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3388 (C > A)

General info

Mitimpact ID
MI.10931
Chr
chrM
Start
3388
Ref
C
Alt
A
Gene symbol
MT-ND1 Extended gene annotation
Gene position
82
Gene start
3307
Gene end
4262
Gene strand
+
Codon substitution
CTA/ATA
AA pos
28
AA ref
L
AA alt
M
Functional effect
missense
OMIM ID
516000
HGVS
NC_012920.1:g.3388C>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
-2.209 Conservation Score
PhyloP 470way
-0.997 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.029 Conservation Score

Pathogenicity predictors

PolyPhen2
Probably damaging 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
.
fathmm
.
AlphaMissense
Likely benign Score and details of the predictor
CADD
Deleterious 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
.
PhD-SNP
.

Pathogenicity meta-predictors

APOGEE1
Neutral 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
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 Frequencies and Phenotypes

Clinvar ID
29998
Clinvar ALLELEID
38953
Clinvar CLNDISDB
Mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506;

mondo:mondo:0010779, medgen:c3151897, omim:500008, orphanet:90641
Clinvar CLNDN
Leigh syndrome;

mitochondrial non-syndromic sensorineural hearing loss
Clinvar CLNSIG
Benign
MITOMAP Allele
3388C>A
MITOMAP Disease Clinical info
Materally inherited nonsyndromic deafness
MITOMAP Disease Status
Reported
MITOMAP Disease Hom/Het
Nr/nr
MITOMAP General GenBank Freq
0.0491%
MITOMAP General GenBank Seqs
30
MITOMAP General GenBank Curated refs
22241583
MITOMAP Variant Class
polymorphism;disease
Gnomad AN
56434
Gnomad AC hom
42
Gnomad AF hom
0.0007442
Gnomad AC het
0
Gnomad AF het
0.0
Gnomad filter
Pass
HelixMTdb AC hom
230
HelixMTdb AF hom
0.0011735
HelixMTdb AC het
1
HelixMTdb AF het
5.1e-06
HelixMTdb mean ARF
0.63226
HelixMTdb max ARF
0.63226
ToMMo JPN54K AC
5
ToMMo JPN54K AF
9.2e-05
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
.

3388 (C > G)

General info

Mitimpact ID
MI.10930
Chr
chrM
Start
3388
Ref
C
Alt
G
Gene symbol
MT-ND1 Extended gene annotation
Gene position
82
Gene start
3307
Gene end
4262
Gene strand
+
Codon substitution
CTA/GTA
AA pos
28
AA ref
L
AA alt
V
Functional effect
missense
OMIM ID
516000
HGVS
NC_012920.1:g.3388C>G
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
-2.209 Conservation Score
PhyloP 470way
-0.997 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.029 Conservation Score

Pathogenicity predictors

PolyPhen2
Probably damaging 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
Damaging 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
Ambiguous Score and details of the predictor
CADD
Deleterious Score and details of the predictor
PROVEAN
Damaging Score and details of the predictor
Mutation Assessor
Medium Score and details of the predictor
EFIN SP
Damaging 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
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
Tolerated Score and details of the meta-predictor
Meta SNP
.

