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12338 (T > C)

General info

Mitimpact ID
MI.19227
Chr
chrM
Start
12338
Ref
T
Alt
C
Gene symbol
MT-ND5 Extended gene annotation
Gene position
2
Gene start
12337
Gene end
14148
Gene strand
+
Codon substitution
ATA/ACA
AA pos
1
AA ref
M
AA alt
T
Functional effect
start_lost
OMIM ID
516005
HGVS
NC_012920.1:g.12338T>C
HGNC ID
7461
RC complex
I
Ensembl gene ID
ENSG00000198786
Ensembl protein ID
ENSP00000354813
Ensembl transcript ID
ENST00000361567
Uniprot ID
P03915
Uniprot name
NU5M_HUMAN
Ncbi gene ID
4540
Ncbi protein ID
YP_003024036.1
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Conservation

PhyloP 100v
2.293 Conservation Score
PhyloP 470way
0.666 Conservation Score
PhastCons 100v
0.992 Conservation Score
PhastCons 470way
0.693 Conservation Score

Pathogenicity predictors

PolyPhen2
Unknown 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
Neutral Score and details of the predictor
PROVEAN
Damaging Score and details of the predictor
Mutation Assessor
.
EFIN SP
Neutral 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
Deleterious 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
29999
Clinvar ALLELEID
38954
Clinvar CLNDISDB
Mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506;

human phenotype ontology:hp:0001086, human phenotype ontology:hp:0001112, mondo:mondo:0010788, medgen:c0917796, omim:535000, orphanet:104
Clinvar CLNDN
Leigh syndrome;

leber optic atrophy
Clinvar CLNSIG
Benign
MITOMAP Allele
12338T>C
MITOMAP Disease Clinical info
Deaf1555 increased penetrance / lhon / midd
MITOMAP Disease Status
Conflicting reports
MITOMAP Disease Hom/Het
+/-
MITOMAP General GenBank Freq
0.3288%
MITOMAP General GenBank Seqs
201
MITOMAP General GenBank Curated refs
18386806 34993838 11507041 29997041 15278763 29387390 16714301 19026397 21482521 29987491 21724059 21419139 12406974 19818876 29579248 21131053
MITOMAP Variant Class
polymorphism;disease
Gnomad AN
56430
Gnomad AC hom
70
Gnomad AF hom
0.0012404
Gnomad AC het
2
Gnomad AF het
3.54e-05
Gnomad filter
Pass
HelixMTdb AC hom
219
HelixMTdb AF hom
0.0011174
HelixMTdb AC het
5
HelixMTdb AF het
2.55e-05
HelixMTdb mean ARF
0.31856
HelixMTdb max ARF
0.57692
ToMMo JPN54K AC
258
ToMMo JPN54K AF
0.004751
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
.

12338 (T > A)

General info

Mitimpact ID
MI.19228
Chr
chrM
Start
12338
Ref
T
Alt
A
Gene symbol
MT-ND5 Extended gene annotation
Gene position
2
Gene start
12337
Gene end
14148
Gene strand
+
Codon substitution
ATA/AAA
AA pos
1
AA ref
M
AA alt
K
Functional effect
start_lost
OMIM ID
516005
HGVS
NC_012920.1:g.12338T>A
HGNC ID
7461
RC complex
I
Ensembl gene ID
ENSG00000198786
Ensembl protein ID
ENSP00000354813
Ensembl transcript ID
ENST00000361567
Uniprot ID
P03915
Uniprot name
NU5M_HUMAN
Ncbi gene ID
4540
Ncbi protein ID
YP_003024036.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
2.293 Conservation Score
PhyloP 470way
0.666 Conservation Score
PhastCons 100v
0.992 Conservation Score
PhastCons 470way
0.693 Conservation Score

