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5178 (C > A)

General info

Mitimpact ID
MI.14253
Chr
chrM
Start
5178
Ref
C
Alt
A
Gene symbol
MT-ND2 Extended gene annotation
Gene position
709
Gene start
4470
Gene end
5511
Gene strand
+
Codon substitution
CTA/ATA
AA pos
237
AA ref
L
AA alt
M
Functional effect
missense
OMIM ID
516001
HGVS
NC_012920.1:g.5178C>A
HGNC ID
7456
RC complex
I
Ensembl gene ID
ENSG00000198763
Ensembl protein ID
ENSP00000355046
Ensembl transcript ID
ENST00000361453
Uniprot ID
P03891
Uniprot name
NU2M_HUMAN
Ncbi gene ID
4536
Ncbi protein ID
YP_003024027.1
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Conservation

PhyloP 100v
-4.27 Conservation Score
PhyloP 470way
-0.921 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.002 Conservation Score

Pathogenicity predictors

PolyPhen2
Possibly damaging 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
.
fathmm
.
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
.
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
Disease Score and details of the predictor
PhD-SNP
Neutral Score and details of the predictor

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
Neutral Score and details of the meta-predictor
COVEC WMV
Neutral Score and details of the meta-predictor
MtoolBox
Deleterious Score and details of the meta-predictor
DEOGEN2
.
Meta SNP
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
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
692551
Clinvar ALLELEID
681087
Clinvar CLNDISDB
Mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506
Clinvar CLNDN
Leigh syndrome
Clinvar CLNSIG
Benign
MITOMAP Allele
5178C>A
MITOMAP Disease Clinical info
Longevity / extraversion / diabetes / ams protection / blood iron metabolism / correlation with myocardial infarction / atherosclerosis
MITOMAP Disease Status
Reported
MITOMAP Disease Hom/Het
+/+
MITOMAP General GenBank Freq
4.5016%
MITOMAP General GenBank Seqs
2752
MITOMAP General GenBank Curated refs
29670672 18545700 19497304 24467713 12384792 8352271 24470521 10924403 8037701 31488191 16624503 10996007 24002810 11179019 17257906 19370763 31478599 15126279 11150049 21099167 8808611 21319252 11573146 15638829 18679013 1346260 8728098 19167085 11669538 17300996 11735027 8016139 18639500 12375058 16271520 18468491 9837836 20067846 21978175 7688932 15211636 21385625 34724985 30242360 12391595 17942074 22487888 10909988 16895436 30592262 24062162 34433719 12436196 15670746 20555337 25834827 12483296 22333566 16048457 12782420 18322915 22781753 9837837 15262184 19130794 19818876 19703591 20306229 15708009 23304069 7521328 28951770 11938495 7646496 16714301 2043137 19733221 35801081 24667788 14604458 29343773 18386806 9449878 19324017 7874114 17259400 29987491 19667492 18194667 17341440 30446962 16982817
MITOMAP Variant Class
polymorphism;disease
Gnomad AN
56426
Gnomad AC hom
603
Gnomad AF hom
0.0106865
Gnomad AC het
0
Gnomad AF het
0.0
Gnomad filter
Pass
HelixMTdb AC hom
2246
HelixMTdb AF hom
0.0114601
HelixMTdb AC het
10
HelixMTdb AF het
5.1e-05
HelixMTdb mean ARF
0.91217
HelixMTdb max ARF
0.96063
ToMMo JPN54K AC
21466
ToMMo JPN54K AF
0.395308
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
.

5178 (C > G)

