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: ENST00000536055
Querying Taster for transcript #2: ENST00000378755
Querying Taster for transcript #3: ENST00000378756
MT speed 0.14 s - this script 2.54631 s

Transcript summary:

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Transcript	Gene symbol	Prediction	Tree vote	Model	Splice site change	Variant type	Protein length	Features at a glance
ENST00000378756(MANE Select)	ATAD3A	Deleterious	91\|9	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000536055	ATAD3A	Deleterious	94\|6	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000378755	ATAD3A	Deleterious	100\|0	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected

MutationT@ster 2025

Variant:

1:1526497G>A_3_ENST00000378756

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 91|9 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr1:1526497G>A (GRCh38)

Gene symbol

ATAD3A

Gene constraints

LOEUF: 0.86, LOF (oe): 0.67, misssense (oe): 0.93, synonymous (oe): 1.00 ? (gnomAD)

Ensembl transcript ID

ENST00000378756.8

Genbank transcript ID

NM_001170535 (exact from MANE)

UniProt / AlphaMissense peptide

ATD3A_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1303G>A
g.14336G>A

AA changes

AAE:	A435T	?
Score:	58

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs763043823
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	12	12

Protein conservation

Species	Match	AA	Alignment
Human		435	K	I	S	E	D	L	R	A	T	L	N	A	F	L	Y	R	T	G	Q	H	S	N	K	F
mutated	not conserved	435	K	I	S	E	D	L	R	A	T	L	N	T	F	L	Y	R	T	G	Q	H	S	N	K
Ptroglodytes	all identical	422							R	A	T	L	N	A	F	L	Y	R	T	G	Q	H	S	N	K
Mmulatta	all identical	435	K	I	S	E	D	L	R	A	T	L	N	A	F	L	Y	R	T	G	Q	H	S	N	K
Fcatus	all identical	434	K	I	S	E	D	L	R	A	T	L	N	A	F	L	H	R	T	G	Q	H	S	S	K
Mmusculus	all identical	434	K	I	S	E	D	L	R	A	T	L	N	A	F	L	H	R	T	G	Q	H	S	S	K
Ggallus	all identical	442	K	I	S	E	D	L	R	A	T	L	N	A	F	L	H	R	T	G	Q	H	S	N	K
Trubripes	all identical	431	K	I	S	E	D	L	R	A	T	L	N	A	F	L	Y	R	T	G	E	Q	S	N	K
Drerio	no homologue
Dmelanogaster	all identical	441	K	I	S	E	D	L	R	A	A	L	N	A	F	L	Y	R	T	S	E	Q	N	P	K
Celegans	no homologue
Xtropicalis	all identical	431	K	I	S	E	D	L	R	A	T	L	N	A	F	L	Y	R	T	G	E	Q	S	N	K

Protein features

Start (aa)	End (aa)	Feature	Details
2	634	CHAIN		lost
313	634	TOPO_DOM	Mitochondrial matrix	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-3.224	0
	8.528	1
(flanking)	6.77	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

