	K	C	F	*
mutated	not conserved	350	D	E	A	G	P	S	I	V	H	R	K	F	F
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)	9.941	1
	7.859	1
(flanking)	9.269	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

1

Strand

-1

Original gDNA sequence snippet

TTCCATCGTCCACCGCAAATGCTTCTAGACACACTCCACCT

Altered gDNA sequence snippet

TTCCATCGTCCACCGCAAATTCTTCTAGACACACTCCACCT

Original cDNA sequence snippet

TTCCATCGTCCACCGCAAATGCTTCTAGACACACTCCACCT

Altered cDNA sequence snippet

TTCCATCGTCCACCGCAAATTCTTCTAGACACACTCCACCT

Wildtype AA sequence

MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA
QSKRGILTLK YPIEHGIITN WDDMEKIWHH TFYNELRVAP EEHPTLLTEA PLNPKANREK
MTQIMFETFN VPAMYVAIQA VLSLYASGRT TGIVLDSGDG VTHNVPIYEG YALPHAIMRL
DLAGRDLTDY LMKILTERGY SFVTTAEREI VRDIKEKLCY VALDFENEMA TAASSSSLEK
SYELPDGQVI TIGNERFRCP ETLFQPSFIG MESAGIHETT YNSIMKCDID IRKDLYANNV
MSGGTTMYPG IADRMQKEIT ALAPSTMKIK MWITKQEYDE AGPSIVHRKC F*

Mutated AA sequence

MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA
QSKRGILTLK YPIEHGIITN WDDMEKIWHH TFYNELRVAP EEHPTLLTEA PLNPKANREK
MTQIMFETFN VPAMYVAIQA VLSLYASGRT TGIVLDSGDG VTHNVPIYEG YALPHAIMRL
DLAGRDLTDY LMKILTERGY SFVTTAEREI VRDIKEKLCY VALDFENEMA TAASSSSLEK
SYELPDGQVI TIGNERFRCP ETLFQPSFIG MESAGIHETT YNSIMKCDID IRKDLYANNV
MSGGTTMYPG IADRMQKEIT ALAPSTMKIK MWITKQEYDE AGPSIVHRKF F*

Position of stopcodon in wt / mu CDS

1056 / 1056

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

352 / 352

Position of stopcodon in wt / mu cDNA

1169 / 1169

Position of start ATG in wt / mu cDNA

114 / 114

Last intron/exon boundary

1103

Theoretical NMD boundary in CDS

939

Length of CDS

1056

Coding sequence (CDS) position

1049

cDNA position

1162

gDNA position

2599

Chromosomal position

229431506

Speed

0.28 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:

1:229431506C>A_2_ENST00000366684

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 801630 (pathogenic)
Protein features (might be) affected

Model: simple_aae
Tree vote: 100|0 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr1:229431506C>A (GRCh38)

Gene symbol

ACTA1

Gene constraints

LOEUF: 0.93, LOF (oe): 0.67, misssense (oe): 0.30, synonymous (oe): 0.92 ? (gnomAD)

Ensembl transcript ID

ENST00000366684.7

Genbank transcript ID

NM_001100 (exact from MANE)

UniProt / AlphaMissense peptide

ACTS_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1127G>T
g.2599G>T

AA changes

AAE:	C376F	?
Score:	205

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Actin accumulation myopathy

pathogenic

ClinVar OMIM

Variant DBs

	Not in dbSNP
	Allele 'A' was not found in gnomAD

Protein conservation

Species	Match	AA	Alignment
Human		376	D	E	A	G	P	S	I	V	H	R	K	C	F	*
mutated	not conserved	376	D	E	A	G	P	S	I	V	H	R	K	F	F
Ptroglodytes	all identical	376	D	E	A	G	P	S	I	V	H	R	K	C	F
Mmulatta	all identical	376	D	E	A	G	P	S	I	V	H	R	K	C	F
Fcatus	no homologue
Mmusculus	all identical	376	D	E	A	G	P	S	I	V	H	R	K	C	F
Ggallus	no homologue
Trubripes	all identical	753	D	E	A	G	P	S	I	V	H	R	K	C	F	m	c	d	d	d	e	t	t	a	l
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

Start (aa)	End (aa)	Feature	Details
2	377	CHAIN		lost
3	377	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	9.941	1
	7.859	1
(flanking)	9.269	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

1

Strand

-1

Original gDNA sequence snippet

TTCCATCGTCCACCGCAAATGCTTCTAGACACACTCCACCT

Altered gDNA sequence snippet

TTCCATCGTCCACCGCAAATTCTTCTAGACACACTCCACCT

Original cDNA sequence snippet

TTCCATCGTCCACCGCAAATGCTTCTAGACACACTCCACCT

Altered cDNA sequence snippet

TTCCATCGTCCACCGCAAATTCTTCTAGACACACTCCACCT

Wildtype AA sequence

MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA
QSKRGILTLK YPIEHGIITN WDDMEKIWHH TFYNELRVAP EEHPTLLTEA PLNPKANREK
MTQIMFETFN VPAMYVAIQA VLSLYASGRT TGIVLDSGDG VTHNVPIYEG YALPHAIMRL
DLAGRDLTDY LMKILTERGY SFVTTAEREI VRDIKEKLCY VALDFENEMA TAASSSSLEK
SYELPDGQVI TIGNERFRCP ETLFQPSFIG MESAGIHETT YNSIMKCDID IRKDLYANNV
MSGGTTMYPG IADRMQKEIT ALAPSTMKIK IIAPPERKYS VWIGGSILAS LSTFQQMWIT
KQEYDEAGPS IVHRKCF*

