MutationT @ ster 2025

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Frameshift
Heterozygous in gnomAD
Known disease mutation: ClinVar ID 95754 (pathogenic)
NMD

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

Analysed issue

Analysis result

Variant

Chr11:126275000_126275001insGAGT (GRCh38)

Gene symbol

Gene constraints

LOEUF: 1.12, LOF (oe): 0.85, misssense (oe): 0.90, synonymous (oe): 1.04 ? (gnomAD)

Ensembl transcript ID

ENST00000692336.1

Genbank transcript ID

NM_001425160 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Insertion

Gene region

CDS

DNA changes

c.634_635insGAGT
g.5977_5978insGAGT

AA changes

A214Sfs*15

Frameshift

Yes

Length of protein

NMD

Pathogenic variant (ClinVar)

Mitochondrial complex I deficiency
Inborn genetic diseases
Leigh syndrome
Mitochondrial complex 1 deficiency, nuclear type 19
Mitochondrial complex I deficiency, nuclear type 1

pathogenic

Variant DBs

dbSNP ID	rs398124308
gnomAD	homozygous (GAGT/GAGT)	heterozygous	allele carriers
	0	502	502

Protein conservation

Species	Match	AA	Alignment
Human		214	N	K	F	P	W	I	N	T	E	G	V	A	L	A	S	Y	G	M	E	D	E	G	W	F
mutated	all conserved	214	N	K	F	P	W	I	N	T	E	G	V	S
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)	7.06	1
(flanking)	3.278	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

22

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

11

Strand

1

Original gDNA sequence snippet

TCCCTGGATAAACACAGAGGGAGTGGCTTTGGCGTCTTAT

Altered gDNA sequence snippet

TCCCTGGATAAACACAGAGGGAGTGAGTGGCTTTGGCGTCTTAT

Original cDNA sequence snippet

TCCCTGGATAAACACAGAGGGAGTGGCTTTGGCGTCTTAT

Altered cDNA sequence snippet

TCCCTGGATAAACACAGAGGGAGTGAGTGGCTTTGGCGTCTTAT

Wildtype AA sequence

MIRRVLPHGM GRGLLTRRPG TRRGGFSLDW DGKVSEIKKK IKSILPGRSC DLLQDTSHLP
PEHSDVVIVG GGVLGLSVAY WLKKLESRRG AIRVLVVERD HTYSQASTGL SVGGICQQFS
LPENIQLSLF SASFLRNINV GASVCTQEYL AVVDAPPLDL RFNPSGYLLL ASEKDAAAME
SNVKVQRQEG AKVSLMSPDQ LRNKFPWINT EGVALASYGM EDEGWFDPWC LLQGLRRKVQ
SLGVLFCQGE VTRFVSSSQR MLTTDDKAVV LKRIHEVHVK MDRSLEYQPV ECAIVINAAG
AWSAQIAALA GVGEGPPGTL QGTKLPVEPR KRYVYVWHCP QGPGLETPLV ADTSGAYFRR
EGLGSNYLGG RSPTEQEEPD PANLEVDHDF FQDKVWPHLA LRVPAFETLK VQSAWAGYYD
YNTFDQNGVV GPHPLVVNMY FATGFSGHGL QQAPGIGRAV AEMVLKGRFQ TIDLSPFLFT
RFYLGEKIQE NNII*

Mutated AA sequence

MIRRVLPHGM GRGLLTRRPG TRRGGFSLDW DGKVSEIKKK IKSILPGRSC DLLQDTSHLP
PEHSDVVIVG GGVLGLSVAY WLKKLESRRG AIRVLVVERD HTYSQASTGL SVGGICQQFS
LPENIQLSLF SASFLRNINV GASVCTQEYL AVVDAPPLDL RFNPSGYLLL ASEKDAAAME
SNVKVQRQEG AKVSLMSPDQ LRNKFPWINT EGVSGFGVLW DGGRRLV*

