13042 (G > A)

General info

Chr
chrM
Start
13042
End
13042
Ref
G
Alt
A
Mitimpact ID
MI.20753
Gene symbol
MT-ND5
RC complex
I
Ensembl gene ID
Ensembl protein ID
Ensembl transcript ID
Uniprot name
Uniprot ID
Ncbi gene ID
Ncbi protein ID
Gene position
706
AA pos
236
AA ref
A
AA alt
T
Codon substitution
Gcc/Acc
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Conservation

PhyloP 100v
-8.99 Conservation Score
PhastCons 100v
0 Conservation Score

Pathogenicity predictors

PolyPhen2
Probably damaging Score and details of the predictor
SIFT
Neutral Score and details of the predictor
FatHmm
Deleterious Score and details of the predictor
FatHMMW
Neutral Score and details of the predictor
PROVEAN
Deleterious Score and details of the predictor
Mutation Assessor
High impact Score and details of the predictor
EFIN SP
Damaging Score and details of the predictor
EFIN HD
Damaging Score and details of the predictor
VEST
Neutral Score and details of the predictor
PANTHER
Disease Score and details of the predictor
PhD-SNP
Disease Score and details of the predictor
MutationTaster
Disease causing automatic Score and details of the predictor
CADD
Deleterious Score and details of the predictor
SNAP
Disease Score and details of the predictor
MitoClass 1
Damaging Score and details of the predictor
SNPDryad
Pathogenic Score and details of the predictor

Pathogenicity meta-predictors

APOGEE
Pathogenic Score and details of the meta-predictor
CAROL
Deleterious Score and details of the meta-predictor
Condel
Neutral Score and details of the meta-predictor
COVEC WMV
Deleterious Score and details of the meta-predictor
Meta SNP
Disease Score and details of the meta-predictor
MtoolBox
Deleterious Score and details of the meta-predictor
DEOGEN2
Neutral Score and details of the meta-predictor

Cancer-specific predictors

PolyPhen2 transf
Low impact Score and details of the cancer-specific predictor
SIFT transf
Medium impact Score and details of the cancer-specific predictor
MutationAssessor transf
High impact Score and details of the cancer-specific predictor
CHASM
Neutral Score and details of the cancer-specific predictor

Databases of Phenotypes

ClinVar March2020 ClinSig
Pathogenic
ClinVar March2020 ClnDBN
Leber's optic atrophy;

juvenile myopathy, encephalopathy, lactic acidosis and stroke;

myoclonus with epilepsy with ragged red fibers;

leigh syndrome due to mitochondrial complex i deficiency
ClinVar March2020 ClnAllele ID
24742
ClinVar March2020 ClnDSDB
Human phenotype ontology:hp:0001112, medgen:c0917796, omim:535000, orphanet:orpha104, snomed ct:58610003;

medgen:c0162671, omim:540000, orphanet:orpha550, snomed ct:39925003;

medgen:c0162672, omim:545000, orphanet:orpha551;

medgen:c1838951
MITOMAP Allele
MITOMAP Phenotype
Optic neuropathy/ retinopathy/ ld
MITOMAP Homoplasmy
-
MITOMAP Heteroplasmy
+
MITOMAP Status
Cfrm
MITOMAP NRef
7
COSMIC 90
COSM5652748
dbSNP 153

Residue interaction

EVmutation
Site A-B InterP
Site A-B IntraP
ΔΔG intra
ΔΔG intra interface
ΔΔG inter

Compensated Pathogenic Deviations

Frequency
.
AA ref
.
CPD AA alt
.
Aln pos
.
RefSeq protein ID
.
Species name
.
Ncbi taxon ID
.

13042 (G > C)

General info

Chr
chrM
Start
13042
End
13042
Ref
G
Alt
C
Mitimpact ID
MI.20754
Gene symbol
MT-ND5
RC complex
I
Ensembl gene ID
Ensembl protein ID
Ensembl transcript ID
Uniprot name
Uniprot ID
Ncbi gene ID
Ncbi protein ID
Gene position
706
AA pos
236
AA ref
A
AA alt
P
Codon substitution
Gcc/Ccc
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Powered by MitoWheel

