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: ENST00000378755
Querying Taster for transcript #2: ENST00000378756
MT speed 0.29 s - this script 2.762145 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
ENST00000378755	ATAD3A	Deleterious	10\|0	complex_aae		No			K60*	Single base exchange		NMD	Amino acid sequence changed NMD Protein features (might be) affected
ENST00000378756(MANE Select)	ATAD3A	Deleterious	10\|0	complex_aae		No			K60*	Single base exchange		NMD	Amino acid sequence changed NMD Protein features (might be) affected

MutationT@ster 2025

Variant:

1:1512446A>T_1_ENST00000378755

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
NMD
Protein features (might be) affected

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

Analysed issue

Analysis result

Variant

Chr1:1512446A>T (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.178A>T
g.285A>T

AA changes

K60* Score: 6.0?

Frameshift

No

Length of protein

NMD

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs1372223273
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	0	13	13

Protein conservation

Species	Match	AA	Alignment
Human		60	N	F	D	P	T	G	L	E	R	A	A	K	A	A	R	E	L	E	H	S	R	Y	A	K
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

Start (aa)	End (aa)	Feature	Details
2	294	TOPO_DOM	Mitochondrial intermembrane	lost
2	634	CHAIN		lost
139	267	COILED		lost
159	181	REGION		lost
295	312	TRANSMEM	Helical	lost
313	634	TOPO_DOM	Mitochondrial matrix	lost
338	353	REGION		lost
369	369	MOD_RES	Phosphoserine	lost
400	407	BINDING	ATP	lost
539	539	MOD_RES	N6-acetyllysine	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.327	0.995
	4.422	1
(flanking)	6.358	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

CCGGCCTGGAGCGCGCCGCCAAGGCGGCGCGCGAGCTGGAG

Altered gDNA sequence snippet

CCGGCCTGGAGCGCGCCGCCTAGGCGGCGCGCGAGCTGGAG

Original cDNA sequence snippet

CCGGCCTGGAGCGCGCCGCCAAGGCGGCGCGCGAGCTGGAG

Altered cDNA sequence snippet

CCGGCCTGGAGCGCGCCGCCTAGGCGGCGCGCGAGCTGGAG

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 DPTGLERAA*

Position of stopcodon in wt / mu CDS

1905 / 180

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

635 / 60

Position of stopcodon in wt / mu cDNA

1999 / 274

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

178

cDNA position

272

gDNA position

285

Chromosomal position

1512446

Speed

0.14 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:

1:1512446A>T_2_ENST00000378756

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
NMD
Protein features (might be) affected

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

Analysed issue

Analysis result

Variant

Chr1:1512446A>T (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.178A>T
g.285A>T

AA changes

K60* Score: 6.0?

Frameshift

No

Length of protein

NMD

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs1372223273
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	0	13	13

