10663 (T > C)

General info

Chr
chrM
Start
10663
End
10663
Ref
T
Alt
C
Mitimpact ID
MI.16101
Gene symbol
MT-ND4L
RC complex
I
Ensembl gene ID
Ensembl protein ID
Ensembl transcript ID
Uniprot name
Uniprot ID
Ncbi gene ID
Ncbi protein ID
Gene position
194
AA pos
65
AA ref
V
AA alt
A
Codon substitution
gTc/gCc
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Conservation

PhyloP 100v
0.98 Conservation Score
PhastCons 100v
0.75 Conservation Score

Pathogenicity predictors

PolyPhen2
Possibly damaging Score and details of the predictor
SIFT
Neutral Score and details of the predictor
FatHmm
Neutral Score and details of the predictor
FatHMMW
Neutral Score and details of the predictor
PROVEAN
Deleterious Score and details of the predictor
Mutation Assessor
Medium 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
Neutral Score and details of the predictor
PhD-SNP
Neutral Score and details of the predictor
MutationTaster
Disease causing automatic Score and details of the predictor
CADD
Neutral Score and details of the predictor
SNAP
Neutral Score and details of the predictor
MitoClass 1
Neutral Score and details of the predictor
SNPDryad
Neutral Score and details of the predictor

Pathogenicity meta-predictors

APOGEE
Pathogenic Score and details of the meta-predictor
CAROL
Neutral Score and details of the meta-predictor
Condel
Neutral Score and details of the meta-predictor
COVEC WMV
. Score and details of the meta-predictor
Meta SNP
Neutral 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
Medium 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
ClinVar March2020 ClnAllele ID
24746
ClinVar March2020 ClnDSDB
Human phenotype ontology:hp:0001112, medgen:c0917796, omim:535000, orphanet:orpha104, snomed ct:58610003
MITOMAP Allele
MITOMAP Phenotype
Lhon
MITOMAP Homoplasmy
+
MITOMAP Heteroplasmy
-
MITOMAP Status
Cfrm
MITOMAP NRef
13
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
.

10663 (T > A)

General info

Chr
chrM
Start
10663
End
10663
Ref
T
Alt
A
Mitimpact ID
MI.16102
Gene symbol
MT-ND4L
RC complex
I
Ensembl gene ID
Ensembl protein ID
Ensembl transcript ID
Uniprot name
Uniprot ID
Ncbi gene ID
Ncbi protein ID
Gene position
194
AA pos
65
AA ref
V
AA alt
D
Codon substitution
gTc/gAc
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Powered by MitoWheel

Conservation

PhyloP 100v
0.98 Conservation Score
PhastCons 100v
0.75 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
Neutral 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
Disease causing 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
Neutral 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
.

10663 (T > G)

