~ | 4219 (G/C) | 4219 (G/A) | 4219 (G/T) |
---|---|---|---|
~ | 4219 (GTC/CTC) | 4219 (GTC/ATC) | 4219 (GTC/TTC) |
MitImpact id | MI.12659 | MI.12660 | MI.12658 |
Chr | chrM | chrM | chrM |
Start | 4219 | 4219 | 4219 |
Ref | G | G | G |
Alt | C | A | T |
Gene symbol | MT-ND1 | MT-ND1 | MT-ND1 |
Extended annotation | mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 1 | mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 1 | mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 1 |
Gene position | 913 | 913 | 913 |
Gene start | 3307 | 3307 | 3307 |
Gene end | 4262 | 4262 | 4262 |
Gene strand | + | + | + |
Codon substitution | GTC/CTC | GTC/ATC | GTC/TTC |
AA position | 305 | 305 | 305 |
AA ref | V | V | V |
AA alt | L | I | F |
Functional effect general | missense | missense | missense |
Functional effect detailed | missense | missense | missense |
OMIM id | 516000 | 516000 | 516000 |
HGVS | NC_012920.1:g.4219G>C | NC_012920.1:g.4219G>A | NC_012920.1:g.4219G>T |
HGNC id | 7455 | 7455 | 7455 |
Respiratory Chain complex | I | I | I |
Ensembl gene id | ENSG00000198888 | ENSG00000198888 | ENSG00000198888 |
Ensembl transcript id | ENST00000361390 | ENST00000361390 | ENST00000361390 |
Ensembl protein id | ENSP00000354687 | ENSP00000354687 | ENSP00000354687 |
Uniprot id | P03886 | P03886 | P03886 |
Uniprot name | NU1M_HUMAN | NU1M_HUMAN | NU1M_HUMAN |
Ncbi gene id | 4535 | 4535 | 4535 |
Ncbi protein id | YP_003024026.1 | YP_003024026.1 | YP_003024026.1 |
PhyloP 100V | 0.066 | 0.066 | 0.066 |
PhyloP 470Way | -0.376 | -0.376 | -0.376 |
PhastCons 100V | 0 | 0 | 0 |
PhastCons 470Way | 0.005 | 0.005 | 0.005 |
PolyPhen2 | benign | benign | benign |
PolyPhen2 score | 0.0 | 0.0 | 0.16 |
SIFT | neutral | neutral | neutral |
SIFT score | 1.0 | 0.48 | 0.43 |
SIFT4G | Tolerated | Tolerated | Damaging |
SIFT4G score | 0.665 | 1.0 | 0.011 |
VEST | Neutral | Neutral | Neutral |
VEST pvalue | 0.22 | 0.35 | 0.06 |
VEST FDR | 0.45 | 0.5 | 0.35 |
Mitoclass.1 | neutral | neutral | neutral |
SNPDryad | Neutral | Neutral | Neutral |
SNPDryad score | 0.39 | 0.03 | 0.65 |
MutationTaster | Polymorphism | Polymorphism | Polymorphism |
MutationTaster score | 1.0 | 1.0 | 1.0 |
MutationTaster converted rankscore | 0.08975 | 0.08975 | 0.08975 |
MutationTaster model | complex_aae | complex_aae | complex_aae |
MutationTaster AAE | V305L | V305I | V305F |
fathmm | Tolerated | Tolerated | Tolerated |
fathmm score | 2.77 | 2.81 | 2.7 |
fathmm converted rankscore | 0.11407 | 0.10975 | 0.12162 |
AlphaMissense | likely_benign | likely_benign | likely_benign |
AlphaMissense score | 0.2327 | 0.0781 | 0.2728 |
CADD | Neutral | Neutral | Neutral |
CADD score | -0.553196 | -0.859453 | 1.947693 |
CADD phred | 0.162 | 0.032 | 15.88 |
PROVEAN | Tolerated | Tolerated | Tolerated |
PROVEAN score | 0.01 | 0.24 | -1.95 |