Conservation

PhyloP 100v
-8.99 Conservation Score
PhastCons 100v
0 Conservation Score

Pathogenicity predictors

PolyPhen2
Probably damaging Score and details of the predictor
SIFT
Neutral Score and details of the predictor
FatHmm
Deleterious Score and details of the predictor
FatHMMW
Neutral Score and details of the predictor
PROVEAN
Deleterious Score and details of the predictor
Mutation Assessor
High impact Score and details of the predictor
EFIN SP
Damaging Score and details of the predictor
EFIN HD
Damaging Score and details of the predictor
VEST
Neutral Score and details of the predictor
PANTHER
Disease Score and details of the predictor
PhD-SNP
Disease Score and details of the predictor
MutationTaster
Polymorphism Score and details of the predictor
CADD
Deleterious Score and details of the predictor
SNAP
Disease Score and details of the predictor
MitoClass 1
Damaging Score and details of the predictor
SNPDryad
Pathogenic Score and details of the predictor

Pathogenicity meta-predictors

APOGEE
Pathogenic Score and details of the meta-predictor
CAROL
Deleterious Score and details of the meta-predictor
Condel
Neutral Score and details of the meta-predictor
COVEC WMV
Deleterious Score and details of the meta-predictor
Meta SNP
Disease Score and details of the meta-predictor
MtoolBox
Deleterious Score and details of the meta-predictor
DEOGEN2
Neutral Score and details of the meta-predictor

Cancer-specific predictors

PolyPhen2 transf
Low impact Score and details of the cancer-specific predictor
SIFT transf
Medium impact Score and details of the cancer-specific predictor
MutationAssessor transf
High impact Score and details of the cancer-specific predictor
CHASM
Neutral Score and details of the cancer-specific predictor

Databases of Phenotypes

ClinVar March2020 ClinSig
.
ClinVar March2020 ClnDBN
.
ClinVar March2020 ClnAllele ID
.
ClinVar March2020 ClnDSDB
.
MITOMAP Allele
.
MITOMAP Phenotype
.
MITOMAP Homoplasmy
.
MITOMAP Heteroplasmy
.
MITOMAP Status
.
MITOMAP NRef
.
COSMIC 90
.
dbSNP 153

Residue interaction

EVmutation
Site A-B InterP
Site A-B IntraP
ΔΔG intra
ΔΔG intra interface
ΔΔG inter

Compensated Pathogenic Deviations

Frequency
.
AA ref
.
CPD AA alt
.
Aln pos
.
RefSeq protein ID
.
Species name
.
Ncbi taxon ID
.

13042 (G > T)

General info

Chr
chrM
Start
13042
End
13042
Ref
G
Alt
T
Mitimpact ID
MI.20755
Gene symbol
MT-ND5
RC complex
I
Ensembl gene ID
Ensembl protein ID
Ensembl transcript ID
Uniprot name
Uniprot ID
Ncbi gene ID
Ncbi protein ID
Gene position
706
AA pos
236
AA ref
A
AA alt
S
Codon substitution
Gcc/Tcc
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
-8.99 Conservation Score
PhastCons 100v
0 Conservation Score

Pathogenicity predictors

PolyPhen2
Probably damaging Score and details of the predictor
SIFT
Neutral Score and details of the predictor
FatHmm
Deleterious Score and details of the predictor
FatHMMW
Neutral Score and details of the predictor
PROVEAN
Deleterious Score and details of the predictor
Mutation Assessor
High impact Score and details of the predictor
EFIN SP
Damaging Score and details of the predictor
EFIN HD
Neutral Score and details of the predictor
VEST
Neutral Score and details of the predictor
PANTHER
Disease Score and details of the predictor
PhD-SNP
Disease Score and details of the predictor
MutationTaster
Polymorphism Score and details of the predictor
CADD
Deleterious Score and details of the predictor
SNAP
Disease Score and details of the predictor
MitoClass 1
Damaging Score and details of the predictor
SNPDryad
Pathogenic Score and details of the predictor

Pathogenicity meta-predictors

APOGEE
Pathogenic Score and details of the meta-predictor
CAROL
Deleterious Score and details of the meta-predictor
Condel
Neutral Score and details of the meta-predictor
COVEC WMV
Deleterious Score and details of the meta-predictor
Meta SNP
Disease Score and details of the meta-predictor
MtoolBox
Deleterious Score and details of the meta-predictor
DEOGEN2
Neutral Score and details of the meta-predictor

