Logo MitImpact
Home Description Output legend Molecular Dynamics How to cite License

3368 (T > C)

General info

Mitimpact ID
MI.10888
Chr
chrM
Start
3368
Ref
T
Alt
C
Gene symbol
MT-ND1 Extended gene annotation
Gene position
62
Gene start
3307
Gene end
4262
Gene strand
+
Codon substitution
ATG/ACG
AA pos
21
AA ref
M
AA alt
T
Functional effect
missense
OMIM ID
516000
HGVS
NC_012920.1:g.3368T>C
HGNC ID
7455
RC complex
I
Ensembl gene ID
ENSG00000198888
Ensembl protein ID
ENSP00000354687
Ensembl transcript ID
ENST00000361390
Uniprot ID
P03886
Uniprot name
NU1M_HUMAN
Ncbi gene ID
4535
Ncbi protein ID
YP_003024026.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
3.756 Conservation Score
PhyloP 470way
-0.507 Conservation Score
PhastCons 100v
0.998 Conservation Score
PhastCons 470way
0.002 Conservation Score

Pathogenicity predictors

PolyPhen2
Benign Score and details of the predictor
SIFT
Neutral Score and details of the predictor
SIFT4G
Tolerated Score and details of the predictor
VEST
Neutral Score and details of the predictor
MitoClass 1
Neutral Score and details of the predictor
SNPDryad
Neutral Score and details of the predictor
MutationTaster
Polymorphism Score and details of the predictor
fathmm
Tolerated Score and details of the predictor
AlphaMissense
Likely benign Score and details of the predictor
CADD
Neutral Score and details of the predictor
PROVEAN
Tolerated Score and details of the predictor
Mutation Assessor
Neutral Score and details of the predictor
EFIN SP
Neutral Score and details of the predictor
EFIN HD
Neutral Score and details of the predictor
MLC
Neutral Score and details of the predictor
PANTHER
.
PhD-SNP
.

Pathogenicity meta-predictors

APOGEE1
Pathogenic Score and details of the meta-predictor
APOGEE2
Benign Score and details of the meta-predictor
CAROL
Neutral Score and details of the meta-predictor
Condel
Deleterious Score and details of the meta-predictor
COVEC WMV
Neutral Score and details of the meta-predictor
MtoolBox
Neutral Score and details of the meta-predictor
DEOGEN2
Tolerated Score and details of the meta-predictor
Meta SNP
.

Cancer-specific predictors

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

Databases of Frequencies and Phenotypes

Clinvar ID
692345
Clinvar ALLELEID
680881
Clinvar CLNDISDB
Mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506
Clinvar CLNDN
Leigh syndrome
Clinvar CLNSIG
Likely benign
MITOMAP Allele
3368T>C
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
0.036%
MITOMAP General GenBank Seqs
22
MITOMAP General GenBank Curated refs
32094358
MITOMAP Variant Class
polymorphism
Gnomad AN
56433
Gnomad AC hom
11
Gnomad AF hom
0.0001949
Gnomad AC het
2
Gnomad AF het
3.54e-05
Gnomad filter
Pass
HelixMTdb AC hom
72
HelixMTdb AF hom
0.0003673
HelixMTdb AC het
2
HelixMTdb AF het
1.02e-05
HelixMTdb mean ARF
0.45132
HelixMTdb max ARF
0.7619
ToMMo JPN54K AC
27
ToMMo JPN54K AF
0.000497
ToMMo JPN54K AN
54302
COSMIC 90
.
dbSNP 156
rs1603218920

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
.

3368 (T > A)

General info

Mitimpact ID
MI.10889
Chr
chrM
Start
3368
Ref
T
Alt
A
Gene symbol
MT-ND1 Extended gene annotation
Gene position
62
Gene start
3307
Gene end
4262
Gene strand
+
Codon substitution
ATG/AAG
AA pos
21
AA ref
M
AA alt
K
Functional effect
missense
OMIM ID
516000
HGVS
NC_012920.1:g.3368T>A
HGNC ID
7455
RC complex
I
Ensembl gene ID
ENSG00000198888
Ensembl protein ID
ENSP00000354687
Ensembl transcript ID
ENST00000361390
Uniprot ID
P03886
Uniprot name
NU1M_HUMAN
Ncbi gene ID
4535
Ncbi protein ID
YP_003024026.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
3.756 Conservation Score
PhyloP 470way
-0.507 Conservation Score
PhastCons 100v
0.998 Conservation Score
PhastCons 470way
0.002 Conservation Score

Pathogenicity predictors

PolyPhen2
Benign Score and details of the predictor
SIFT
Neutral Score and details of the predictor
SIFT4G
Damaging Score and details of the predictor
VEST
Neutral Score and details of the predictor
MitoClass 1
Neutral Score and details of the predictor
SNPDryad
Neutral Score and details of the predictor
MutationTaster
Disease Score and details of the predictor
fathmm
Tolerated Score and details of the predictor
AlphaMissense
Likely pathogenic Score and details of the predictor
CADD
Deleterious Score and details of the predictor
PROVEAN
Tolerated Score and details of the predictor
Mutation Assessor
Neutral Score and details of the predictor
EFIN SP
Neutral Score and details of the predictor
EFIN HD
Neutral Score and details of the predictor
MLC
Neutral Score and details of the predictor
PANTHER
.
PhD-SNP
.