ACCTCAGGGCCACACTGAACGCCTTCCTGTACCGCACGGGC

Altered gDNA sequence snippet

ACCTCAGGGCCACACTGAACACCTTCCTGTACCGCACGGGC

Original cDNA sequence snippet

ACCTCAGGGCCACACTGAACGCCTTCCTGTACCGCACGGGC

Altered cDNA sequence snippet

ACCTCAGGGCCACACTGAACACCTTCCTGTACCGCACGGGC

Wildtype AA sequence

MSWLFGINKG PKGEGAGPPP PLPPAQPGAE GGGDRGLGDR PAPKDKWSNF DPTGLERAAK
AARELEHSRY AKDALNLAQM QEQTLQLEQQ SKLKEYEAAV EQLKSEQIRA QAEERRKTLS
EETRQHQARA QYQDKLARQR YEDQLKQQQL LNEENLRKQE ESVQKQEAMR RATVEREMEL
RHKNEMLRVE AEARARAKAE RENADIIREQ IRLKAAEHRQ TVLESIRTAG TLFGEGFRAF
VTDWDKVTAT VAGLTLLAVG VYSAKNATLV AGRFIEARLG KPSLVRETSR ITVLEALRHP
IQVSRRLLSR PQDALEGVVL SPSLEARVRD IAIATRNTKK NRSLYRNILM YGPPGTGKTL
FAKKLALHSG MDYAIMTGGD VAPMGREGVT AMHKLFDWAN TSRRGLLLFV DEADAFLRKR
ATEKISEDLR ATLNAFLYRT GQHSNKFMLV LASNQPEQFD WAINDRINEM VHFDLPGQEE
RERLVRMYFD KYVLKPATEG KQRLKLAQFD YGRKCSEVAR LTEGMSGREI AQLAVSWQAT
AYASEDGVLT EAMMDTRVQD AVQQHQQKMC WLKAEGPGRG DEPSPS*

Mutated AA sequence

MSWLFGINKG PKGEGAGPPP PLPPAQPGAE GGGDRGLGDR PAPKDKWSNF DPTGLERAAK
AARELEHSRY AKDALNLAQM QEQTLQLEQQ SKLKEYEAAV EQLKSEQIRA QAEERRKTLS
EETRQHQARA QYQDKLARQR YEDQLKQQQL LNEENLRKQE ESVQKQEAMR RATVEREMEL
RHKNEMLRVE AEARARAKAE RENADIIREQ IRLKAAEHRQ TVLESIRTAG TLFGEGFRAF
VTDWDKVTAT VAGLTLLAVG VYSAKNATLV AGRFIEARLG KPSLVRETSR ITVLEALRHP
IQVSRRLLSR PQDALEGVVL SPSLEARVRD IAIATRNTKK NRSLYRNILM YGPPGTGKTL
FAKKLALHSG MDYAIMTGGD VAPMGREGVT AMHKLFDWAN TSRRGLLLFV DEADAFLRKR
ATEKISEDLR ATLNTFLYRT GQHSNKFMLV LASNQPEQFD WAINDRINEM VHFDLPGQEE
RERLVRMYFD KYVLKPATEG KQRLKLAQFD YGRKCSEVAR LTEGMSGREI AQLAVSWQAT
AYASEDGVLT EAMMDTRVQD AVQQHQQKMC WLKAEGPGRG DEPSPS*

Position of stopcodon in wt / mu CDS

1761 / 1761

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

587 / 587

Position of stopcodon in wt / mu cDNA

1868 / 1868

Position of start ATG in wt / mu cDNA

108 / 108

Last intron/exon boundary

1721

Theoretical NMD boundary in CDS

1563

Length of CDS

1761

Coding sequence (CDS) position

1303

cDNA position

1410

gDNA position

14336

Chromosomal position

1526497

Speed

0.06 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:

1:1526497G>A_1_ENST00000536055

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 94|6 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr1:1526497G>A (GRCh38)

Gene symbol

ATAD3A

Gene constraints

LOEUF: 0.72, LOF (oe): 0.54, misssense (oe): 0.91, synonymous (oe): 0.97 ? (gnomAD)

Ensembl transcript ID

ENST00000536055.6

Genbank transcript ID

NM_001170536 (by similarity)

UniProt / AlphaMissense peptide

ATD3A_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1066G>A
g.14336G>A

AA changes

AAE:	A356T	?
Score:	58

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs763043823
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	12	12

Protein conservation

Species	Match	AA	Alignment
Human		356	K	I	S	E	D	L	R	A	T	L	N	A	F	L	Y	R	T	G	Q	H	S	N	K	F
mutated	not conserved	356	K	I	S	E	D	L	R	A	T	L	N	T	F	L	Y	R
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

Start (aa)	End (aa)	Feature	Details
2	634	CHAIN		lost
313	634	TOPO_DOM	Mitochondrial matrix	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-3.224	0
	8.528	1
(flanking)	6.77	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

