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3308 (T > A)

General info

Mitimpact ID
MI.10759
Chr
chrM
Start
3308
Ref
T
Alt
A
Gene symbol
MT-ND1 Extended gene annotation
Gene position
2
Gene start
3307
Gene end
4262
Gene strand
+
Codon substitution
ATA/AAA
AA pos
1
AA ref
M
AA alt
K
Functional effect
start_lost
OMIM ID
516000
HGVS
NC_012920.1:g.3308T>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
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Conservation

PhyloP 100v
4.722 Conservation Score
PhyloP 470way
0.458 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.156 Conservation Score

Pathogenicity predictors

PolyPhen2
Probably damaging Score and details of the predictor
SIFT
Deleterious Score and details of the predictor
SIFT4G
Damaging Score and details of the predictor
VEST
Neutral Score and details of the predictor
MitoClass 1
Damaging Score and details of the predictor
SNPDryad
Neutral Score and details of the predictor
MutationTaster
.
fathmm
.
AlphaMissense
.
CADD
Deleterious Score and details of the predictor
PROVEAN
Tolerated Score and details of the predictor
Mutation Assessor
.
EFIN SP
Damaging Score and details of the predictor
EFIN HD
Damaging Score and details of the predictor
MLC
Deleterious 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
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
MtoolBox
Deleterious Score and details of the meta-predictor
DEOGEN2
.
Meta SNP
.

Cancer-specific predictors

PolyPhen2 transf
.
SIFT transf
.
MutationAssessor transf
.
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
3308T>A
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
0.0016%
MITOMAP General GenBank Seqs
1
MITOMAP General GenBank Curated refs
18335039
MITOMAP Variant Class
polymorphism
Gnomad AN
56434
Gnomad AC hom
0
Gnomad AF hom
0.0
Gnomad AC het
1
Gnomad AF het
1.77e-05
Gnomad filter
Pass
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
.

3308 (T > C)

General info

Mitimpact ID
MI.10758
Chr
chrM
Start
3308
Ref
T
Alt
C
Gene symbol
MT-ND1 Extended gene annotation
Gene position
2
Gene start
3307
Gene end
4262
Gene strand
+
Codon substitution
ATA/ACA
AA pos
1
AA ref
M
AA alt
T
Functional effect
start_lost
OMIM ID
516000
HGVS
NC_012920.1:g.3308T>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
4.722 Conservation Score
PhyloP 470way
0.458 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.156 Conservation Score

Pathogenicity predictors

PolyPhen2
Probably damaging Score and details of the predictor
SIFT
Deleterious 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
.
fathmm
.
AlphaMissense
.
CADD
Neutral Score and details of the predictor
PROVEAN
Tolerated Score and details of the predictor
Mutation Assessor
.
EFIN SP
Damaging Score and details of the predictor
EFIN HD
Damaging Score and details of the predictor
MLC
Deleterious 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
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
MtoolBox
Deleterious Score and details of the meta-predictor
DEOGEN2
.
Meta SNP
.

Cancer-specific predictors

PolyPhen2 transf
.
SIFT transf
.
MutationAssessor transf
.
CHASM
Neutral Score and details of the cancer-specific predictor

Databases of Frequencies and Phenotypes

Clinvar ID
9728
Clinvar ALLELEID
24767
Clinvar CLNDISDB
Medgen:cn169374;

efo:efo 0005303, mesh:d013398, medgen:c0038644, omim:272120;

mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506;

mondo:mondo:0002032, medgen:c0699790
Clinvar CLNDN
Not specified;

sudden infant death syndrome;

leigh syndrome;