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 Frequencies and Phenotypes

Clinvar ID
.
Clinvar ALLELEID
.
Clinvar CLNDISDB
.
Clinvar CLNDN
.
Clinvar CLNSIG
.
MITOMAP Allele
3388C>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
.
~ 3388 (C/A) 3388 (C/G)
~ 3388 (CTA/ATA) 3388 (CTA/GTA)
MitImpact id MI.10931 MI.10930
Chr chrM chrM
Start 3388 3388
Ref C C
Alt A G
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 82 82
Gene start 3307 3307
Gene end 4262 4262
Gene strand + +
Codon substitution CTA/ATA CTA/GTA
AA position 28 28
AA ref L L
AA alt M V
Functional effect general missense missense
Functional effect detailed missense missense
OMIM id 516000 516000
HGVS NC_012920.1:g.3388C>A NC_012920.1:g.3388C>G
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 -2.209 -2.209
PhyloP 470Way -0.997 -0.997
PhastCons 100V 0 0
PhastCons 470Way 0.029 0.029
PolyPhen2 probably_damaging probably_damaging
PolyPhen2 score 1.0 1.0
SIFT neutral neutral
SIFT score 0.12 0.4
SIFT4G Damaging Damaging
SIFT4G score 0.001 0.001
VEST Neutral Neutral
VEST pvalue 0.31 0.28
VEST FDR 0.45 0.45
Mitoclass.1 neutral damaging
SNPDryad Neutral Neutral
SNPDryad score 0.89 0.84
MutationTaster . Polymorphism
MutationTaster score . 0.999999
MutationTaster converted rankscore . 0.08975
MutationTaster model . complex_aae
MutationTaster AAE . L28V
fathmm . Tolerated
fathmm score . 2.6
fathmm converted rankscore . 0.13204
AlphaMissense likely_benign ambiguous
AlphaMissense score 0.2974 0.371
CADD Deleterious Deleterious
CADD score 3.594937 3.278251
CADD phred 23.2 22.8
PROVEAN Tolerated Damaging
PROVEAN score -1.75 -2.61
MutationAssessor . medium
MutationAssessor score . 3.11
EFIN SP Neutral Damaging
EFIN SP score 0.604 0.596
EFIN HD Neutral Neutral
EFIN HD score 0.608 0.472
MLC Neutral Neutral
MLC score 0.14780614 0.14780614
PANTHER score . .
PhD-SNP score . .
APOGEE1 Neutral Neutral
APOGEE1 score 0.45 0.46
APOGEE2 VUS- VUS+
APOGEE2 score 0.393917605967577 0.628303939318245
CAROL deleterious deleterious
CAROL score 1.0 1.0
Condel neutral neutral
Condel score 0.06 0.2
COVEC WMV deleterious deleterious
COVEC WMV score 1 2
MtoolBox deleterious deleterious
MtoolBox DS 0.81 0.87
DEOGEN2 . Tolerated
DEOGEN2 score . 0.119147
DEOGEN2 converted rankscore . 0.44047
Meta-SNP . .
Meta-SNP score . .
PolyPhen2 transf low impact low impact
PolyPhen2 transf score -3.57 -3.57
SIFT_transf medium impact medium impact
SIFT transf score -0.21 0.18
MutationAssessor transf medium impact high impact
MutationAssessor transf score 1.23 2.62
CHASM Neutral Neutral
CHASM pvalue 0.55 0.52
CHASM FDR 0.8 0.8
ClinVar id 29998.0 .
ClinVar Allele id 38953.0 .
ClinVar CLNDISDB MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506|MONDO:MONDO:0010779,MedGen:C3151897,OMIM:500008,Orphanet:90641 .
ClinVar CLNDN Leigh_syndrome|Mitochondrial_non-syndromic_sensorineural_hearing_loss .
ClinVar CLNSIG Benign .
MITOMAP Disease Clinical info Materally Inherited Nonsyndromic Deafness .
MITOMAP Disease Status Reported .
MITOMAP Disease Hom/Het nr/nr ./.
MITOMAP General GenBank Freq 0.0491% .
MITOMAP General GenBank Seqs 30 .
MITOMAP General Curated refs 22241583 .
MITOMAP Variant Class polymorphism;disease .
gnomAD 3.1 AN 56434.0 .
gnomAD 3.1 AC Homo 42.0 .
gnomAD 3.1 AF Hom 0.0007442319999999999 .
gnomAD 3.1 AC Het 0.0 .
gnomAD 3.1 AF Het 0.0 .
gnomAD 3.1 filter PASS .
HelixMTdb AC Hom 230.0 .
HelixMTdb AF Hom 0.0011735712 .
HelixMTdb AC Het 1.0 .
HelixMTdb AF Het 5.1024836e-06 .
HelixMTdb mean ARF 0.63226 .
HelixMTdb max ARF 0.63226 .
ToMMo 54KJPN AC 5 .
ToMMo 54KJPN AF 9.2e-05 .
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