| MitImpact id |
MI.10522 |
MI.10523 |
MI.10521 |
| Chr |
chrM |
chrM |
chrM |
| Start |
15777 |
15777 |
15777 |
| Ref |
G |
G |
G |
| Alt |
A |
C |
T |
| Gene symbol |
MT-CYB |
MT-CYB |
MT-CYB |
| Extended annotation |
mitochondrially encoded cytochrome b |
mitochondrially encoded cytochrome b |
mitochondrially encoded cytochrome b |
| Gene position |
1031 |
1031 |
1031 |
| Gene start |
14747 |
14747 |
14747 |
| Gene end |
15887 |
15887 |
15887 |
| Gene strand |
+ |
+ |
+ |
| Codon substitution |
AGC/AAC |
AGC/ACC |
AGC/ATC |
| AA position |
344 |
344 |
344 |
| AA ref |
S |
S |
S |
| AA alt |
N |
T |
I |
| Functional effect general |
missense |
missense |
missense |
| Functional effect detailed |
missense |
missense |
missense |
| OMIM id |
516020 |
516020 |
516020 |
| HGVS |
NC_012920.1:g.15777G>A |
NC_012920.1:g.15777G>C |
NC_012920.1:g.15777G>T |
| HGNC id |
7427 |
7427 |
7427 |
| Respiratory Chain complex |
III |
III |
III |
| Ensembl gene id |
ENSG00000198727 |
ENSG00000198727 |
ENSG00000198727 |
| Ensembl transcript id |
ENST00000361789 |
ENST00000361789 |
ENST00000361789 |
| Ensembl protein id |
ENSP00000354554 |
ENSP00000354554 |
ENSP00000354554 |
| Uniprot id |
P00156 |
P00156 |
P00156 |
| Uniprot name |
CYB_HUMAN |
CYB_HUMAN |
CYB_HUMAN |
| Ncbi gene id |
4519 |
4519 |
4519 |
| Ncbi protein id |
YP_003024038.1 |
YP_003024038.1 |
YP_003024038.1 |
| PhyloP 100V |
4.743 |
4.743 |
4.743 |
| PhyloP 470Way |
-0.139 |
-0.139 |
-0.139 |
| PhastCons 100V |
1 |
1 |
1 |
| PhastCons 470Way |
0.185 |
0.185 |
0.185 |
| PolyPhen2 |
benign |
benign |
possibly_damaging |
| PolyPhen2 score |
0.03 |
0.4 |
0.89 |
| SIFT |
neutral |
neutral |
neutral |
| SIFT score |
0.34 |
0.45 |
0.46 |
| SIFT4G |
Damaging |
Damaging |
Damaging |
| SIFT4G score |
0.011 |
0.009 |
0.0 |
| VEST |
Neutral |
Neutral |
Neutral |
| VEST pvalue |
0.56 |
0.45 |
0.1 |
| VEST FDR |
0.6 |
0.55 |
0.4 |
| Mitoclass.1 |
neutral |
neutral |
neutral |
| SNPDryad |
Neutral |
Neutral |
Neutral |
| SNPDryad score |
0.37 |
0.19 |
0.66 |
| MutationTaster |
. |
. |
. |
| MutationTaster score |
. |
. |
. |
| MutationTaster converted rankscore |
. |
. |
. |
| MutationTaster model |
. |
. |
. |
| MutationTaster AAE |
. |
. |
. |
| fathmm |
. |
. |
. |
| fathmm score |
. |
. |
. |
| fathmm converted rankscore |
. |
. |
. |
| AlphaMissense |
likely_benign |
likely_benign |
likely_benign |
| AlphaMissense score |
0.1048 |
0.0923 |
0.1773 |
| CADD |
Neutral |
Neutral |
Deleterious |
| CADD score |
2.129689 |
1.881933 |
2.588491 |
| CADD phred |
17.05 |
15.48 |
20.1 |
| PROVEAN |
Tolerated |
Tolerated |
Tolerated |
| PROVEAN score |
-0.17 |
-0.67 |
-1.91 |
| MutationAssessor |
low |
neutral |
medium |
| MutationAssessor score |
1.175 |
0.09 |
2.33 |
| EFIN SP |
Neutral |
Neutral |
Neutral |
| EFIN SP score |
0.896 |
0.922 |
0.936 |
| EFIN HD |
Neutral |