Cancer-specific predictors

PolyPhen2 transf
Low impact Score and details of the cancer-specific predictor
SIFT transf
Medium impact Score and details of the cancer-specific predictor
MutationAssessor transf
High impact Score and details of the cancer-specific predictor
CHASM
Neutral Score and details of the cancer-specific predictor

Databases of Phenotypes

ClinVar March2020 ClinSig
.
ClinVar March2020 ClnDBN
.
ClinVar March2020 ClnAllele ID
.
ClinVar March2020 ClnDSDB
.
MITOMAP Allele
.
MITOMAP Phenotype
.
MITOMAP Homoplasmy
.
MITOMAP Heteroplasmy
.
MITOMAP Status
.
MITOMAP NRef
.
COSMIC 90
.
dbSNP 153

Residue interaction

EVmutation
Site A-B InterP
Site A-B IntraP
ΔΔG intra
ΔΔG intra interface
ΔΔG inter

Compensated Pathogenic Deviations

Frequency
.
AA ref
.
CPD AA alt
.
Aln pos
.
RefSeq protein ID
.
Species name
.
Ncbi taxon ID
.
~ 13042 (G/A) 13042 (G/C) 13042 (G/T)
~ 13042 (Gcc/Acc) 13042 (Gcc/Ccc) 13042 (Gcc/Tcc)
Chr chrM chrM chrM
Start 13042 13042 13042
End 13042 13042 13042
Ref G G G
Alt A C T
MitImpact id MI.20753 MI.20754 MI.20755
Gene symbol MT-ND5 MT-ND5 MT-ND5
Respiratory Chain complex I I I
Ensembl gene id ENSG00000198786 ENSG00000198786 ENSG00000198786
Ensembl protein id ENSP00000354813 ENSP00000354813 ENSP00000354813
Ensembl transcript id ENST00000361567 ENST00000361567 ENST00000361567
Uniprot name NU5M_HUMAN NU5M_HUMAN NU5M_HUMAN
Uniprot id P03915 P03915 P03915
Ncbi gene id 4540 4540 4540
Ncbi protein id YP_003024036.1 YP_003024036.1 YP_003024036.1
Gene position 706 706 706
AA position 236 236 236
AA ref A A A
AA alt T P S
Codon substitution Gcc/Acc Gcc/Ccc Gcc/Tcc
PhyloP 100V -8.99 -8.99 -8.99
PhastCons 100V 0 0 0
PolyPhen2 probably_damaging probably_damaging probably_damaging
PolyPhen2 score 1 1 1
SIFT neutral neutral neutral
SIFT score 0.42 0.24 0.45
FatHmm deleterious deleterious deleterious
FatHmm score -4.58 -6.89 -4.3
FatHmmW neutral neutral neutral
FatHmmW score 4.12 4.02 4.23
PROVEAN deleterious deleterious deleterious
PROVEAN score -3.72 -4.65 -2.79
MutationAssessor high impact high impact high impact
MutationAssessor score 4.87 4.41 3.64
EFIN SP damaging damaging damaging
EFIN SP score 0.25 0.27 0.32
EFIN HD damaging damaging neutral
EFIN HD score 0.19 0.27 0.39
CADD deleterious deleterious deleterious
CADD score 4.2 3.84 3.68
CADD phred 23.9 23.4 23.3
VEST pvalue 0.33 0.24 0.22
VEST FDR 0.5 0.45 0.45
PANTHER disease disease disease
PANTHER score 0.61 0.86 0.76
PhD-SNP disease disease disease
PhD-SNP score 0.56 0.59 0.51
SNAP disease disease disease
SNAP score 0.75 0.83 0.71
Meta-SNP disease disease disease
Meta-SNP score 0.71 0.73 0.64
Meta-SNP RI 4 5 3
CAROL deleterious deleterious deleterious
CAROL score 1 1 1
Condel neutral neutral neutral
Condel score 0.21 0.12 0.23
COVEC WMV deleterious deleterious deleterious
COVEC WMV score 2 2 2
MtoolBox deleterious deleterious deleterious
MtoolBox DS 0.78 0.83 0.8
PolyPhen2 transf low impact low impact low impact
PolyPhen2 transf score -3.6 -3.6 -3.6
SIFT_transf medium impact medium impact medium impact
SIFT transf score 0.16 -0.04 0.18
MutationAssessor transf high impact high impact high impact