MutationAssessor | neutral | neutral | neutral |
MutationAssessor score | -0.415 | -1.185 | 0.285 |
EFIN SP | Neutral | Neutral | Neutral |
EFIN SP score | 0.806 | 0.726 | 0.764 |
EFIN HD | Neutral | Neutral | Neutral |
EFIN HD score | 0.672 | 0.942 | 0.626 |
MLC | Neutral | Neutral | Neutral |
MLC score | 0.20411612 | 0.20411612 | 0.20411612 |
PANTHER score | . | . | . |
PhD-SNP score | . | . | . |
APOGEE1 | Neutral | Neutral | Neutral |
APOGEE1 score | 0.3 | 0.42 | 0.36 |
APOGEE2 | Likely-benign | Benign | Likely-benign |
APOGEE2 score | 0.0829289572330553 | 0.0178600066502164 | 0.247953448807371 |
CAROL | neutral | neutral | neutral |
CAROL score | 0.0 | 0.52 | 0.49 |
Condel | deleterious | deleterious | deleterious |
Condel score | 1.0 | 0.74 | 0.64 |
COVEC WMV | neutral | neutral | neutral |
COVEC WMV score | -6 | -6 | -6 |
MtoolBox | neutral | neutral | neutral |
MtoolBox DS | 0.08 | 0.08 | 0.16 |
DEOGEN2 | Tolerated | Tolerated | Tolerated |
DEOGEN2 score | 0.008009 | 0.0078 | 0.04136 |
DEOGEN2 converted rankscore | 0.07373 | 0.07183 | 0.25834 |
Meta-SNP | . | . | . |
Meta-SNP score | . | . | . |
PolyPhen2 transf | high impact | high impact | medium impact |
PolyPhen2 transf score | 2.07 | 2.07 | -0.08 |
SIFT_transf | high impact | medium impact | medium impact |
SIFT transf score | 1.96 | 0.26 | 0.21 |
MutationAssessor transf | medium impact | low impact | medium impact |
MutationAssessor transf score | -0.86 | -2.08 | -0.62 |
CHASM | Neutral | Neutral | Neutral |
CHASM pvalue | 0.52 | 0.77 | 0.36 |
CHASM FDR | 0.8 | 0.85 | 0.8 |
ClinVar id | . | 235315.0 | . |
ClinVar Allele id | . | 237002.0 | . |
ClinVar CLNDISDB | . | MedGen:CN517202|MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506 | . |
ClinVar CLNDN | . | not_provided|Leigh_syndrome | . |
ClinVar CLNSIG | . | Benign/Likely_benign | . |
MITOMAP Disease Clinical info | . | . | . |
MITOMAP Disease Status | . | . | . |
MITOMAP Disease Hom/Het | ./. | ./. | ./. |
MITOMAP General GenBank Freq | 0.0% | 0.0802% | . |
MITOMAP General GenBank Seqs | 0 | 49 | . |
MITOMAP General Curated refs | . | 20975840;31797714 | . |
MITOMAP Variant Class | polymorphism | polymorphism | . |
gnomAD 3.1 AN | 56431.0 | 56416.0 | . |
gnomAD 3.1 AC Homo | 0.0 | 57.0 | . |
gnomAD 3.1 AF Hom | 0.0 | 0.00101035 | . |
gnomAD 3.1 AC Het | 0.0 | 3.0 | . |
gnomAD 3.1 AF Het | 0.0 | 5.31764e-05 | . |
gnomAD 3.1 filter | npg | PASS | . |
HelixMTdb AC Hom | 0.0 | 59.0 | . |
HelixMTdb AF Hom | 0.0 | 0.00030104653 | . |
HelixMTdb AC Het | 2.0 | 16.0 | . |
HelixMTdb AF Het | 1.0204967e-05 | 8.163974e-05 | . |
HelixMTdb mean ARF | 0.23311 | 0.40884 | . |
HelixMTdb max ARF | 0.3375 | 0.97368 | . |
ToMMo 54KJPN AC | . | 35 | . |
ToMMo 54KJPN AF | . | 0.000645 | . |
ToMMo 54KJPN AN | . | 54302 | . |
COSMIC 90 | . | . | . |
dbSNP 156 id | . | rs878853008 | . |