Neutral |
Neutral |
| EFIN HD score |
0.788 |
0.634 |
0.674 |
| MLC |
Neutral |
Neutral |
Neutral |
| MLC score |
0.12306114 |
0.12306114 |
0.12306114 |
| PANTHER score |
. |
. |
. |
| PhD-SNP score |
. |
. |
. |
| APOGEE1 |
Pathogenic |
Neutral |
Neutral |
| APOGEE1 score |
0.52 |
0.48 |
0.48 |
| APOGEE2 |
Benign |
Benign |
Likely-benign |
| APOGEE2 score |
0.0148913376005909 |
0.0110603362036623 |
0.0997132530930406 |
| CAROL |
neutral |
neutral |
neutral |
| CAROL score |
0.64 |
0.49 |
0.88 |
| Condel |
deleterious |
deleterious |
neutral |
| Condel score |
0.66 |
0.53 |
0.29 |
| COVEC WMV |
neutral |
neutral |
. |
| COVEC WMV score |
-6 |
-6 |
0 |
| MtoolBox |
neutral |
neutral |
deleterious |
| MtoolBox DS |
0.19 |
0.4 |
0.73 |
| DEOGEN2 |
. |
. |
. |
| DEOGEN2 score |
. |
. |
. |
| DEOGEN2 converted rankscore |
. |
. |
. |
| Meta-SNP |
. |
. |
. |
| Meta-SNP score |
. |
. |
. |
| PolyPhen2 transf |
medium impact |
medium impact |
low impact |
| PolyPhen2 transf score |
0.68 |
-0.57 |
-1.58 |
| SIFT_transf |
medium impact |
medium impact |
medium impact |
| SIFT transf score |
0.07 |
0.18 |
0.18 |
| MutationAssessor transf |
medium impact |
low impact |
medium impact |
| MutationAssessor transf score |
-0.67 |
-1.65 |
0.7 |
| CHASM |
Neutral |
Neutral |
Neutral |
| CHASM pvalue |
0.29 |
0.34 |
0.19 |
| CHASM FDR |
0.8 |
0.8 |
0.8 |
| ClinVar id |
377195.0 |
693950.0 |
. |
| ClinVar Allele id |
364073.0 |
680840.0 |
. |
| ClinVar CLNDISDB |
MedGen:CN517202|MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506 |
MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506 |
. |
| ClinVar CLNDN |
not_provided|Leigh_syndrome |
Leigh_syndrome |
. |
| ClinVar CLNSIG |
Benign/Likely_benign |
Benign |
. |
| MITOMAP Disease Clinical info |
. |
. |
. |
| MITOMAP Disease Status |
. |
. |
. |
| MITOMAP Disease Hom/Het |
./. |
./. |
./. |
| MITOMAP General GenBank Freq |
0.1832% |
0.0523% |
. |
| MITOMAP General GenBank Seqs |
112 |
32 |
. |
| MITOMAP General Curated refs |
21281460;24467713;18477584;18335039;16901986 |
18691441 |
. |
| MITOMAP Variant Class |
polymorphism |
polymorphism |
. |
| gnomAD 3.1 AN |
56414.0 |
56432.0 |
56433.0 |
| gnomAD 3.1 AC Homo |
38.0 |
138.0 |
0.0 |
| gnomAD 3.1 AF Hom |
0.000673592 |
0.00244542 |
0.0 |
| gnomAD 3.1 AC Het |
8.0 |
0.0 |
0.0 |
| gnomAD 3.1 AF Het |
0.000141809 |
0.0 |
0.0 |
| gnomAD 3.1 filter |
PASS |
PASS |
npg |
| HelixMTdb AC Hom |
140.0 |
68.0 |
. |
| HelixMTdb AF Hom |
0.0007143477 |
0.00034696888 |
. |
| HelixMTdb AC Het |
26.0 |
2.0 |
. |
| HelixMTdb AF Het |
0.00013266457 |
1.0204967e-05 |
. |
| HelixMTdb mean ARF |
0.40239 |
0.24793 |
. |
| HelixMTdb max ARF |
0.87421 |
0.3098 |
. |
| ToMMo 54KJPN AC |
33 |
0 |
. |
| ToMMo 54KJPN AF |
0.000608 |
0 |
. |
| ToMMo 54KJPN AN |
54302 |
54302 |
. |
| COSMIC 90 |
. |
. |
. |
| dbSNP 156 id |
. |
. |
. |