Pathogenicity predictors

PolyPhen2
Unknown 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
Pathogenic Score and details of the predictor
MutationTaster
.
fathmm
.
AlphaMissense
.
CADD
Neutral Score and details of the predictor
PROVEAN
Damaging 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
Deleterious 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
Deleterious 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
12338T>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
.
~ 12338 (T/C) 12338 (T/A)
~ 12338 (ATA/ACA) 12338 (ATA/AAA)
MitImpact id MI.19227 MI.19228
Chr chrM chrM
Start 12338 12338
Ref T T
Alt C A
Gene symbol MT-ND5 MT-ND5
Extended annotation mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 5 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 5
Gene position 2 2
Gene start 12337 12337
Gene end 14148 14148
Gene strand + +
Codon substitution ATA/ACA ATA/AAA
AA position 1 1
AA ref M M
AA alt T K
Functional effect general start_lost start_lost
Functional effect detailed start_lost start_lost
OMIM id 516005 516005
HGVS NC_012920.1:g.12338T>C NC_012920.1:g.12338T>A
HGNC id 7461 7461
Respiratory Chain complex I I
Ensembl gene id ENSG00000198786 ENSG00000198786
Ensembl transcript id ENST00000361567 ENST00000361567
Ensembl protein id ENSP00000354813 ENSP00000354813
Uniprot id P03915 P03915
Uniprot name NU5M_HUMAN NU5M_HUMAN
Ncbi gene id 4540 4540
Ncbi protein id YP_003024036.1 YP_003024036.1
PhyloP 100V 2.293 2.293
PhyloP 470Way 0.666 0.666
PhastCons 100V 0.992 0.992
PhastCons 470Way 0.693 0.693
PolyPhen2 unknown unknown
PolyPhen2 score . .
SIFT deleterious deleterious
SIFT score 0.0 0.0
SIFT4G Damaging Damaging
SIFT4G score 0.0 0.0
VEST Neutral Neutral
VEST pvalue 0.38 0.21
VEST FDR 0.5 0.45
Mitoclass.1 damaging damaging
SNPDryad Neutral Pathogenic
SNPDryad score 0.78 0.9
MutationTaster . .
MutationTaster score . .
MutationTaster converted rankscore . .
MutationTaster model . .
MutationTaster AAE . .
fathmm . .
fathmm score . .
fathmm converted rankscore . .
AlphaMissense . .
AlphaMissense score . .
CADD Neutral Neutral
CADD score 1.103053 2.168086
CADD phred 11.23 17.3
PROVEAN Damaging Damaging
PROVEAN score -3.8 -3.91
MutationAssessor . .
MutationAssessor score . .
EFIN SP Neutral Neutral
EFIN SP score 0.754 0.736
EFIN HD Damaging Neutral
EFIN HD score 0.268 0.292
MLC Deleterious Deleterious
MLC score 0.7 0.7
PANTHER score . .
PhD-SNP score . .
APOGEE1 Pathogenic Neutral
APOGEE1 score 0.61 0.49
APOGEE2 VUS- VUS-
APOGEE2 score 0.287159847475625 0.34155652361722
CAROL deleterious deleterious
CAROL score 1.0 1.0
Condel deleterious deleterious
Condel score 0.5 0.5
COVEC WMV deleterious deleterious
COVEC WMV score 2 2
MtoolBox deleterious deleterious
MtoolBox DS 0.49 0.52
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 0.28 0.42
CHASM FDR 0.8 0.8
ClinVar id 29999.0 .
ClinVar Allele id 38954.0 .
ClinVar CLNDISDB MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506|Human_Phenotype_Ontology:HP:0001086,Human_Phenotype_Ontology:HP:0001112,MONDO:MONDO:0010788,MedGen:C0917796,OMIM:535000,Orphanet:104 .
ClinVar CLNDN Leigh_syndrome|Leber_optic_atrophy .
ClinVar CLNSIG Benign .
MITOMAP Disease Clinical info DEAF1555 increased penetrance / LHON / MIDD .
MITOMAP Disease Status Conflicting reports .
MITOMAP Disease Hom/Het +/- ./.
MITOMAP General GenBank Freq 0.3288% .
MITOMAP General GenBank Seqs 201 .
MITOMAP General Curated refs 18386806;34993838;11507041;29997041;15278763;29387390;16714301;19026397;21482521;29987491;21724059;21419139;12406974;19818876;29579248;21131053 .
MITOMAP Variant Class polymorphism;disease .
gnomAD 3.1 AN 56430.0 .
gnomAD 3.1 AC Homo 70.0 .
gnomAD 3.1 AF Hom 0.00124047 .
gnomAD 3.1 AC Het 2.0 .
gnomAD 3.1 AF Het 3.54421e-05 .
gnomAD 3.1 filter PASS .
HelixMTdb AC Hom 219.0 .
HelixMTdb AF Hom 0.0011174439 .
HelixMTdb AC Het 5.0 .
HelixMTdb AF Het 2.5512418e-05 .
HelixMTdb mean ARF 0.31856 .
HelixMTdb max ARF 0.57692 .
ToMMo 54KJPN AC 258 .
ToMMo 54KJPN AF 0.004751 .
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