Position of stopcodon in wt / mu CDS

1485 / 684

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

495 / 228

Position of stopcodon in wt / mu cDNA

1663 / 862

Position of start ATG in wt / mu cDNA

179 / 179

Last intron/exon boundary

1408

Theoretical NMD boundary in CDS

1179

Length of CDS

1485

Coding sequence (CDS) position

634 / 635

cDNA position

812 / 813

gDNA position

5977 / 5978

Chromosomal position

126275000 / 126275001

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

MutationT@ster 2025

Variant:

11:126275000G>GGAGT_4_ENST00000532125

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Frameshift
Heterozygous in gnomAD
Known disease mutation: ClinVar ID 95754 (pathogenic)
NMD

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

Analysed issue

Analysis result

Variant

Chr11:126275000_126275001insGAGT (GRCh38)

Gene symbol

Gene constraints

LOEUF: 1.12, LOF (oe): 0.85, misssense (oe): 0.90, synonymous (oe): 1.04 ? (gnomAD)

Ensembl transcript ID

ENST00000532125.2

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Insertion

Gene region

CDS

DNA changes

c.607_608insGAGT
g.5977_5978insGAGT

AA changes

A205Sfs*15

Frameshift

Yes

Length of protein

NMD

Pathogenic variant (ClinVar)

Mitochondrial complex I deficiency
Inborn genetic diseases
Leigh syndrome
Mitochondrial complex 1 deficiency, nuclear type 19
Mitochondrial complex I deficiency, nuclear type 1

pathogenic

Variant DBs

dbSNP ID	rs398124308
gnomAD	homozygous (GAGT/GAGT)	heterozygous	allele carriers
	0	502	502

Protein conservation

Species	Match	AA	Alignment
Human		205	N	K	F	P	W	I	N	T	E	G	V	A	L	A	S	Y	G	M	E	D	E	G	W	F
mutated	all conserved	205	N	K	F	P	W	I	N	T	E	G	V	S
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)	7.06	1
(flanking)	3.278	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

22

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

11

Strand

1

Original gDNA sequence snippet

TCCCTGGATAAACACAGAGGGAGTGGCTTTGGCGTCTTAT

Altered gDNA sequence snippet

TCCCTGGATAAACACAGAGGGAGTGAGTGGCTTTGGCGTCTTAT

Original cDNA sequence snippet

TCCCTGGATAAACACAGAGGGAGTGGCTTTGGCGTCTTAT

Altered cDNA sequence snippet

TCCCTGGATAAACACAGAGGGAGTGAGTGGCTTTGGCGTCTTAT

Wildtype AA sequence

MIRRVLPHGM GRGLLTRRPG TRRGGFSLDW DGKVSEIKKK IKSILPGRSC DLLQDTSHLP
PEHSDVVIVG GGVLGLSVAY WLKKLESRRG AIRVLVVERD HTYSQASTGL SVGGICQQFS
LPENIQLSLF SASFLRNINY LAVVDAPPLD LRFNPSGYLL LASEKDAAAM ESNVKVQRQE
GAKVSLMSPD QLRNKFPWIN TEGVALASYG MEDEGWFDPW CLLQGLRRKV QSLGVLFCQG
EVTRFVSSSQ RMLTTDDKAV VLKRIHEVHV KMDRSLEYQP VECAIVINAA GAWSAQIAAL
AGVGEGPPGT LQGTKLPVEP RKRYVYVWHC PQGPGLETPL VADTSGAYFR REGLGSNYLG
GRSPTEQEEP DPANLEVDHD FFQDKVWPHL ALRVPAFETL KVQSAWAGYY DYNTFDQNGV
VGPHPLVVNM YFATGFSGHG LQQAPGIGRA VAEMVLKGRF QTIDLSPFLF TRFYLGEKIQ
ENNII*

Mutated AA sequence

MIRRVLPHGM GRGLLTRRPG TRRGGFSLDW DGKVSEIKKK IKSILPGRSC DLLQDTSHLP
PEHSDVVIVG GGVLGLSVAY WLKKLESRRG AIRVLVVERD HTYSQASTGL SVGGICQQFS
LPENIQLSLF SASFLRNINY LAVVDAPPLD LRFNPSGYLL LASEKDAAAM ESNVKVQRQE
GAKVSLMSPD QLRNKFPWIN TEGVSGFGVL WDGGRRLV*