General info

Chr
chrM
Start
10663
End
10663
Ref
T
Alt
G
Mitimpact ID
MI.16103
Gene symbol
MT-ND4L
RC complex
I
Ensembl gene ID
Ensembl protein ID
Ensembl transcript ID
Uniprot name
Uniprot ID
Ncbi gene ID
Ncbi protein ID
Gene position
194
AA pos
65
AA ref
V
AA alt
G
Codon substitution
gTc/gGc
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
0.98 Conservation Score
PhastCons 100v
0.75 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
Medium impact Score and details of the predictor
EFIN SP
Neutral 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
Disease causing 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
Neutral Score and details of the meta-predictor
CAROL
Neutral 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
Medium 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
.
~ 10663 (T/C) 10663 (T/A) 10663 (T/G)
~ 10663 (gTc/gCc) 10663 (gTc/gAc) 10663 (gTc/gGc)
Chr chrM chrM chrM
Start 10663 10663 10663
End 10663 10663 10663
Ref T T T
Alt C A G
MitImpact id MI.16101 MI.16102 MI.16103
Gene symbol MT-ND4L MT-ND4L MT-ND4L
Respiratory Chain complex I I I
Ensembl gene id ENSG00000212907 ENSG00000212907 ENSG00000212907
Ensembl protein id ENSP00000354728 ENSP00000354728 ENSP00000354728
Ensembl transcript id ENST00000361335 ENST00000361335 ENST00000361335
Uniprot name NU4LM_HUMAN NU4LM_HUMAN NU4LM_HUMAN
Uniprot id P03901 P03901 P03901
Ncbi gene id 4539 4539 4539
Ncbi protein id YP_003024034.1 YP_003024034.1 YP_003024034.1
Gene position 194 194 194
AA position 65 65 65
AA ref V V V
AA alt A D G
Codon substitution gTc/gCc gTc/gAc gTc/gGc
PhyloP 100V 0.98 0.98 0.98
PhastCons 100V 0.75 0.75 0.75
PolyPhen2 possibly_damaging probably_damaging probably_damaging
PolyPhen2 score 0.8 0.98 0.97
SIFT neutral neutral neutral
SIFT score 0.62 0.2 0.36
FatHmm neutral deleterious deleterious
FatHmm score -2.23 -6.18 -4.9
FatHmmW neutral neutral neutral
FatHmmW score 1.53 1.39 1.4
PROVEAN deleterious deleterious deleterious
PROVEAN score -3.98 -6.89 -6.96
MutationAssessor medium impact high impact medium impact
MutationAssessor score 2.15 3.97 2.82
EFIN SP damaging neutral neutral
EFIN SP score 0.28 0.7 0.74
EFIN HD damaging neutral neutral
EFIN HD score 0.25 0.37 0.45
CADD neutral deleterious deleterious
CADD score 1.28 4.68 3.8
CADD phred 12.18 24.6 23.4
VEST pvalue 0.43 0.11 0.27
VEST FDR 0.55 0.4 0.45
PANTHER neutral disease disease
PANTHER score 0.19 0.65 0.52
PhD-SNP neutral disease disease
PhD-SNP score 0.28 0.94 0.91
SNAP neutral disease disease
SNAP score 0.36 0.7 0.57
Meta-SNP neutral disease disease
Meta-SNP score 0.43 0.86 0.79
Meta-SNP RI 1 7 6
CAROL neutral deleterious neutral
CAROL score 0.77 0.99 0.97
Condel neutral neutral neutral
Condel score 0.41 0.11 0.2
COVEC WMV . deleterious deleterious
COVEC WMV score 0 2 1
MtoolBox deleterious deleterious deleterious
MtoolBox DS 0.58 0.85 0.79
PolyPhen2 transf low impact low impact low impact
PolyPhen2 transf score -1.35 -2.35 -2.19
SIFT_transf medium impact medium impact medium impact
SIFT transf score 0.33 -0.12 0.07
MutationAssessor transf medium impact high impact medium impact
MutationAssessor transf score 0.66 2.19 1.23
CHASM pvalue 0.33 0.53 0.5
CHASM FDR 0.8 0.8 0.8
APOGEE Pathogenic Neutral Neutral
APOGEE score 0.9 0.42 0.35
SNPDryad score 0.89 0.98 0.97
MutationTaster disease_causing_automatic disease_causing disease_causing
MutationTaster score 0.12 1 1
DEOGEN2 score 0.1 0.32 0.11
Mitoclass.1 neutral damaging damaging
