~ | 10197 (G/C) | 10197 (G/A) | 10197 (G/T) |
---|---|---|---|
~ | 10197 (GCC/CCC) | 10197 (GCC/ACC) | 10197 (GCC/TCC) |
MitImpact id | MI.15260 | MI.15259 | MI.15258 |
Chr | chrM | chrM | chrM |
Start | 10197 | 10197 | 10197 |
Ref | G | G | G |
Alt | C | A | T |
Gene symbol | MT-ND3 | MT-ND3 | MT-ND3 |
Extended annotation | mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 3 | mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 3 | mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 3 |
Gene position | 139 | 139 | 139 |
Gene start | 10059 | 10059 | 10059 |
Gene end | 10404 | 10404 | 10404 |
Gene strand | + | + | + |
Codon substitution | GCC/CCC | GCC/ACC | GCC/TCC |
AA position | 47 | 47 | 47 |
AA ref | A | A | A |
AA alt | P | T | S |
Functional effect general | missense | missense | missense |
Functional effect detailed | missense | missense | missense |
OMIM id | 516002 | 516002 | 516002 |
HGVS | NC_012920.1:g.10197G>C | NC_012920.1:g.10197G>A | NC_012920.1:g.10197G>T |
HGNC id | 7458 | 7458 | 7458 |
Respiratory Chain complex | I | I | I |
Ensembl gene id | ENSG00000198840 | ENSG00000198840 | ENSG00000198840 |
Ensembl transcript id | ENST00000361227 | ENST00000361227 | ENST00000361227 |
Ensembl protein id | ENSP00000355206 | ENSP00000355206 | ENSP00000355206 |
Uniprot id | P03897 | P03897 | P03897 |
Uniprot name | NU3M_HUMAN | NU3M_HUMAN | NU3M_HUMAN |
Ncbi gene id | 4537 | 4537 | 4537 |
Ncbi protein id | YP_003024033.1 | YP_003024033.1 | YP_003024033.1 |
PhyloP 100V | 4.687 | 4.687 | 4.687 |
PhyloP 470Way | 0.848 | 0.848 | 0.848 |
PhastCons 100V | 1 | 1 | 1 |
PhastCons 470Way | 0.007 | 0.007 | 0.007 |
PolyPhen2 | probably_damaging | probably_damaging | probably_damaging |
PolyPhen2 score | 1.0 | 1.0 | 1.0 |
SIFT | neutral | neutral | neutral |
SIFT score | 0.32 | 0.52 | 1.0 |
SIFT4G | Damaging | Damaging | Damaging |
SIFT4G score | 0.001 | 0.0 | 0.007 |
VEST | Pathogenic | Neutral | Neutral |
VEST pvalue | 0.04 | 0.17 | 0.26 |
VEST FDR | 0.35 | 0.45 | 0.45 |
Mitoclass.1 | damaging | damaging | neutral |
SNPDryad | Pathogenic | Pathogenic | Pathogenic |
SNPDryad score | 0.96 | 0.93 | 0.98 |
MutationTaster | Polymorphism | Disease automatic | Polymorphism |
MutationTaster score | 1 | 3.23265e-07 | 0.999992 |
MutationTaster converted rankscore | 0.08975 | 0.08975 | 0.08975 |
MutationTaster model | complex_aae | complex_aae | complex_aae |
MutationTaster AAE | A47P | A47T | A47S |
fathmm | Tolerated | Tolerated | Tolerated |
fathmm score | 0.82 | 0.89 | 0.98 |
fathmm converted rankscore | 0.48142 | 0.45636 | 0.42122 |
AlphaMissense | ambiguous | likely_benign | likely_benign |
AlphaMissense score | 0.4019 | 0.2513 | 0.1583 |
CADD | Deleterious | Deleterious | Deleterious |
CADD score | 3.865291 | 4.196092 | 3.717795 |
CADD phred | 23.5 | 23.9 | 23.3 |
PROVEAN | Damaging | Damaging | Damaging |
PROVEAN score | -4.73 | -3.52 | -2.76 |
MutationAssessor | medium | medium | low |
MutationAssessor score | 2.03 | 2.045 | 1.14 |
EFIN SP | Damaging | Damaging | Damaging |
EFIN SP score | 0.39 | 0.094 | 0.456 |
EFIN HD | Damaging | Neutral | Neutral |
EFIN HD score | 0.236 | 0.38 | 0.366 |