Protein conservation

Species	Match	AA	Alignment
Human		60	N	F	D	P	T	G	L	E	R	A	A	K	A	A	R	E	L	E	H	S	R	Y	A	K	D	A	L	N	L	A	Q	M	Q	E	Q	T	L	Q	L	E	Q	Q	S	K	L	K	E	Y	E	A	A	V	E	Q	L	K	S	E	Q	I	R	A	Q	A	E	E	R	R	K	T	L	S	E	E	T	R	Q	H	Q	A	R	A	Q	Y	Q	D	K	L	A	R	Q	R	Y	E	D	Q	L	K	Q	Q	Q	L	L	N	E	E	N	L	R	K	Q	E	E	S	V	Q	K	Q	E	A	M	R	R	A	T	V	E	R	E	M	E	L	R	H	K	N	E	M	L
mutated	no alignment	n/a
Ptroglodytes	no alignment	n/a
Mmulatta	partly conserved	60	N	F	D	P	T	G	L	E	R	A	A	K	A	A	R	E	L	E	Q	S	R	Y	A	K	D	A	L	N	L	A	Q	M	Q	E	Q	T	L	Q	L	E	Q	Q	S	K	L	K	E	Y	E	A	A	V	E	Q	L	R	S	E	Q	I	R	A	Q	A	E	E	R	R	K	T	L	S
Fcatus	partly conserved	60	N	F	D	P	T	G	L	E	R	A	A	K	A	A	R	E	L	E	H	S	R	H	A	K	E	A	L	S	L	A	Q	M	Q	E	Q	T	L	Q	L	E	Q	Q	S	K	L	K	E	Y	E	A	A	V	E	Q	L	K	S	E	Q	I	R	V	Q	A	E	E	R	R	K	T	L	G
Mmusculus	partly conserved	60	N	F	D	P	T	G	L	E	R	A	A	K	A	A	R	E	L	E	H	S	R	H	A	K	E	A	L	S	L	A	Q	M	Q	E	Q	T	L	Q	L	E	Q	Q	S	K	L	K	E	Y	E	A	A	V	E	Q	L	K	S	E	Q	I	R	V	Q	A	E	E	R	R	K	T	L	T
Ggallus	partly conserved	67					T	G	L	E	R	A	A	K	A	A	R	E	L	D	A	S	R	H	A	K	D	A	L	S	L	A	Q	M	Q	E	Q	T	L	Q	L	E	Q	Q	A	K	L	K	E	Y	E	A	A	I	E	Q	L	K	N	E	Q	I	R	V	Q	A	E	E	R	R	K	T	L	S	E	E	T	K	Q	H	Q	A	R	A	Q	Y	Q	D	K	L	A	R	Q	R	Y	D	E	Q	M	R	Q	Q	Q	L	A	N	E	E	N	L	R	K	Q	E	E	S	V	Q	K	Q	E	A	M	R	R	A
Trubripes	partly conserved	56									R	A	A	Q	A	A	K	E	L	D	K	S	R	H	A	K	E	A	L	D	L	A	R	M	Q	E	Q	T	S	H	L	E	Y	Q	S	K	I	K	E	Y	E	A	A	V	E	Q	L	K	G	D	Q	I	R	T	Q	A	E	E	R	R	K	T	L	N	E	E	T	K	Q	N	Q	A	R	A	Q	Y	Q	D	K	L	A	R	Q	R	Y	E	D	Q	L	R	Q	Q	Q	A	L	N	E	E	N	L	R	K	Q	E	E	S	V	Q	K	Q	E	A	M	R	K	A	T	I	E	H
Drerio	no homologue
Dmelanogaster	partly conserved	66					S	A	L	E	R	A	A	D	A	A	K	T	L	E	R	S	K	H	A	R	E	A	L	E	L	S	K	M	Q	E	A	T	R	Q	T	E	Y	N	T	K	V	K	E	Y	E	A	H	I	E	Q	A	K	V	E	Q	K	R	I	D	H	E	E	R	R	K	T	L	I	E	E	T	K	Q	Q	Q	Q	R	A	Q	Y	Q	D	Q	L	S	R	K	R	Y	E	D	Q	L	L	Q	Q	Q	R	V	Q	E	E	N	L	R	K	Q	E	E	S	V	Q	R	Q	E	A	M	R	R	Q
Celegans	no homologue
Xtropicalis	partly conserved	60	N	F	D	P	T	G	L	E	R	A	A	K	A	A	R	E	L	D	Q	S	R	H	A	K	E	A	L	N	L	A	K	V	Q	E	E	T	L	Q	L	E	Q	Q	S	K	I	K	E	Y	E	A	A	V	E	Q	L	K	N	E	Q	I	R	V	Q	A	E	E	R	R	K	T	L	N

Protein features

Start (aa)	End (aa)	Feature	Details
2	294	TOPO_DOM	Mitochondrial intermembrane	lost
2	634	CHAIN		lost
139	267	COILED		lost
159	181	REGION		lost
295	312	TRANSMEM	Helical	lost
313	634	TOPO_DOM	Mitochondrial matrix	lost
338	353	REGION		lost
369	369	MOD_RES	Phosphoserine	lost
400	407	BINDING	ATP	lost
539	539	MOD_RES	N6-acetyllysine	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.327	0.995
	4.422	1
(flanking)	6.358	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

CCGGCCTGGAGCGCGCCGCCAAGGCGGCGCGCGAGCTGGAG

Altered gDNA sequence snippet

CCGGCCTGGAGCGCGCCGCCTAGGCGGCGCGCGAGCTGGAG

Original cDNA sequence snippet

CCGGCCTGGAGCGCGCCGCCAAGGCGGCGCGCGAGCTGGAG

Altered cDNA sequence snippet

CCGGCCTGGAGCGCGCCGCCTAGGCGGCGCGCGAGCTGGAG

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 DPTGLERAA*

Position of stopcodon in wt / mu CDS

1761 / 180

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

587 / 60

Position of stopcodon in wt / mu cDNA

1868 / 287

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

178

cDNA position

285

gDNA position

285

Chromosomal position

1512446

Speed

0.15 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