ACCTCAGGGCCACACTGAACGCCTTCCTGTACCGCACGGGC

Altered gDNA sequence snippet

ACCTCAGGGCCACACTGAACACCTTCCTGTACCGCACGGGC

Original cDNA sequence snippet

ACCTCAGGGCCACACTGAACGCCTTCCTGTACCGCACGGGC

Altered cDNA sequence snippet

ACCTCAGGGCCACACTGAACACCTTCCTGTACCGCACGGGC

Wildtype AA sequence

MQEQTLQLEQ QSKLKEYEAA VEQLKSEQIR AQAEERRKTL SEETRQHQAR AQYQDKLARQ
RYEDQLKQQQ LLNEENLRKQ EESVQKQEAM RRATVEREME LRHKNEMLRV EAEARARAKA
ERENADIIRE QIRLKAAEHR QTVLESIRTA GTLFGEGFRA FVTDWDKVTA TVAGLTLLAV
GVYSAKNATL VAGRFIEARL GKPSLVRETS RITVLEALRH PIQVSRRLLS RPQDALEGVV
LSPSLEARVR DIAIATRNTK KNRSLYRNIL MYGPPGTGKT LFAKKLALHS GMDYAIMTGG
DVAPMGREGV TAMHKLFDWA NTSRRGLLLF VDEADAFLRK RATEKISEDL RATLNAFLYR
TGQHSNKFML VLASNQPEQF DWAINDRINE MVHFDLPGQE ERERLVRMYF DKYVLKPATE
GKQRLKLAQF DYGRKCSEVA RLTEGMSGRE IAQLAVSWQA TAYASEDGVL TEAMMDTRVQ
DAVQQHQQKM CWLKAEGPGR GDEPSPS*

Mutated AA sequence

MQEQTLQLEQ QSKLKEYEAA VEQLKSEQIR AQAEERRKTL SEETRQHQAR AQYQDKLARQ
RYEDQLKQQQ LLNEENLRKQ EESVQKQEAM RRATVEREME LRHKNEMLRV EAEARARAKA
ERENADIIRE QIRLKAAEHR QTVLESIRTA GTLFGEGFRA FVTDWDKVTA TVAGLTLLAV
GVYSAKNATL VAGRFIEARL GKPSLVRETS RITVLEALRH PIQVSRRLLS RPQDALEGVV
LSPSLEARVR DIAIATRNTK KNRSLYRNIL MYGPPGTGKT LFAKKLALHS GMDYAIMTGG
DVAPMGREGV TAMHKLFDWA NTSRRGLLLF VDEADAFLRK RATEKISEDL RATLNTFLYR
TGQHSNKFML VLASNQPEQF DWAINDRINE MVHFDLPGQE ERERLVRMYF DKYVLKPATE
GKQRLKLAQF DYGRKCSEVA RLTEGMSGRE IAQLAVSWQA TAYASEDGVL TEAMMDTRVQ
DAVQQHQQKM CWLKAEGPGR GDEPSPS*

Position of stopcodon in wt / mu CDS

1524 / 1524

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

508 / 508

Position of stopcodon in wt / mu cDNA

1717 / 1717

Position of start ATG in wt / mu cDNA

194 / 194

Last intron/exon boundary

1570

Theoretical NMD boundary in CDS

1326

Length of CDS

1524

Coding sequence (CDS) position

1066

cDNA position

1259

gDNA position

14336

Chromosomal position

1526497

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

MutationT@ster 2025

Variant:

1:1526497G>A_2_ENST00000378755

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 100|0 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr1:1526497G>A (GRCh38)

Gene symbol

ATAD3A

Gene constraints

LOEUF: 0.88, LOF (oe): 0.69, misssense (oe): 0.93, synonymous (oe): 1.00 ? (gnomAD)

Ensembl transcript ID

ENST00000378755.9

Genbank transcript ID

NM_018188 (by similarity)

UniProt / AlphaMissense peptide

ATD3A_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1447G>A
g.14336G>A

AA changes

AAE:	A483T	?
Score:	58

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs763043823
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	12	12

Protein conservation

Species	Match	AA	Alignment
Human		483	K	I	S	E	D	L	R	A	T	L	N	A	F	L	Y	R	T	G	Q	H	S	N	K	F
mutated	not conserved	483										L	N	T	F	L	Y	R	T	G	Q	H	S	N	K
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

Start (aa)	End (aa)	Feature	Details
2	634	CHAIN		lost
313	634	TOPO_DOM	Mitochondrial matrix	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-3.224	0
	8.528	1
(flanking)	6.77	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