MLC | Deleterious | Deleterious | Deleterious |
MLC score | 0.55232663 | 0.55232663 | 0.55232663 |
PANTHER score | . | 0.309 | . |
PhD-SNP score | . | 0.797 | . |
APOGEE1 | Neutral | Pathogenic | Neutral |
APOGEE1 score | 0.46 | 0.88 | 0.39 |
APOGEE2 | VUS+ | Likely-pathogenic | VUS |
APOGEE2 score | 0.645176820055587 | 0.843686040876126 | 0.498126916021381 |
CAROL | deleterious | deleterious | deleterious |
CAROL score | 1.0 | 1.0 | 1.0 |
Condel | neutral | neutral | deleterious |
Condel score | 0.16 | 0.26 | 0.5 |
COVEC WMV | deleterious | deleterious | neutral |
COVEC WMV score | 1 | 1 | -2 |
MtoolBox | deleterious | deleterious | deleterious |
MtoolBox DS | 0.84 | 0.79 | 0.75 |
DEOGEN2 | Damaging | Damaging | Tolerated |
DEOGEN2 score | 0.539619 | 0.52544 | 0.495506 |
DEOGEN2 converted rankscore | 0.84213 | 0.83481 | 0.81820 |
Meta-SNP | . | Disease | . |
Meta-SNP score | . | 0.623 | . |
PolyPhen2 transf | low impact | low impact | low impact |
PolyPhen2 transf score | -3.43 | -3.43 | -3.43 |
SIFT_transf | medium impact | medium impact | high impact |
SIFT transf score | 0.01 | 0.21 | 1.85 |
MutationAssessor transf | medium impact | medium impact | medium impact |
MutationAssessor transf score | 1.39 | 1.22 | 0.51 |
CHASM | Neutral | Neutral | Neutral |
CHASM pvalue | 0.31 | 0.76 | 0.21 |
CHASM FDR | 0.8 | 0.85 | 0.8 |
ClinVar id | . | 9715.0 | . |
ClinVar Allele id | . | 24754.0 | . |
ClinVar CLNDISDB | . | MONDO:MONDO:0027068,MedGen:C4746992,OMIM:500014|MedGen:CN169374|MedGen:CN517202|MONDO:MONDO:0044970,MedGen:C0751651,Orphanet:68380|MedGen:CN043634|MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506|MONDO:MONDO:0010772,MedGen:C1839040,OMIM:500001,Orphanet:99718 | . |
ClinVar CLNDN | . | Mitochondrial_complex_1_deficiency,_mitochondrial_type_1|not_specified|not_provided|Mitochondrial_disease|Mitochondrial_DNA-Associated_Leigh_Syndrome_and_NARP|Leigh_syndrome|Leber_optic_atrophy_and_dystonia | . |
ClinVar CLNSIG | . | Pathogenic | . |
MITOMAP Disease Clinical info | Leigh Disease | Leigh Disease / Dystonia / Stroke / LDYT | . |
MITOMAP Disease Status | Reported | Cfrm [P] | . |
MITOMAP Disease Hom/Het | -/+ | +/+ | ./. |
MITOMAP General GenBank Freq | 0.0% | 0.0049% | . |
MITOMAP General GenBank Seqs | 0 | 3 | . |
MITOMAP General Curated refs | 38437941 | 21978175;37038312;30899856;28429146;30461153;30128709;17413873;18800376;17152068;18977334;35715829;30978515;15372108;19458970;29253894;11130070;30199507;32045392;38465286;20064630;12509511;21364701;30095618;30978516;20972245 | . |
MITOMAP Variant Class | disease | disease | . |
gnomAD 3.1 AN | 56433.0 | 56422.0 | . |
gnomAD 3.1 AC Homo | 0.0 | 0.0 | . |
gnomAD 3.1 AF Hom | 0.0 | 0.0 | . |
gnomAD 3.1 AC Het | 0.0 | 0.0 | . |
gnomAD 3.1 AF Het | 0.0 | 0.0 | . |
gnomAD 3.1 filter | npg | npg | . |
HelixMTdb AC Hom | . | 0.0 | . |
HelixMTdb AF Hom | . | 0.0 | . |
HelixMTdb AC Het | . | 7.0 | . |
HelixMTdb AF Het | . | 3.5717385e-05 | . |
HelixMTdb mean ARF | . | 0.15194 | . |
HelixMTdb max ARF | . | 0.25 | . |
ToMMo 54KJPN AC | . | . | . |
ToMMo 54KJPN AF | . | . | . |
ToMMo 54KJPN AN | . | . | . |
COSMIC 90 | . | . | . |
dbSNP 156 id | . | rs267606891 | . |