General info

Mitimpact ID
MI.14252
Chr
chrM
Start
5178
Ref
C
Alt
G
Gene symbol
MT-ND2 Extended gene annotation
Gene position
709
Gene start
4470
Gene end
5511
Gene strand
+
Codon substitution
CTA/GTA
AA pos
237
AA ref
L
AA alt
V
Functional effect
missense
OMIM ID
516001
HGVS
NC_012920.1:g.5178C>G
HGNC ID
7456
RC complex
I
Ensembl gene ID
ENSG00000198763
Ensembl protein ID
ENSP00000355046
Ensembl transcript ID
ENST00000361453
Uniprot ID
P03891
Uniprot name
NU2M_HUMAN
Ncbi gene ID
4536
Ncbi protein ID
YP_003024027.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
-4.27 Conservation Score
PhyloP 470way
-0.921 Conservation Score
PhastCons 100v
0 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
Low 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
Neutral 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
Deleterious 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
Medium 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
5178C>G
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
.
~ 5178 (C/A) 5178 (C/G)
~ 5178 (CTA/ATA) 5178 (CTA/GTA)
MitImpact id MI.14253 MI.14252
Chr chrM chrM
Start 5178 5178
Ref C C
Alt A G
Gene symbol MT-ND2 MT-ND2
Extended annotation mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 2 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 2
Gene position 709 709
Gene start 4470 4470
Gene end 5511 5511
Gene strand + +
Codon substitution CTA/ATA CTA/GTA
AA position 237 237
AA ref L L
AA alt M V
Functional effect general missense missense
Functional effect detailed missense missense
OMIM id 516001 516001
HGVS NC_012920.1:g.5178C>A NC_012920.1:g.5178C>G
HGNC id 7456 7456
Respiratory Chain complex I I
Ensembl gene id ENSG00000198763 ENSG00000198763
Ensembl transcript id ENST00000361453 ENST00000361453
Ensembl protein id ENSP00000355046 ENSP00000355046
Uniprot id P03891 P03891
Uniprot name NU2M_HUMAN NU2M_HUMAN
Ncbi gene id 4536 4536
Ncbi protein id YP_003024027.1 YP_003024027.1
PhyloP 100V -4.27 -4.27
PhyloP 470Way -0.921 -0.921
PhastCons 100V 0 0
PhastCons 470Way 0.002 0.002
PolyPhen2 possibly_damaging benign
PolyPhen2 score 0.9 0.3
SIFT neutral neutral
SIFT score 0.25 0.51
SIFT4G Tolerated Tolerated
SIFT4G score 0.435 0.101
VEST Neutral Neutral
VEST pvalue 0.32 0.35
VEST FDR 0.5 0.5
Mitoclass.1 neutral neutral
SNPDryad Neutral Neutral
SNPDryad score 0.43 0.22
MutationTaster . Polymorphism
MutationTaster score . 1.0
MutationTaster converted rankscore . 0.08975
MutationTaster model . complex_aae
MutationTaster AAE . L237V
fathmm . Tolerated
fathmm score . 4.6
fathmm converted rankscore . 0.01868
AlphaMissense likely_benign likely_benign
AlphaMissense score 0.0633 0.112
CADD Neutral Neutral
CADD score 2.364958 2.355273
CADD phred 18.59 18.53
PROVEAN Tolerated Tolerated
PROVEAN score 0.39 -0.24
MutationAssessor . low
MutationAssessor score . 1.375
EFIN SP Neutral Neutral
EFIN SP score 0.986 0.88
EFIN HD Neutral Neutral
EFIN HD score 0.826 0.758
MLC Neutral Neutral
MLC score 0.36743316 0.36743316
PANTHER score 0.636 .
PhD-SNP score 0.128 .
APOGEE1 Pathogenic Neutral
APOGEE1 score 0.68 0.38
APOGEE2 Benign Benign
APOGEE2 score 0.0309644098990708 0.0605315709291483
CAROL neutral neutral
CAROL score 0.92 0.39
Condel neutral deleterious
Condel score 0.18 0.61
COVEC WMV neutral neutral
COVEC WMV score -3 -6
MtoolBox deleterious deleterious
MtoolBox DS 0.63 0.46
DEOGEN2 . Tolerated
DEOGEN2 score . 0.009375
DEOGEN2 converted rankscore . 0.08542
Meta-SNP Neutral .
Meta-SNP score 0.208 .
PolyPhen2 transf low impact medium impact
PolyPhen2 transf score -1.67 -0.46
SIFT_transf medium impact medium impact
SIFT transf score -0.06 0.22
MutationAssessor transf low impact medium impact
MutationAssessor transf score -1.03 -0.72
CHASM Neutral Neutral
CHASM pvalue 0.51 0.3
CHASM FDR 0.8 0.8
ClinVar id 692551.0 .
ClinVar Allele id 681087.0 .
ClinVar CLNDISDB MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506 .
ClinVar CLNDN Leigh_syndrome .
ClinVar CLNSIG Benign .
MITOMAP Disease Clinical info Longevity / Extraversion / diabetes / AMS protection / blood iron metabolism / correlation with myocardial infarction / atherosclerosis .
MITOMAP Disease Status Reported .
MITOMAP Disease Hom/Het +/+ ./.
MITOMAP General GenBank Freq 4.5016% .
MITOMAP General GenBank Seqs 2752 .
MITOMAP General Curated refs 29670672;18545700;19497304;24467713;12384792;8352271;24470521;10924403;8037701;31488191;16624503;10996007;24002810;11179019;17257906;19370763;31478599;15126279;11150049;21099167;8808611;21319252;11573146;15638829;18679013;1346260;8728098;19167085;11669538;17300996;11735027;8016139;18639500;12375058;16271520;18468491;9837836;20067846;21978175;7688932;15211636;21385625;34724985;30242360;12391595;17942074;22487888;10909988;16895436;30592262;24062162;34433719;12436196;15670746;20555337;25834827;12483296;22333566;16048457;12782420;18322915;22781753;9837837;15262184;19130794;19818876;19703591;20306229;15708009;23304069;7521328;28951770;11938495;7646496;16714301;2043137;19733221;35801081;24667788;14604458;29343773;18386806;9449878;19324017;7874114;17259400;29987491;19667492;18194667;17341440;30446962;16982817 .
MITOMAP Variant Class polymorphism;disease .
gnomAD 3.1 AN 56426.0 .
gnomAD 3.1 AC Homo 603.0 .
gnomAD 3.1 AF Hom 0.0106866 .
gnomAD 3.1 AC Het 0.0 .
gnomAD 3.1 AF Het 0.0 .
gnomAD 3.1 filter PASS .
HelixMTdb AC Hom 2246.0 .
HelixMTdb AF Hom 0.011460178 .
HelixMTdb AC Het 10.0 .
HelixMTdb AF Het 5.1024836e-05 .
HelixMTdb mean ARF 0.91217 .
HelixMTdb max ARF 0.96063 .
ToMMo 54KJPN AC 21466 .
ToMMo 54KJPN AF 0.395308 .
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