dbSNP 153 id rs1556423844 . .
ClinVar March2020 ClinSig Pathogenic . .
ClinVar March2020 ClnDBN Leber's_optic_atrophy . .
ClinVar March2020 ClnAllele id 24746 . .
ClinVar March2020 ClnDSDB Human_Phenotype_Ontology:HP:0001112,MedGen:C0917796,OMIM:535000,Orphanet:ORPHA104,SNOMED_CT:58610003 . .
COSMIC 90 . . .
CPD Frequency . . .
MITOMAP Allele T10663C . .
MITOMAP Phenotype LHON . .
MITOMAP Homoplasmy + . .
MITOMAP Heteroplasmy - . .
MITOMAP Status Cfrm . .
MITOMAP NRef 13 . .
EVmutation MT-ND4L_65V|68A:0.312138;80S:0.268146;66F:0.160226;83N:0.155337;73V:0.117822;72A:0.110734;74G:0.083326 MT-ND4L_65V|68A:0.312138;80S:0.268146;66F:0.160226;83N:0.155337;73V:0.117822;72A:0.110734;74G:0.083326 MT-ND4L_65V|68A:0.312138;80S:0.268146;66F:0.160226;83N:0.155337;73V:0.117822;72A:0.110734;74G:0.083326
Site A InterP ND4L_65 ND4L_65 ND4L_65
Site B InterP ND3_70 ND3_70 ND3_70
Covariation Score InterP mfDCA_25.0 mfDCA_25.0 mfDCA_25.0
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 MT-ND4L:MT-ND3:5ldw:K:A:V65A:A70T:0.996944:1.07140863:-0.10531006;MT-ND4L:MT-ND3:5ldw:K:A:V65A:A70P:1.12169:1.07140863:0.136969954;MT-ND4L:MT-ND3:5ldw:K:A:V65A:A70G:1.079168:1.07140863:0.0606499687;MT-ND4L:MT-ND3:5ldw:K:A:V65A:A70D:1.281703:1.07140863:0.237130165;MT-ND4L:MT-ND3:5ldw:K:A:V65A:A70V:0.975782:1.07140863:-0.165289968;MT-ND4L:MT-ND3:5ldw:K:A:V65A:A70S:1.078009:1.07140863:-0.0444901474;MT-ND4L:MT-ND3:5ldx:K:A:V65A:A70T:0.921544:0.983483911:-0.166613057;MT-ND4L:MT-ND3:5ldx:K:A:V65A:A70P:1.03586:0.983483911:0.103146836;MT-ND4L:MT-ND3:5ldx:K:A:V65A:A70G:0.996203:0.983483911:0.0906528458;MT-ND4L:MT-ND3:5ldx:K:A:V65A:A70D:1.163597:0.983483911:0.198536918;MT-ND4L:MT-ND3:5ldx:K:A:V65A:A70V:0.724451:0.983483911:-0.608348012;MT-ND4L:MT-ND3:5ldx:K:A:V65A:A70S:0.988545:0.983483911:-0.0454552174 MT-ND4L:MT-ND3:5ldw:K:A:V65D:A70V:2.600093:2.76944804:-0.165289968;MT-ND4L:MT-ND3:5ldw:K:A:V65D:A70T:2.537823:2.76944804:-0.10531006;MT-ND4L:MT-ND3:5ldw:K:A:V65D:A70S:2.7872:2.76944804:-0.0444901474;MT-ND4L:MT-ND3:5ldw:K:A:V65D:A70G:2.720839:2.76944804:0.0606499687;MT-ND4L:MT-ND3:5ldw:K:A:V65D:A70P:2.772003:2.76944804:0.136969954;MT-ND4L:MT-ND3:5ldw:K:A:V65D:A70D:3.255235:2.76944804:0.237130165;MT-ND4L:MT-ND3:5ldx:K:A:V65D:A70V:2.455729:2.66725397:-0.608348012;MT-ND4L:MT-ND3:5ldx:K:A:V65D:A70T:2.502454:2.66725397:-0.166613057;MT-ND4L:MT-ND3:5ldx:K:A:V65D:A70S:2.730646:2.66725397:-0.0454552174;MT-ND4L:MT-ND3:5ldx:K:A:V65D:A70G:2.711726:2.66725397:0.0906528458;MT-ND4L:MT-ND3:5ldx:K:A:V65D:A70P:2.80799:2.66725397:0.103146836;MT-ND4L:MT-ND3:5ldx:K:A:V65D:A70D:3.277618:2.66725397:0.198536918 MT-ND4L:MT-ND3:5ldw:K:A:V65G:A70S:1.353553:1.34940958:-0.0444901474;MT-ND4L:MT-ND3:5ldw:K:A:V65G:A70G:1.362801:1.34940958:0.0606499687;MT-ND4L:MT-ND3:5ldw:K:A:V65G:A70V:1.251895:1.34940958:-0.165289968;MT-ND4L:MT-ND3:5ldw:K:A:V65G:A70T:1.255951:1.34940958:-0.10531006;MT-ND4L:MT-ND3:5ldw:K:A:V65G:A70D:1.552873:1.34940958:0.237130165;MT-ND4L:MT-ND3:5ldw:K:A:V65G:A70P:1.411591:1.34940958:0.136969954;MT-ND4L:MT-ND3:5ldx:K:A:V65G:A70S:1.245295:1.23225188:-0.0454552174;MT-ND4L:MT-ND3:5ldx:K:A:V65G:A70G:1.243825:1.23225188:0.0906528458;MT-ND4L:MT-ND3:5ldx:K:A:V65G:A70V:1.109897:1.23225188:-0.608348012;MT-ND4L:MT-ND3:5ldx:K:A:V65G:A70T:1.180902:1.23225188:-0.166613057;MT-ND4L:MT-ND3:5ldx:K:A:V65G:A70D:1.403211:1.23225188:0.198536918;MT-ND4L:MT-ND3:5ldx:K:A:V65G:A70P:1.269099:1.23225188:0.103146836
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