ACCTCAGGGCCACACTGAACGCCTTCCTGTACCGCACGGGC

Altered gDNA sequence snippet

ACCTCAGGGCCACACTGAACACCTTCCTGTACCGCACGGGC

Original cDNA sequence snippet

ACCTCAGGGCCACACTGAACGCCTTCCTGTACCGCACGGGC

Altered cDNA sequence snippet

ACCTCAGGGCCACACTGAACACCTTCCTGTACCGCACGGGC

Wildtype AA sequence

MSWLFGINKG PKGEGAGPPP PLPPAQPGAE GGGDRGLGDR PAPKDKWSNF DPTGLERAAK
AARELEHSRY AKDALNLAQM QEQTLQLEQQ SKLKMRLEAL SLLHTLVWAW SLCRAGAVQT
QERLSGSASP EQVPAGECCA LQEYEAAVEQ LKSEQIRAQA EERRKTLSEE TRQHQARAQY
QDKLARQRYE DQLKQQQLLN EENLRKQEES VQKQEAMRRA TVEREMELRH KNEMLRVEAE
ARARAKAERE NADIIREQIR LKAAEHRQTV LESIRTAGTL FGEGFRAFVT DWDKVTATVA
GLTLLAVGVY SAKNATLVAG RFIEARLGKP SLVRETSRIT VLEALRHPIQ VSRRLLSRPQ
DALEGVVLSP SLEARVRDIA IATRNTKKNR SLYRNILMYG PPGTGKTLFA KKLALHSGMD
YAIMTGGDVA PMGREGVTAM HKLFDWANTS RRGLLLFVDE ADAFLRKRAT EKISEDLRAT
LNAFLYRTGQ HSNKFMLVLA SNQPEQFDWA INDRINEMVH FDLPGQEERE RLVRMYFDKY
VLKPATEGKQ RLKLAQFDYG RKCSEVARLT EGMSGREIAQ LAVSWQATAY ASEDGVLTEA
MMDTRVQDAV QQHQQKMCWL KAEGPGRGDE PSPS*

Mutated AA sequence

MSWLFGINKG PKGEGAGPPP PLPPAQPGAE GGGDRGLGDR PAPKDKWSNF DPTGLERAAK
AARELEHSRY AKDALNLAQM QEQTLQLEQQ SKLKMRLEAL SLLHTLVWAW SLCRAGAVQT
QERLSGSASP EQVPAGECCA LQEYEAAVEQ LKSEQIRAQA EERRKTLSEE TRQHQARAQY
QDKLARQRYE DQLKQQQLLN EENLRKQEES VQKQEAMRRA TVEREMELRH KNEMLRVEAE
ARARAKAERE NADIIREQIR LKAAEHRQTV LESIRTAGTL FGEGFRAFVT DWDKVTATVA
GLTLLAVGVY SAKNATLVAG RFIEARLGKP SLVRETSRIT VLEALRHPIQ VSRRLLSRPQ
DALEGVVLSP SLEARVRDIA IATRNTKKNR SLYRNILMYG PPGTGKTLFA KKLALHSGMD
YAIMTGGDVA PMGREGVTAM HKLFDWANTS RRGLLLFVDE ADAFLRKRAT EKISEDLRAT
LNTFLYRTGQ HSNKFMLVLA SNQPEQFDWA INDRINEMVH FDLPGQEERE RLVRMYFDKY
VLKPATEGKQ RLKLAQFDYG RKCSEVARLT EGMSGREIAQ LAVSWQATAY ASEDGVLTEA
MMDTRVQDAV QQHQQKMCWL KAEGPGRGDE PSPS*

Position of stopcodon in wt / mu CDS

1905 / 1905

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

635 / 635

Position of stopcodon in wt / mu cDNA

1999 / 1999

Position of start ATG in wt / mu cDNA

95 / 95

Last intron/exon boundary

1852

Theoretical NMD boundary in CDS

1707

Length of CDS

1905

Coding sequence (CDS) position

1447

cDNA position

1541

gDNA position

14336

Chromosomal position

1526497

Speed

0.03 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