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10609 (T > C)

General info

Mitimpact ID
MI.15983
Chr
chrM
Start
10609
Ref
T
Alt
C
Gene symbol
MT-ND4L Extended gene annotation
Gene position
140
Gene start
10470
Gene end
10766
Gene strand
+
Codon substitution
ATA/ACA
AA pos
47
AA ref
M
AA alt
T
Functional effect
missense
OMIM ID
516004
HGVS
NC_012920.1:g.10609T>C
HGNC ID
7460
RC complex
I
Ensembl gene ID
ENSG00000212907
Ensembl protein ID
ENSP00000354728
Ensembl transcript ID
ENST00000361335
Uniprot ID
P03901
Uniprot name
NU4LM_HUMAN
Ncbi gene ID
4539
Ncbi protein ID
YP_003024034.1
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Conservation

PhyloP 100v
-0.299 Conservation Score
PhyloP 470way
0.666 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.015 Conservation Score

Pathogenicity predictors

PolyPhen2
Benign Score and details of the predictor
SIFT
Neutral Score and details of the predictor
SIFT4G
Tolerated Score and details of the predictor
VEST
Neutral Score and details of the predictor
MitoClass 1
Neutral Score and details of the predictor
SNPDryad
Neutral Score and details of the predictor
MutationTaster
.
fathmm
.
AlphaMissense
Likely benign Score and details of the predictor
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
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
Benign Score and details of the meta-predictor
CAROL
Neutral Score and details of the meta-predictor
Condel
Deleterious Score and details of the meta-predictor
COVEC WMV
Neutral Score and details of the meta-predictor
MtoolBox
Neutral Score and details of the meta-predictor
DEOGEN2
.
Meta SNP
.

Cancer-specific predictors

PolyPhen2 transf
Medium impact Score and details of the cancer-specific predictor
SIFT transf
Medium impact Score and details of the cancer-specific predictor
MutationAssessor transf
Low impact Score and details of the cancer-specific predictor
CHASM
Neutral Score and details of the cancer-specific predictor

Databases of Frequencies and Phenotypes

Clinvar ID
693302
Clinvar ALLELEID
680192
Clinvar CLNDISDB
Mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506
Clinvar CLNDN
Leigh syndrome
Clinvar CLNSIG
Benign
MITOMAP Allele
10609T>C
MITOMAP Disease Clinical info
Type 2 diabetes patients with underlying 3243g / lhon patient with 10663c
MITOMAP Disease Status
Reported
MITOMAP Disease Hom/Het
Nr/nr
MITOMAP General GenBank Freq
2.3424%
MITOMAP General GenBank Seqs
1432
MITOMAP General GenBank Curated refs
21281460 29997041 19732751 18545700 19818876 9443868 23304069 19026397 17434445 17942074 16714301 24568867 24667788 17698299 12436196 33402819 24002810 20153673 16048457 20067846 17341440
MITOMAP Variant Class
polymorphism;disease
Gnomad AN
56425
Gnomad AC hom
208
Gnomad AF hom
0.0036863
Gnomad AC het
1
Gnomad AF het
1.77e-05
Gnomad filter
Pass
HelixMTdb AC hom
830
HelixMTdb AF hom
0.004235
HelixMTdb AC het
11
HelixMTdb AF het
5.61e-05
HelixMTdb mean ARF
0.45976
HelixMTdb max ARF
0.92
ToMMo JPN54K AC
3286
ToMMo JPN54K AF
0.060513
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
.

10609 (T > A)

General info

Mitimpact ID
MI.15982
Chr
chrM
Start
10609
Ref
T
Alt
A
Gene symbol
MT-ND4L Extended gene annotation
Gene position
140
Gene start
10470
Gene end
10766
Gene strand
+
Codon substitution
ATA/AAA
AA pos
47
AA ref
M
AA alt
K
Functional effect
missense
OMIM ID
516004
HGVS
NC_012920.1:g.10609T>A
HGNC ID
7460
RC complex
I
Ensembl gene ID
ENSG00000212907
Ensembl protein ID
ENSP00000354728
Ensembl transcript ID
ENST00000361335
Uniprot ID
P03901
Uniprot name
NU4LM_HUMAN
Ncbi gene ID
4539
Ncbi protein ID
YP_003024034.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
-0.299 Conservation Score
PhyloP 470way
0.666 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.015 Conservation Score

Pathogenicity predictors

PolyPhen2
Benign Score and details of the predictor
SIFT
Neutral 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
Ambiguous Score and details of the predictor
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
Neutral Score and details of the meta-predictor
Condel
Deleterious Score and details of the meta-predictor
COVEC WMV
Neutral Score and details of the meta-predictor
MtoolBox
Neutral Score and details of the meta-predictor
DEOGEN2
.
Meta SNP
.