carcinoma of colon
Clinvar CLNSIG
Benign/likely benign
MITOMAP Allele
3308T>C
MITOMAP Disease Clinical info
Melas / deaf enhancer / hypertension / lvnc / putative lhon
MITOMAP Disease Status
Reported - possibly synergistic; hg l1b and a2i marker
MITOMAP Disease Hom/Het
-/+
MITOMAP General GenBank Freq
0.6968%
MITOMAP General GenBank Seqs
426
MITOMAP General GenBank Curated refs
10720328 18335039 15466077 22777272 32094358 10521313 11938495 15972314 9299504 21968326 14960712 12160969 10070626 10924280 10371545 22777278 21041797 10519336 10803467 24002810 29987491 21625124 21457906 18194667
MITOMAP Variant Class
polymorphism;disease
Gnomad AN
56409
Gnomad AC hom
1609
Gnomad AF hom
0.0285238
Gnomad AC het
5
Gnomad AF het
8.86e-05
Gnomad filter
Pass
HelixMTdb AC hom
1126
HelixMTdb AF hom
0.0057453
HelixMTdb AC het
26
HelixMTdb AF het
0.0001326
HelixMTdb mean ARF
0.50148
HelixMTdb max ARF
0.94643
ToMMo JPN54K AC
32
ToMMo JPN54K AF
0.000589
ToMMo JPN54K AN
54302
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
.
~ 3308 (T/A) 3308 (T/C)
~ 3308 (ATA/AAA) 3308 (ATA/ACA)
MitImpact id MI.10759 MI.10758
Chr chrM chrM
Start 3308 3308
Ref T T
Alt A C
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 2 2
Gene start 3307 3307
Gene end 4262 4262
Gene strand + +
Codon substitution ATA/AAA ATA/ACA
AA position 1 1
AA ref M M
AA alt K T
Functional effect general start_lost start_lost
Functional effect detailed start_lost start_lost
OMIM id 516000 516000
HGVS NC_012920.1:g.3308T>A NC_012920.1:g.3308T>C
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 4.722 4.722
PhyloP 470Way 0.458 0.458
PhastCons 100V 1 1
PhastCons 470Way 0.156 0.156
PolyPhen2 probably_damaging probably_damaging
PolyPhen2 score 0.99 0.99
SIFT deleterious deleterious
SIFT score 0.0 0.0
SIFT4G Damaging Damaging
SIFT4G score 0.0 0.0
VEST Neutral Neutral
VEST pvalue 0.06 0.07
VEST FDR 0.35 0.35
Mitoclass.1 damaging neutral
SNPDryad Neutral Neutral
SNPDryad score 0.79 0.05
MutationTaster . .
MutationTaster score . .
MutationTaster converted rankscore . .
MutationTaster model . .
MutationTaster AAE . .
fathmm . .
fathmm score . .
fathmm converted rankscore . .
AlphaMissense . .
AlphaMissense score . .
CADD Deleterious Neutral
CADD score 3.387294 2.362247
CADD phred 23.0 18.57
PROVEAN Tolerated Tolerated
PROVEAN score -1.86 -0.26
MutationAssessor . .
MutationAssessor score . .
EFIN SP Damaging Damaging
EFIN SP score 0.516 0.528
EFIN HD Damaging Damaging
EFIN HD score 0.152 0.196
MLC Deleterious Deleterious
MLC score 0.7 0.7
PANTHER score . .
PhD-SNP score . .
APOGEE1 Pathogenic Pathogenic
APOGEE1 score 0.71 0.75
APOGEE2 VUS VUS-
APOGEE2 score 0.4248831060166 0.32785796242486
CAROL deleterious deleterious
CAROL score 1.0 1.0
Condel neutral neutral
Condel score 0.01 0.01
COVEC WMV deleterious deleterious
COVEC WMV score 4 4
MtoolBox deleterious deleterious
MtoolBox DS 0.76 0.74
DEOGEN2 . .
DEOGEN2 score . .
DEOGEN2 converted rankscore . .
Meta-SNP . .
Meta-SNP score . .
PolyPhen2 transf . .
PolyPhen2 transf score . .
SIFT_transf . .
SIFT transf score . .
MutationAssessor transf . .
MutationAssessor transf score . .
CHASM Neutral Neutral
CHASM pvalue 0.17 0.08
CHASM FDR 0.8 0.8
ClinVar id . 9728.0
ClinVar Allele id . 24767.0
ClinVar CLNDISDB . MedGen:CN169374|EFO:EFO_0005303,MeSH:D013398,MedGen:C0038644,OMIM:272120|MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506|MONDO:MONDO:0002032,MedGen:C0699790
ClinVar CLNDN . not_specified|SUDDEN_INFANT_DEATH_SYNDROME|Leigh_syndrome|Carcinoma_of_colon
ClinVar CLNSIG . Benign/Likely_benign
MITOMAP Disease Clinical info . MELAS / DEAF enhancer / hypertension / LVNC / putative LHON
MITOMAP Disease Status . Reported - possibly synergistic; hg L1b and A2i marker
MITOMAP Disease Hom/Het ./. -/+
MITOMAP General GenBank Freq 0.0016% 0.6968%
MITOMAP General GenBank Seqs 1 426
MITOMAP General Curated refs 18335039 10720328;18335039;15466077;22777272;32094358;10521313;11938495;15972314;9299504;21968326;14960712;12160969;10070626;10924280;10371545;22777278;21041797;10519336;10803467;24002810;29987491;21625124;21457906;18194667
MITOMAP Variant Class polymorphism polymorphism;disease
gnomAD 3.1 AN 56434.0 56409.0
gnomAD 3.1 AC Homo 0.0 1609.0
gnomAD 3.1 AF Hom 0.0 0.0285238
gnomAD 3.1 AC Het 1.0 5.0
gnomAD 3.1 AF Het 1.77198e-05 8.86383e-05
gnomAD 3.1 filter PASS PASS
HelixMTdb AC Hom . 1126.0
HelixMTdb AF Hom . 0.0057453965
HelixMTdb AC Het . 26.0
HelixMTdb AF Het . 0.00013266457
HelixMTdb mean ARF . 0.50148
HelixMTdb max ARF . 0.94643
ToMMo 54KJPN AC . 32
ToMMo 54KJPN AF . 0.000589
ToMMo 54KJPN AN . 54302
COSMIC 90 . .
dbSNP 156 id . .
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