Pathogenicity meta-predictors

APOGEE1
Pathogenic Score and details of the meta-predictor
APOGEE2
Vus- Score and details of the meta-predictor
CAROL
Neutral Score and details of the meta-predictor
Condel
Deleterious Score and details of the meta-predictor
COVEC WMV
Neutral Score and details of the meta-predictor
MtoolBox
Neutral Score and details of the meta-predictor
DEOGEN2
Tolerated Score and details of the meta-predictor
Meta SNP
.

Cancer-specific predictors

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

Databases of Frequencies and Phenotypes

Clinvar ID
.
Clinvar ALLELEID
.
Clinvar CLNDISDB
.
Clinvar CLNDN
.
Clinvar CLNSIG
.
MITOMAP Allele
3368T>A
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
.
MITOMAP General GenBank Seqs
.
MITOMAP General GenBank Curated refs
.
MITOMAP Variant Class
.
Gnomad AN
0
Gnomad AC hom
0
Gnomad AF hom
0.0
Gnomad AC het
.
Gnomad AF het
.
Gnomad filter
.
HelixMTdb AC hom
0
HelixMTdb AF hom
0.0
HelixMTdb AC het
.
HelixMTdb AF het
0.0
HelixMTdb mean ARF
0.0
HelixMTdb max ARF
.
ToMMo JPN54K AC
.
ToMMo JPN54K AF
.
ToMMo JPN54K AN
.
COSMIC 90
.
dbSNP 156
.