Mutated AA sequence

MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA
QSKRGILTLK YPIEHGIITN WDDMEKIWHH TFYNELRVAP EEHPTLLTEA PLNPKANREK
MTQIMFETFN VPAMYVAIQA VLSLYASGRT TGIVLDSGDG VTHNVPIYEG YALPHAIMRL
DLAGRDLTDY LMKILTERGY SFVTTAEREI VRDIKEKLCY VALDFENEMA TAASSSSLEK
SYELPDGQVI TIGNERFRCP ETLFQPSFIG MESAGIHETT YNSIMKCDID IRKDLYANNV
MSGGTTMYPG IADRMQKEIT ALAPSTMKIK IIAPPERKYS VWIGGSILAS LSTFQQMWIT
KQEYDEAGPS IVHRKFF*

Position of stopcodon in wt / mu CDS

1134 / 1134

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

378 / 378

Position of stopcodon in wt / mu cDNA

1237 / 1237

Position of start ATG in wt / mu cDNA

104 / 104

Last intron/exon boundary

1093

Theoretical NMD boundary in CDS

939

Length of CDS

1134

Coding sequence (CDS) position

1127

cDNA position

1230

gDNA position

2599

Chromosomal position

229431506

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:

1:229431506C>A_3_ENST00000684723

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 801630 (pathogenic)

Model: simple_aae
Tree vote: 100|0 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr1:229431506C>A (GRCh38)

Gene symbol

ACTA1

Gene constraints

LOEUF: 0.90, LOF (oe): 0.62, misssense (oe): 0.30, synonymous (oe): 0.89 ? (gnomAD)

Ensembl transcript ID

ENST00000684723.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.992G>T
g.2599G>T

AA changes

AAE:	C331F	?
Score:	205

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Actin accumulation myopathy

pathogenic

ClinVar OMIM

Variant DBs

	Not in dbSNP
	Allele 'A' was not found in gnomAD

Protein conservation

Species	Match	AA	Alignment
Human		331	D	E	A	G	P	S	I	V	H	R	K	C	F	*
mutated	not conserved	331	D	E	A	G	P	S	I	V	H	R	K	F	F
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)	9.941	1
	7.859	1
(flanking)	9.269	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

1

Strand

-1

Original gDNA sequence snippet

TTCCATCGTCCACCGCAAATGCTTCTAGACACACTCCACCT

Altered gDNA sequence snippet

TTCCATCGTCCACCGCAAATTCTTCTAGACACACTCCACCT

Original cDNA sequence snippet

TTCCATCGTCCACCGCAAATGCTTCTAGACACACTCCACCT

Altered cDNA sequence snippet

TTCCATCGTCCACCGCAAATTCTTCTAGACACACTCCACCT

Wildtype AA sequence

MVGMGQKDSY VGDEAQSKRG ILTLKYPIEH GIITNWDDME KIWHHTFYNE LRVAPEEHPT
LLTEAPLNPK ANREKMTQIM FETFNVPAMY VAIQAVLSLY ASGRTTGIVL DSGDGVTHNV
PIYEGYALPH AIMRLDLAGR DLTDYLMKIL TERGYSFVTT AEREIVRDIK EKLCYVALDF
ENEMATAASS SSLEKSYELP DGQVITIGNE RFRCPETLFQ PSFIGMESAG IHETTYNSIM
KCDIDIRKDL YANNVMSGGT TMYPGIADRM QKEITALAPS TMKIKIIAPP ERKYSVWIGG
SILASLSTFQ QMWITKQEYD EAGPSIVHRK CF*

Mutated AA sequence

MVGMGQKDSY VGDEAQSKRG ILTLKYPIEH GIITNWDDME KIWHHTFYNE LRVAPEEHPT
LLTEAPLNPK ANREKMTQIM FETFNVPAMY VAIQAVLSLY ASGRTTGIVL DSGDGVTHNV
PIYEGYALPH AIMRLDLAGR DLTDYLMKIL TERGYSFVTT AEREIVRDIK EKLCYVALDF
ENEMATAASS SSLEKSYELP DGQVITIGNE RFRCPETLFQ PSFIGMESAG IHETTYNSIM
KCDIDIRKDL YANNVMSGGT TMYPGIADRM QKEITALAPS TMKIKIIAPP ERKYSVWIGG
SILASLSTFQ QMWITKQEYD EAGPSIVHRK FF*

Position of stopcodon in wt / mu CDS

999 / 999

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

333 / 333

Position of stopcodon in wt / mu cDNA

1102 / 1102

Position of start ATG in wt / mu cDNA

104 / 104

Last intron/exon boundary

958

Theoretical NMD boundary in CDS

804

Length of CDS

999

Coding sequence (CDS) position

992

cDNA position

1095

gDNA position

2599

Chromosomal position

229431506

Speed

0.18 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