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

14748 (T > C)

General info

Mitimpact ID
MI.8319
Chr
chrM
Start
14748
Ref
T
Alt
C
Gene symbol
MT-CYB Extended gene annotation
Gene position
2
Gene start
14747
Gene end
15887
Gene strand
+
Codon substitution
ATG/ACG
AA pos
1
AA ref
M
AA alt
T
Functional effect
start_lost
OMIM ID
516020
HGVS
NC_012920.1:g.14748T>C
HGNC ID
7427
RC complex
III
Ensembl gene ID
ENSG00000198727
Ensembl protein ID
ENSP00000354554
Ensembl transcript ID
ENST00000361789
Uniprot ID
P00156
Uniprot name
CYB_HUMAN
Ncbi gene ID
4519
Ncbi protein ID
YP_003024038.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
7.153 Conservation Score
PhyloP 470way
0.666 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.947 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
Pathogenic 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
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
Likely-benign 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
693753
Clinvar ALLELEID
680643
Clinvar CLNDISDB
Mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506
Clinvar CLNDN
Leigh syndrome
Clinvar CLNSIG
Uncertain significance
MITOMAP Allele
14748T>C
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
0.0%
MITOMAP General GenBank Seqs
0
MITOMAP General GenBank Curated refs
.
MITOMAP Variant Class
polymorphism
Gnomad AN
56433
Gnomad AC hom
0
Gnomad AF hom
0.0
Gnomad AC het
0
Gnomad AF het
0.0
Gnomad filter
Npg
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
.

14748 (T > A)

General info

Mitimpact ID
MI.8318
Chr
chrM
Start
14748
Ref
T
Alt
A
Gene symbol
MT-CYB Extended gene annotation
Gene position
2
Gene start
14747
Gene end
15887
Gene strand
+
Codon substitution
ATG/AAG
AA pos
1
AA ref
M
AA alt
K
Functional effect
start_lost
OMIM ID
516020
HGVS
NC_012920.1:g.14748T>A
HGNC ID
7427
RC complex
III
Ensembl gene ID
ENSG00000198727
Ensembl protein ID
ENSP00000354554
Ensembl transcript ID
ENST00000361789
Uniprot ID
P00156
Uniprot name
CYB_HUMAN
Ncbi gene ID
4519
Ncbi protein ID
YP_003024038.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
7.153 Conservation Score
PhyloP 470way
0.666 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.947 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
Pathogenic 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
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
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
14748T>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
.
~ 14748 (T/C) 14748 (T/A)
~ 14748 (ATG/ACG) 14748 (ATG/AAG)
MitImpact id MI.8319 MI.8318
Chr chrM chrM
Start 14748 14748
Ref T T
Alt C A
Gene symbol MT-CYB MT-CYB
Extended annotation mitochondrially encoded cytochrome b mitochondrially encoded cytochrome b
Gene position 2 2
Gene start 14747 14747
Gene end 15887 15887
Gene strand + +
Codon substitution ATG/ACG ATG/AAG
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 516020 516020
HGVS NC_012920.1:g.14748T>C NC_012920.1:g.14748T>A
HGNC id 7427 7427
Respiratory Chain complex III III
Ensembl gene id ENSG00000198727 ENSG00000198727
Ensembl transcript id ENST00000361789 ENST00000361789
Ensembl protein id ENSP00000354554 ENSP00000354554
Uniprot id P00156 P00156
Uniprot name CYB_HUMAN CYB_HUMAN
Ncbi gene id 4519 4519
Ncbi protein id YP_003024038.1 YP_003024038.1
PhyloP 100V 7.153 7.153
PhyloP 470Way 0.666 0.666
PhastCons 100V 1 1
PhastCons 470Way 0.947 0.947
PolyPhen2 probably_damaging probably_damaging
PolyPhen2 score 0.92 0.92
SIFT deleterious deleterious
SIFT score 0.0 0.0
SIFT4G Damaging Damaging
SIFT4G score 0.0 0.0
VEST Neutral Neutral
VEST pvalue 0.11 0.1
VEST FDR 0.4 0.4
Mitoclass.1 damaging damaging
SNPDryad Pathogenic Pathogenic
SNPDryad score 0.99 0.99
MutationTaster . .
MutationTaster score . .
MutationTaster converted rankscore . .
MutationTaster model . .
MutationTaster AAE . .
fathmm . .
fathmm score . .
fathmm converted rankscore . .
AlphaMissense . .
AlphaMissense score . .
CADD Neutral Neutral
CADD score 0.877898 2.022484
CADD phred 9.936 16.35
PROVEAN Tolerated Tolerated
PROVEAN score -1.48 -1.93
MutationAssessor . .
MutationAssessor score . .
EFIN SP Neutral Neutral
EFIN SP score 0.878 0.87
EFIN HD Damaging Damaging
EFIN HD score 0.094 0.068
MLC Deleterious Deleterious
MLC score 0.7 0.7
PANTHER score . .
PhD-SNP score . .
APOGEE1 Pathogenic Pathogenic
APOGEE1 score 0.52 0.54
APOGEE2 Likely-benign VUS-
APOGEE2 score 0.217408965348625 0.284810621034483
CAROL deleterious deleterious
CAROL score 1.0 1.0
Condel neutral neutral
Condel score 0.04 0.04
COVEC WMV deleterious deleterious
COVEC WMV score 4 4
MtoolBox deleterious deleterious
MtoolBox DS 0.73 0.73
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 0.03 0.06
CHASM FDR 0.8 0.8
ClinVar id 693753.0 .
ClinVar Allele id 680643.0 .
ClinVar CLNDISDB MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506 .
ClinVar CLNDN Leigh_syndrome .
ClinVar CLNSIG Uncertain_significance .
MITOMAP Disease Clinical info . .
MITOMAP Disease Status . .
MITOMAP Disease Hom/Het ./. ./.
MITOMAP General GenBank Freq 0.0% .
MITOMAP General GenBank Seqs 0 .
MITOMAP General Curated refs . .
MITOMAP Variant Class polymorphism .
gnomAD 3.1 AN 56433.0 .
gnomAD 3.1 AC Homo 0.0 .
gnomAD 3.1 AF Hom 0.0 .
gnomAD 3.1 AC Het 0.0 .
gnomAD 3.1 AF Het 0.0 .
gnomAD 3.1 filter npg .
HelixMTdb AC Hom . .
HelixMTdb AF Hom . .
HelixMTdb AC Het . .
HelixMTdb AF Het . .
HelixMTdb mean ARF . .
HelixMTdb max ARF . .
ToMMo 54KJPN AC . .
ToMMo 54KJPN AF . .
ToMMo 54KJPN AN . .
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