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
.
~ 3368 (T/C) 3368 (T/A)
~ 3368 (ATG/ACG) 3368 (ATG/AAG)
MitImpact id MI.10888 MI.10889
Chr chrM chrM
Start 3368 3368
Ref T T
Alt C A
Gene symbol MT-ND1 MT-ND1
Extended annotation mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 1 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 1
Gene position 62 62
Gene start 3307 3307
Gene end 4262 4262
Gene strand + +
Codon substitution ATG/ACG ATG/AAG
AA position 21 21
AA ref M M
AA alt T K
Functional effect general missense missense
Functional effect detailed missense missense
OMIM id 516000 516000
HGVS NC_012920.1:g.3368T>C NC_012920.1:g.3368T>A
HGNC id 7455 7455
Respiratory Chain complex I I
Ensembl gene id ENSG00000198888 ENSG00000198888
Ensembl transcript id ENST00000361390 ENST00000361390
Ensembl protein id ENSP00000354687 ENSP00000354687
Uniprot id P03886 P03886
Uniprot name NU1M_HUMAN NU1M_HUMAN
Ncbi gene id 4535 4535
Ncbi protein id YP_003024026.1 YP_003024026.1
PhyloP 100V 3.756 3.756
PhyloP 470Way -0.507 -0.507
PhastCons 100V 0.998 0.998
PhastCons 470Way 0.002 0.002
PolyPhen2 benign benign
PolyPhen2 score 0.0 0.11
SIFT neutral neutral
SIFT score 0.33 0.05
SIFT4G Tolerated Damaging
SIFT4G score 1.0 0.0
VEST Neutral Neutral
VEST pvalue 0.15 0.06
VEST FDR 0.4 0.35
Mitoclass.1 neutral neutral
SNPDryad Neutral Neutral
SNPDryad score 0.02 0.63
MutationTaster Polymorphism Disease
MutationTaster score 1 1
MutationTaster converted rankscore 0.08975 0.81001
MutationTaster model complex_aae complex_aae
MutationTaster AAE M21T M21K
fathmm Tolerated Tolerated
fathmm score 3.03 2.82
fathmm converted rankscore 0.08898 0.10871
AlphaMissense likely_benign likely_pathogenic
AlphaMissense score 0.1688 0.9417
CADD Neutral Deleterious
CADD score 0.087578 3.929339
CADD phred 3.476 23.5
PROVEAN Tolerated Tolerated
PROVEAN score 5.02 -0.16
MutationAssessor neutral neutral
MutationAssessor score -4.145 0.695
EFIN SP Neutral Neutral
EFIN SP score 0.692 0.616
EFIN HD Neutral Neutral
EFIN HD score 0.75 0.504
MLC Neutral Neutral
MLC score 0.29953528 0.29953528
PANTHER score . .
PhD-SNP score . .
APOGEE1 Pathogenic Pathogenic
APOGEE1 score 0.57 0.6
APOGEE2 Benign VUS-
APOGEE2 score 0.0558242238754968 0.280021106075549
CAROL neutral neutral
CAROL score 0.67 0.94
Condel deleterious deleterious
Condel score 0.67 0.47
COVEC WMV neutral neutral
COVEC WMV score -6 -6
MtoolBox neutral neutral
MtoolBox DS 0.12 0.39
DEOGEN2 Tolerated Tolerated
DEOGEN2 score 0.011371 0.015345
DEOGEN2 converted rankscore 0.10151 0.12888
Meta-SNP . .
Meta-SNP score . .
PolyPhen2 transf high impact medium impact
PolyPhen2 transf score 2.07 0.1
SIFT_transf medium impact medium impact
SIFT transf score 0.1 -0.44
MutationAssessor transf low impact low impact
MutationAssessor transf score -5.33 -1.19
CHASM Neutral Neutral
CHASM pvalue 0.12 0.19
CHASM FDR 0.8 0.8
ClinVar id 692345.0 .
ClinVar Allele id 680881.0 .
ClinVar CLNDISDB MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506 .
ClinVar CLNDN Leigh_syndrome .
ClinVar CLNSIG Likely_benign .
MITOMAP Disease Clinical info . .
MITOMAP Disease Status . .
MITOMAP Disease Hom/Het ./. ./.
MITOMAP General GenBank Freq 0.036% .
MITOMAP General GenBank Seqs 22 .
MITOMAP General Curated refs 32094358 .
MITOMAP Variant Class polymorphism .
gnomAD 3.1 AN 56433.0 .
gnomAD 3.1 AC Homo 11.0 .
gnomAD 3.1 AF Hom 0.000194921 .
gnomAD 3.1 AC Het 2.0 .
gnomAD 3.1 AF Het 3.54403e-05 .
gnomAD 3.1 filter PASS .
HelixMTdb AC Hom 72.0 .
HelixMTdb AF Hom 0.00036737882 .
HelixMTdb AC Het 2.0 .
HelixMTdb AF Het 1.0204967e-05 .
HelixMTdb mean ARF 0.45132 .
HelixMTdb max ARF 0.7619 .
ToMMo 54KJPN AC 27 .
ToMMo 54KJPN AF 0.000497 .
ToMMo 54KJPN AN 54302 .
COSMIC 90 . .
dbSNP 156 id rs1603218920 .
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.
0
Details:
0
Score:  
0
  [min -20, max 10]
  • Predicted accelerated evolution:  score <= 0
  • Conserved:  score > 0
Score:  
0
  [min -20, max 12]
  • Predicted accelerated evolution:  score <= 0
  • Conserved:  score > 0
Score:  
0
  [min 0, max 1]
  • Non-conserved:  score <= 0.7
  • Conserved:  score > 0.7 (soft threshold)
Score:  
0
  [min 0, max 1]
  • Non-conserved:  score <= 0.7
  • Conserved:  score > 0.7 (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 0, max 1]
  • Neutral:  score > 0.05
  • Deleterious:  score <= 0.05
Score:  
0
  [min -16.13, max 10.64]
  • Neutral:  score > 1.5
  • Deleterious:  score <= 1.5
Score:  
0
  [min 0.0, max 1.0]
  • Likely benign:  score <= 0.34
  • Ambiguous:  0.34 < score < 0.56
  • Likely pathogenic:  score >= 0.56
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 Unlimited]
  • Neutral:  score < 20 (soft threshold)
  • Deleterious:  score >= 20
Score:  
0
  [min 0, max 1]
  • Neutral:  score < 0.5 (soft threshold)
  • Deleterious:  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
Pathogenicity score:  
0
  [min 0, max 1]
  • Neutral:  score ≤ 0.5
  • Pathogenic:  score > 0.5


Pathogenicity score for this variant:  
0
  [min 0, max 1]
ACMG-AMP curations for mitochondrial variants should use the raw scores. Standalone probabilities are shown below:
  • Benign:  score ≤ 0.062 (prob. ≤ 0.001)
  • Likely-benign:  0.062 < score ≤ 0.265 (0.001 < prob. ≤ 0.1)
  • Low-scoring VUS (VUS-):  0.265 < score ≤ 0.396 (0.1 < prob. ≤ 0.33)
  • VUS:  0.396 < score ≤ 0.544 (0.33 < prob. ≤ 0.66)
  • High-scoring VUS (VUS+):  0.544 < score < 0.716 (0.66 < prob. < 0.9)
  • Likely-pathogenic:  0.716 ≤ score < 0.907 (0.9 ≤ prob. < 0.99)
  • Pathogenic:  score ≥ 0.907 (prob. ≥ 0.99)
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