MutationAssessor transf score 3.25 2.83 2.12
CHASM pvalue 0.72 0.6 0.69
CHASM FDR 0.85 0.8 0.85
APOGEE Pathogenic Pathogenic Pathogenic
APOGEE score 0.85 0.83 0.62
SNPDryad score 0.94 0.96 0.98
MutationTaster disease_causing_automatic polymorphism polymorphism
MutationTaster score 0.03 0.9 0.99
DEOGEN2 score 0.22 0.43 0.22
Mitoclass.1 damaging damaging damaging
dbSNP 153 id rs267606898 . .
ClinVar March2020 ClinSig Pathogenic . .
ClinVar March2020 ClnDBN Leber's_optic_atrophy|Juvenile_myopathy,_encephalopathy,_lactic_acidosis_AND_stroke|Myoclonus_with_epilepsy_with_ragged_red_fibers|Leigh_syndrome_due_to_mitochondrial_complex_I_deficiency . .
ClinVar March2020 ClnAllele id 24742 . .
ClinVar March2020 ClnDSDB Human_Phenotype_Ontology:HP:0001112,MedGen:C0917796,OMIM:535000,Orphanet:ORPHA104,SNOMED_CT:58610003|MedGen:C0162671,OMIM:540000,Orphanet:ORPHA550,SNOMED_CT:39925003|MedGen:C0162672,OMIM:545000,Orphanet:ORPHA551|MedGen:C1838951 . .
COSMIC 90 COSM5652748 . .
CPD Frequency . . .
MITOMAP Allele G13042A . .
MITOMAP Phenotype Optic neuropathy/ retinopathy/ LD . .
MITOMAP Homoplasmy - . .
MITOMAP Heteroplasmy + . .
MITOMAP Status Cfrm . .
MITOMAP NRef 7 . .
EVmutation MT-ND5_236A|244S:0.182016;237M:0.177634;303A:0.176312;299K:0.117245;396I:0.107623;247L:0.097882;333A:0.093703;241T:0.090735;339L:0.08794;306T:0.085258;340F:0.082234;249S:0.079462;251T:0.079315;243V:0.075992;253V:0.07389;332H:0.069038;300K:0.066845 MT-ND5_236A|244S:0.182016;237M:0.177634;303A:0.176312;299K:0.117245;396I:0.107623;247L:0.097882;333A:0.093703;241T:0.090735;339L:0.08794;306T:0.085258;340F:0.082234;249S:0.079462;251T:0.079315;243V:0.075992;253V:0.07389;332H:0.069038;300K:0.066845 MT-ND5_236A|244S:0.182016;237M:0.177634;303A:0.176312;299K:0.117245;396I:0.107623;247L:0.097882;333A:0.093703;241T:0.090735;339L:0.08794;306T:0.085258;340F:0.082234;249S:0.079462;251T:0.079315;243V:0.075992;253V:0.07389;332H:0.069038;300K:0.066845
Site A InterP . . .
Site B InterP . . .
Covariation Score InterP . . .
Site A IntraP . . .
Site B IntraP . . .
Covariation Score IntraP . . .
CPD AA ref . . .
CPD AA alt . . .
CPD Aln pos . . .
CPD Species name . . .
CPD RefSeq Protein ID . . .
CPD Ncbi Taxon id . . .
DDG intra . . .
DDG intra interface . . .
DDG inter . . .
For more info, please check the output legend.
ΔΔG values >±0.61 Kcal/mol are indicative of disrupting variants.
ΔΔG values close to zero (<±0.1 Kcal/mol) are indicative of possibly
compensating double mutants.
For more info, please check the output legend.
ΔΔG values >±0.61 Kcal/mol are indicative of disrupting variants.
ΔΔG values close to zero (<±0.1 Kcal/mol) are indicative of possibly
compensating double mutants.
For more info, please check the output legend.
ΔΔG values >±0.61 Kcal/mol are indicative of disrupting variants.
ΔΔG values close to zero (<±0.1 Kcal/mol) are indicative of possibly
compensating double mutants.
For more info, please check the output legend.
For more info, please check the output legend.
Score:  
0
  [min -20, max 10]
  • Predicted accelerated evolution:  score <= 0
  • Conserved:  score > 0
Score:  
0
  [min 0, max 1]