Position of stopcodon in wt / mu CDS

1458 / 657

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

486 / 219

Position of stopcodon in wt / mu cDNA

1636 / 835

Position of start ATG in wt / mu cDNA

179 / 179

Last intron/exon boundary

1381

Theoretical NMD boundary in CDS

1152

Length of CDS

1458

Coding sequence (CDS) position

607 / 608

cDNA position

785 / 786

gDNA position

5977 / 5978

Chromosomal position

126275000 / 126275001

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

MutationT@ster 2025

Variant:

11:126275000G>GGAGT_5_ENST00000688588

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Frameshift
Heterozygous in gnomAD
Known disease mutation: ClinVar ID 95754 (pathogenic)
NMD

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

Analysed issue

Analysis result

Variant

Chr11:126275000_126275001insGAGT (GRCh38)

Gene symbol

Gene constraints

LOEUF: 1.16, LOF (oe): 0.84, misssense (oe): 0.92, synonymous (oe): 1.01 ? (gnomAD)

Ensembl transcript ID

ENST00000688588.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Insertion

Gene region

CDS

DNA changes

c.610_611insGAGT
g.5977_5978insGAGT

AA changes

A206Sfs*15

Frameshift

Yes

Length of protein

NMD

Pathogenic variant (ClinVar)

Mitochondrial complex I deficiency
Inborn genetic diseases
Leigh syndrome
Mitochondrial complex 1 deficiency, nuclear type 19
Mitochondrial complex I deficiency, nuclear type 1

pathogenic

Variant DBs

dbSNP ID	rs398124308
gnomAD	homozygous (GAGT/GAGT)	heterozygous	allele carriers
	0	502	502

Protein conservation

Species	Match	AA	Alignment
Human		206	N	K	F	P	W	I	N	T	E	G	V	A	L	A	S	Y	G	M	E	D	E	G	W	F
mutated	all conserved	206	N	K	F	P	W	I	N	T	E	G	V	S
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)	7.06	1
(flanking)	3.278	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

22

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

11

Strand

1

Original gDNA sequence snippet

TCCCTGGATAAACACAGAGGGAGTGGCTTTGGCGTCTTAT

Altered gDNA sequence snippet

TCCCTGGATAAACACAGAGGGAGTGAGTGGCTTTGGCGTCTTAT

Original cDNA sequence snippet

TCCCTGGATAAACACAGAGGGAGTGGCTTTGGCGTCTTAT

Altered cDNA sequence snippet

TCCCTGGATAAACACAGAGGGAGTGAGTGGCTTTGGCGTCTTAT

Wildtype AA sequence

MIRRVLPHGM GRGLLTRRPG TRRGGFSLDW DGKVSEIKKK IKSILPGRSC DLLQDTSHLP
PEHSDVVIVG GGVLGLSVAY WLKKLESRRG AIRVLVVERD HTYSQASTGL SVGGICQQFS
LPENIQLSLF SASFLRNINE YLAVVDAPPL DLRFNPSGYL LLASEKDAAA MESNVKVQRQ
EGAKVSLMSP DQLRNKFPWI NTEGVALASY GMEDEGWFDP WCLLQGLRRK VQSLGVLFCQ
GEVTRFVSSS QRMLTTDDKA VVLKRIHEVH VKMDRSLEYQ PVECAIVINA AGAWSAQIAA
LAGVGEGPPG TLQGTKLPVE PRKSRKNRTR RTWKWTMISS RTRCGPIWP*

Mutated AA sequence

MIRRVLPHGM GRGLLTRRPG TRRGGFSLDW DGKVSEIKKK IKSILPGRSC DLLQDTSHLP
PEHSDVVIVG GGVLGLSVAY WLKKLESRRG AIRVLVVERD HTYSQASTGL SVGGICQQFS
LPENIQLSLF SASFLRNINE YLAVVDAPPL DLRFNPSGYL LLASEKDAAA MESNVKVQRQ
EGAKVSLMSP DQLRNKFPWI NTEGVSGFGV LWDGGRRLV*