Cancer-specific predictors

PolyPhen2 transf
Medium impact Score and details of the cancer-specific predictor
SIFT transf
Medium impact Score and details of the cancer-specific predictor
MutationAssessor transf
Medium impact Score and details of the cancer-specific predictor
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
10609T>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
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
.
~ 10609 (T/C) 10609 (T/A)
~ 10609 (ATA/ACA) 10609 (ATA/AAA)
MitImpact id MI.15983 MI.15982
Chr chrM chrM
Start 10609 10609
Ref T T
Alt C A
Gene symbol MT-ND4L MT-ND4L
Extended annotation mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 4L mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 4L
Gene position 140 140
Gene start 10470 10470
Gene end 10766 10766
Gene strand + +
Codon substitution ATA/ACA ATA/AAA
AA position 47 47
AA ref M M
AA alt T K
Functional effect general missense missense
Functional effect detailed missense missense
OMIM id 516004 516004
HGVS NC_012920.1:g.10609T>C NC_012920.1:g.10609T>A
HGNC id 7460 7460
Respiratory Chain complex I I
Ensembl gene id ENSG00000212907 ENSG00000212907
Ensembl transcript id ENST00000361335 ENST00000361335
Ensembl protein id ENSP00000354728 ENSP00000354728
Uniprot id P03901 P03901
Uniprot name NU4LM_HUMAN NU4LM_HUMAN
Ncbi gene id 4539 4539
Ncbi protein id YP_003024034.1 YP_003024034.1
PhyloP 100V -0.299 -0.299
PhyloP 470Way 0.666 0.666
PhastCons 100V 0 0
PhastCons 470Way 0.015 0.015
PolyPhen2 benign benign
PolyPhen2 score 0.01 0.26
SIFT neutral neutral
SIFT score 0.43 0.23
SIFT4G Tolerated Damaging
SIFT4G score 0.356 0.019
VEST Neutral Neutral
VEST pvalue 0.55 0.29
VEST FDR 0.6 0.45
Mitoclass.1 neutral damaging
SNPDryad Neutral Neutral
SNPDryad score 0.03 0.49
MutationTaster . .
MutationTaster score . .
MutationTaster converted rankscore . .
MutationTaster model . .
MutationTaster AAE . .
fathmm . .
fathmm score . .
fathmm converted rankscore . .
AlphaMissense likely_benign ambiguous
AlphaMissense score 0.095 0.4252
CADD Neutral Neutral
CADD score -0.671772 2.173793
CADD phred 0.084 17.34
PROVEAN Tolerated Damaging
PROVEAN score -0.76 -2.78
MutationAssessor . .
MutationAssessor score . .
EFIN SP Neutral Neutral
EFIN SP score 0.852 0.678
EFIN HD Neutral Neutral
EFIN HD score 0.98 0.48
MLC Deleterious Deleterious
MLC score 0.78649888 0.78649888
PANTHER score . .
PhD-SNP score . .
APOGEE1 Neutral Neutral
APOGEE1 score 0.25 0.35
APOGEE2 Benign VUS
APOGEE2 score 0.0163429871540779 0.541449227555864
CAROL neutral neutral
CAROL score 0.56 0.72
Condel deleterious deleterious
Condel score 0.71 0.49
COVEC WMV neutral neutral
COVEC WMV score -6 -6
MtoolBox neutral neutral
MtoolBox DS 0.11 0.33
DEOGEN2 . .
DEOGEN2 score . .
DEOGEN2 converted rankscore . .
Meta-SNP . .
Meta-SNP score . .
PolyPhen2 transf medium impact medium impact
PolyPhen2 transf score 1.03 -0.39
SIFT_transf medium impact medium impact
SIFT transf score 0.14 -0.08
MutationAssessor transf low impact medium impact
MutationAssessor transf score -2.05 0.25
CHASM Neutral Neutral
CHASM pvalue 0.34 0.55
CHASM FDR 0.8 0.8
ClinVar id 693302.0 .
ClinVar Allele id 680192.0 .
ClinVar CLNDISDB MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506 .
ClinVar CLNDN Leigh_syndrome .
ClinVar CLNSIG Benign .
MITOMAP Disease Clinical info Type 2 diabetes patients with underlying 3243G / LHON patient with 10663C .
MITOMAP Disease Status Reported .
MITOMAP Disease Hom/Het nr/nr ./.
MITOMAP General GenBank Freq 2.3424% .
MITOMAP General GenBank Seqs 1432 .
MITOMAP General Curated refs 21281460;29997041;19732751;18545700;19818876;9443868;23304069;19026397;17434445;17942074;16714301;24568867;24667788;17698299;12436196;33402819;24002810;20153673;16048457;20067846;17341440 .
MITOMAP Variant Class polymorphism;disease .
gnomAD 3.1 AN 56425.0 56433.0
gnomAD 3.1 AC Homo 208.0 0.0
gnomAD 3.1 AF Hom 0.00368631 0.0
gnomAD 3.1 AC Het 1.0 0.0
gnomAD 3.1 AF Het 1.77226e-05 0.0
gnomAD 3.1 filter PASS npg
HelixMTdb AC Hom 830.0 .
HelixMTdb AF Hom 0.0042350614 .
HelixMTdb AC Het 11.0 .
HelixMTdb AF Het 5.6127315e-05 .
HelixMTdb mean ARF 0.45976 .
HelixMTdb max ARF 0.92 .
ToMMo 54KJPN AC 3286 .
ToMMo 54KJPN AF 0.060513 .
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