  • Non-conserved:  score <= 0.9
  • Conserved:  score > 0.9 (soft threshold)
Score:  
0
  [min 0, max 1]
  • Neutral:  score <= 0.15
  • Possibly damaging:  0.15 < score <= 0.85
  • Probably damaging:  score > 0.85
Score:  
0
  [min 0, max 1]
  • Neutral:  score > 0.05
  • Deleterious:  score <= 0.05
Score:  
0
  [min -15, max 10]
  • Neutral:  score > -3
  • Deleterious:  score <= -3
Score:  
0
  [min -3, max 6]
  • Neutral:  score > -1.5
  • Deleterious:  score <= -1.5
Score:  
0
  [min -14, max 14]
  • Neutral:  score > -2.5
  • Deleterious:  score <= -2.5 (soft threshold)
Score:  
0
  [min -6, max 6]
  • Neutral:  score <= 0.8
  • Low impact:  0.8 < score <= 1.9
  • Medium impact:  1.9 < score <= 3.5
  • High impact:  score > 3.5
Score:  
0
  [min 0, max 1]
  • Neutral:  score > 0.6
  • Damaging:  score <= 0.6
Score:  
0
  [min 0, max 1]
  • Neutral:  score > 0.28
  • Damaging:  score <= 0.28
Phred score:  
0
  [min 0, max 35]
  • Neutral:  score < 20 (soft threshold)
  • Deleterious:  score >= 20
Score:  
0
  [min 0, max 1]
  • Neutral:  score < 0.5
  • Disease:  score >= 0.5
Score:  
0
  [min 0, max 1]
  • Neutral:  score < 0.5
  • Disease:  score >= 0.5
Score:  
0
  [min 0, max 1]
  • Neutral:  score < 0.5
  • Disease:  score >= 0.5
Score:  
0
  [min 0, max 1]
  • Polymorphism:  score < 0.5
  • Disease causing:  score >= 0.5
P-value:  
0
  [min 0, max 1]
  • Neutral:  p-value > 0.05
  • Pathogenic:  p-value <= 0.05
Score:  
0
  [min 0, max 1]
No hard-thresholds were indicated by authors (ref). Indicatively:
  • Neutral:  score < 0.9
  • Pathogenic:  score >= 0.9
No score. Categorical only
Please refer to Additional File 14: Table S10 for further details.
Score:  
0
  [min 0, max 1]
  • Neutral:  score < 0.98
  • Deleterious:  score >= 0.98
Score:  
0
  [min 0, max 1]
  • Neutral:  score < 0.5
  • Disease:  score >= 0.5
Score:  
0
  [min 0, max 1]
  • Neutral:  score < 0.5
  • Deleterious:  score >= 0.5
Score:  
0
  [min -6, max 6]
  • Neutral:  score < 0
  • Deleterious:  score > 0
  • Inaccurate prediction:  score = 0
Score:  
0
  [min 0, max 1]
  • Neutral:  score < 0.5
  • Deleterious:  score >= 0.5
DS score:  
0
  [min 0, max 1]
  • Neutral:  score < 0.43
  • Deleterious:  score >= 0.43
Score:  
0
  [min 0, max 1]
  • Neutral:  score <= 0.5
  • Pathogenic:  score > 0.5
Score:  
0
  [min -5, max 5]
  • Low impact:  score <= -1 (soft threshold)
  • Medium impact:  -1 < score < 1.5 (soft threshold)
  • High impact:  score >= 1.5 (soft threshold)
Score:  
0
  [min -5, max 5]
  • Low impact:  score <= -1
  • Medium impact:  -1 < score < 2 (soft threshold)
  • High impact:  score >= 2 (soft threshold)
Score:  
0
  [min -5, max 5]
  • Low impact:  score <= -1
  • Medium impact:  -1 < score < 2 (soft threshold)
  • High impact:  score >= 2 (soft threshold)
P-value:  
0
  [min 0, max 1]
  • Neutral:  FDR > 0.2
  • Driver:  FDR <= 0.2
The frequency of a CPD variant is proportional to the
number of aligned orthologous sequences that
carry a specific human pathogenic variant as
wild-type amino acid on the total number of aligned
sequences.

For more info, please check the output legend