Position of stopcodon in wt / mu CDS

1050 / 660

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

350 / 220

Position of stopcodon in wt / mu cDNA

1228 / 838

Position of start ATG in wt / mu cDNA

179 / 179

Last intron/exon boundary

1254

Theoretical NMD boundary in CDS

1025

Length of CDS

1050

Coding sequence (CDS) position

610 / 611

cDNA position

788 / 789

gDNA position

5977 / 5978

Chromosomal position

126275000 / 126275001

Speed

0.08 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

MutationT@ster 2025

Variant:

11:126275000G>GGAGT_2_ENST00000263578

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Frameshift
Heterozygous in gnomAD
Known disease mutation: ClinVar ID 95754 (pathogenic)
NMD
Protein features (might be) affected

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

Analysed issue

Analysis result

Variant

Chr11:126275000_126275001insGAGT (GRCh38)

Gene symbol

Gene constraints

LOEUF: 1.12, LOF (oe): 0.85, misssense (oe): 0.90, synonymous (oe): 1.04 ? (gnomAD)

Ensembl transcript ID

ENST00000263578.10

Genbank transcript ID

NM_017547 (exact from MANE), NM_001425165 (by similarity), NM_001425161 (by similarity), NM_001425164 (by similarity), NM_001425163 (by similarity), NM_001425171 (by similarity)

UniProt / AlphaMissense peptide

FXRD1_HUMAN | AlphaMissense: transcript, gene

Variant type

Insertion

Gene region

CDS

DNA changes

c.610_611insGAGT
g.5977_5978insGAGT

AA changes

A206Sfs*15

Frameshift

Yes

Length of protein

NMD

Pathogenic variant (ClinVar)

Mitochondrial complex I deficiency
Inborn genetic diseases
Leigh syndrome
Mitochondrial complex 1 deficiency, nuclear type 19
Mitochondrial complex I deficiency, nuclear type 1

pathogenic

Variant DBs

dbSNP ID	rs398124308
gnomAD	homozygous (GAGT/GAGT)	heterozygous	allele carriers
	0	502	502

Protein conservation

Species	Match	AA	Alignment
Human		206	N	K	F	P	W	I	N	T	E	G	V	A	L	A	S	Y	G	M	E	D	E	G	W	F	D	P	W	C	L	L	Q	G	L	R	R	K	V	Q	S	L	G	V	L	F	C	Q	G	E	V	T	R	F	V	S	S	S	Q	R	M	L	T	T	D	D	K	A	V	V	L	K	R	I	H	E	V	H	V	K	M	D	R	S	L	E	Y	Q	P	V	E	C	A	I	V	I	N	A	A	G	A	W	S	A	Q	I	A	A	L	A	G	V	G	E	G	P	P	G	T	L	Q	G	T	K	L	P	V	E	P	R	K	R	Y	V	Y	V	W	H	C	P	Q	G
mutated	all conserved	206	N	K	F	P	W	I	N	T	E	G	V	S
Ptroglodytes	all identical	196	N	K	F	P	W	I	N	T	E	G	V	A	L	A	S	Y	G	M	E	D	E	G	W	F	D	P	W	C	L	L	Q	G	L	R	R	K	V	Q	S	L	G	V	L	F	C	Q	G	E	V	T	R	F	V	S	S	S	Q	R	M	L	T	T	D	D	K	A	V	V	L	K	R	I	H	E	V	H	V	K	M	D	R	S	L	E	Y	Q	P	V	E	C	A	I	V	I	N	A	A	G	A	W	S	A	Q	I
Mmulatta	partly conserved	206	N	K	F	P	W	I	N	T	E	G	V	A	L	A	S	Y	G	M	E	N	E	G	W	F	D	P	W	C	L	L	H	G	L	R	Q	K	L	M	S	M	G	V	F	F	C	Q	G	E	V	T	R	F	V	T	S	S	Q	R	M	M	T	T	D	D	E	M	V	T	L	K	S	I	H	E	V	H	V	K	M	D	H	S	L	E	Y	Q	P	V	E	C	A	I	V	I	N	A	A	G	A	W	S	A	Q	I	A	A
Fcatus	partly conserved	206	N	K	F	P	W	I	N	T	E	G	V	A	L	A	S	Y	G	M	E	H	E	G	W	F	D	P	W	C	L	L	Q	G	L	R	R	K	V	Q	S	M	G	V	L	F	C	R	G	E	V	T	R	F	V	S	S	S	N	L	M	K	T	A	S	G	E	E	V	N	V	K	R	I	H	E	V	H	V	K	I	D	Q	S	L	E	Y	Q	P	V	E	C	A	I	V	I	N	A	A	G	A	W	S	G	Q	V	A	E
Mmusculus	partly conserved	207	T	K	F	P	W	I	N	V	E	G	V	A	L	A	S	Y	G	L	E	D	E	G	W	F	D	A	W	S	L	L	Q	G	L	R	R	K	V	Q	S	M	G	V	F	F	C	Q	G	E	V	T	R	F	I	T	S	S	T	P	M	K	T	P	T	G	E	H	V	V	L	R	R	I	N	N	V	H	V	K	M	D	K	S	L	E	Y	Q	P	V	E	C	A	V	V	I	N	A	A	G	A	W	S	G	K	I	A
Ggallus	partly conserved	225	A	K	F	P	W	I	N	T	E	N	V	A	V	A	S	Y	G	L	E	N	E	G	W	F	D	P	W	S	L	L	N	A	F	R	R	K	A	M	S	L	G	V	Y	S	C	V	G	E	V	T	S	F	V	A	D	T	A	D	-	-	N	T	P	G	M	P	R	G	V	G	R	V	K	Y	V	N	V	R	L	P	D	S	P	E	Q	Q	P	V	S	C	A	I	V	V	A	A	A	G	A	W	T	G	K	L	-	-	L	D	S	A	T
Trubripes	partly conserved	229									E	G	V	A	L	A	S	Q	G	L	E	N	E	G	W	F	D	P	W	S	L	L	N	A	F	R	R	K	S	I	S	M	G	V	V	S	C	H	G	E	V	T	D	F	K	Y	T	M	N	V	V	T	T	I	D	D	D	K	L	Q	L	R	R	I	Q	S	V	K	V	Q	M	P	N	S	L	E	Y	Q	P	V	E	C	S	I	V	V	N	A	A	G	A	F	S	A	N	L	V	E	K	L	G	V	G	A	G	T	K	D	A	V	A	G	I	A	V	P	V	E	P	R
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	partly conserved	224								T	N	G	V	A	L	A	S	Y	G	L	E	N	E	G	W	F	D	P	W	T	L	L	N	A	F	R	R	K	A	L	S	M	G	V	Y	H	C	H	G	E	V	T	D	F	S	T	T	K	R	E	M	M	T	A	D	G	D	P	V	T	F	S	R	I	G	H	V	T	V	L	M	P	N	S	L	E	S	Q	N	V	E	C	A	L	V	I	N	A	A	G	A	W	S	S	N	V	A	E	L	A	G	I	G	I	G	P	S	D	S	L	E	S	V	K	L	P	V	E	P

Protein features

Start (aa)	End (aa)	Feature	Details
1	486	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	7.06	1
(flanking)	3.278	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

22

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

11

Strand

1

Original gDNA sequence snippet

TCCCTGGATAAACACAGAGGGAGTGGCTTTGGCGTCTTAT

Altered gDNA sequence snippet

TCCCTGGATAAACACAGAGGGAGTGAGTGGCTTTGGCGTCTTAT

Original cDNA sequence snippet

TCCCTGGATAAACACAGAGGGAGTGGCTTTGGCGTCTTAT

Altered cDNA sequence snippet

TCCCTGGATAAACACAGAGGGAGTGAGTGGCTTTGGCGTCTTAT

Wildtype AA sequence

MIRRVLPHGM GRGLLTRRPG TRRGGFSLDW DGKVSEIKKK IKSILPGRSC DLLQDTSHLP
PEHSDVVIVG GGVLGLSVAY WLKKLESRRG AIRVLVVERD HTYSQASTGL SVGGICQQFS
LPENIQLSLF SASFLRNINE YLAVVDAPPL DLRFNPSGYL LLASEKDAAA MESNVKVQRQ
EGAKVSLMSP DQLRNKFPWI NTEGVALASY GMEDEGWFDP WCLLQGLRRK VQSLGVLFCQ
GEVTRFVSSS QRMLTTDDKA VVLKRIHEVH VKMDRSLEYQ PVECAIVINA AGAWSAQIAA
LAGVGEGPPG TLQGTKLPVE PRKRYVYVWH CPQGPGLETP LVADTSGAYF RREGLGSNYL
GGRSPTEQEE PDPANLEVDH DFFQDKVWPH LALRVPAFET LKVQSAWAGY YDYNTFDQNG
VVGPHPLVVN MYFATGFSGH GLQQAPGIGR AVAEMVLKGR FQTIDLSPFL FTRFYLGEKI
QENNII*

Mutated AA sequence

MIRRVLPHGM GRGLLTRRPG TRRGGFSLDW DGKVSEIKKK IKSILPGRSC DLLQDTSHLP
PEHSDVVIVG GGVLGLSVAY WLKKLESRRG AIRVLVVERD HTYSQASTGL SVGGICQQFS
LPENIQLSLF SASFLRNINE YLAVVDAPPL DLRFNPSGYL LLASEKDAAA MESNVKVQRQ
EGAKVSLMSP DQLRNKFPWI NTEGVSGFGV LWDGGRRLV*

Position of stopcodon in wt / mu CDS

1461 / 660

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

487 / 220

Position of stopcodon in wt / mu cDNA

1514 / 713

Position of start ATG in wt / mu cDNA

54 / 54

Last intron/exon boundary

1259

Theoretical NMD boundary in CDS

1155

Length of CDS

1461

Coding sequence (CDS) position

610 / 611

cDNA position

663 / 664

gDNA position

5977 / 5978

Chromosomal position

126275000 / 126275001

Speed

0.13 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

MutationT@ster 2025

Variant:

11:126275000G>GGAGT_6_ENST00000685484

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Frameshift
Heterozygous in gnomAD
Known disease mutation: ClinVar ID 95754 (pathogenic)
NMD

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

Analysed issue

Analysis result

Variant

Chr11:126275000_126275001insGAGT (GRCh38)

Gene symbol

Gene constraints

LOEUF: 1.22, LOF (oe): 0.90, misssense (oe): 0.90, synonymous (oe): 1.04 ? (gnomAD)

Ensembl transcript ID

ENST00000685484.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Insertion

Gene region

CDS

DNA changes

c.610_611insGAGT
g.5977_5978insGAGT

AA changes

A206Sfs*15

Frameshift

Yes

Length of protein

NMD

Pathogenic variant (ClinVar)

Mitochondrial complex I deficiency
Inborn genetic diseases
Leigh syndrome
Mitochondrial complex 1 deficiency, nuclear type 19
Mitochondrial complex I deficiency, nuclear type 1

pathogenic

Variant DBs

dbSNP ID	rs398124308
gnomAD	homozygous (GAGT/GAGT)	heterozygous	allele carriers
	0	502	502

Protein conservation

Species	Match	AA	Alignment
Human		206	N	K	F	P	W	I	N	T	E	G	V	A	L	A	S	Y	G	M	E	D	E	G	W	F
mutated	all conserved	206	N	K	F	P	W	I	N	T	E	G	V	S
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)	7.06	1
(flanking)	3.278	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

22

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

11

Strand

1

Original gDNA sequence snippet

TCCCTGGATAAACACAGAGGGAGTGGCTTTGGCGTCTTAT

Altered gDNA sequence snippet

TCCCTGGATAAACACAGAGGGAGTGAGTGGCTTTGGCGTCTTAT

Original cDNA sequence snippet

TCCCTGGATAAACACAGAGGGAGTGGCTTTGGCGTCTTAT

Altered cDNA sequence snippet

TCCCTGGATAAACACAGAGGGAGTGAGTGGCTTTGGCGTCTTAT

Wildtype AA sequence

MIRRVLPHGM GRGLLTRRPG TRRGGFSLDW DGKVSEIKKK IKSILPGRSC DLLQDTSHLP
PEHSDVVIVG GGVLGLSVAY WLKKLESRRG AIRVLVVERD HTYSQASTGL SVGGICQQFS
LPENIQLSLF SASFLRNINE YLAVVDAPPL DLRFNPSGYL LLASEKDAAA MESNVKVQRQ
EGAKVSLMSP DQLRNKFPWI NTEGVALASY GMEDEGWFDP WCLLQGLRRK VQSLGVLFCQ
GEVTRFVSSS QRMLTTDDKA VVLKRIHEVH VKMDRSLEYQ PVECAIVINA AGAWSAQIAA
LAGVGEGPPG TLQGTKLPVE PRKRYVYVWH CPQGPGLETP LVADTSGAYF RREGLGSNYL
GGRSPTEQEE PDPANLEVDH DFFQDKVWPH LALRVPAFET LKVTGKGWFS FLFLDIGWDR
*

Mutated AA sequence

MIRRVLPHGM GRGLLTRRPG TRRGGFSLDW DGKVSEIKKK IKSILPGRSC DLLQDTSHLP
PEHSDVVIVG GGVLGLSVAY WLKKLESRRG AIRVLVVERD HTYSQASTGL SVGGICQQFS
LPENIQLSLF SASFLRNINE YLAVVDAPPL DLRFNPSGYL LLASEKDAAA MESNVKVQRQ
EGAKVSLMSP DQLRNKFPWI NTEGVSGFGV LWDGGRRLV*

Position of stopcodon in wt / mu CDS

1263 / 660

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

421 / 220

Position of stopcodon in wt / mu cDNA

1441 / 838

Position of start ATG in wt / mu cDNA

179 / 179

Last intron/exon boundary

1279

Theoretical NMD boundary in CDS

1050

Length of CDS

1263

Coding sequence (CDS) position

610 / 611

cDNA position

788 / 789

gDNA position

5977 / 5978

Chromosomal position

126275000 / 126275001

Speed

0.10 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

MutationT@ster 2025

Variant:

11:126275000G>GGAGT_3_ENST00000533839

Prediction:

DeleteriousPermalink

Summary:

Heterozygous in gnomAD
Known disease mutation: ClinVar ID 95754 (pathogenic)

Model: without_aae
Tree vote: 164|36 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr11:126275000_126275001insGAGT (GRCh38)

Gene symbol

Gene constraints

LOEUF: 1.30, LOF (oe): 0.92, misssense (oe): 0.93, synonymous (oe): 1.07 ? (gnomAD)

Ensembl transcript ID

ENST00000533839.6

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Insertion

Gene region

intron

DNA changes

c.86-794_86-793insGAGT
g.5977_5978insGAGT

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Mitochondrial complex I deficiency
Inborn genetic diseases
Leigh syndrome
Mitochondrial complex 1 deficiency, nuclear type 19
Mitochondrial complex I deficiency, nuclear type 1

pathogenic

Variant DBs

dbSNP ID	rs398124308
gnomAD	homozygous (GAGT/GAGT)	heterozygous	allele carriers
	0	502	502

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	7.06	1
(flanking)	3.278	1

?

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

N/A

AA sequence altered

N/A

Chromosome

11

Strand

1

Original gDNA sequence snippet

TCCCTGGATAAACACAGAGGGAGTGGCTTTGGCGTCTTAT

Altered gDNA sequence snippet

TCCCTGGATAAACACAGAGGGAGTGAGTGGCTTTGGCGTCTTAT

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MIRRVLPHGM GRGLLTRRPG TRRGGFSLGF VSSSQRMLTT DDKAVVLKRI HEVHVKMDRS
LEYQPVECAI VINAAGAWSA QIAALAGVGE GPPGTLQGTK LPVEPRKRYV YVWHCPQGPG
LETPLVADTS GAYFRREGLG SNYLGGRSPT EQEEPDPANL EVDHDFFQDK VWPHLALRVP
AFETLKVQSA WAGYYDYNTF DQNGVVGPHP LVVNMYFATG FSGHGLQQAP GIGRAVAEMV
LKGRFQTIDL SPFLFTRFYL GEKIQENNII *

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

153 / 153

Last intron/exon boundary

710

Theoretical NMD boundary in CDS

507

Length of CDS

813

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

5977 / 5978

Chromosomal position

126275000 / 126275001

Speed

0.02 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