9861 (T > C)

General info

Mitimpact ID

MI.8031

Chr

chrM

Start

9861

Ref

Alt

Gene symbol

MT-CO3

Gene position

655

Gene start

9207

Gene end

9990

Gene strand

Codon substitution

TTC/CTC

AA pos

219

AA ref

AA alt

Functional effect

missense

OMIM ID

516050

HGVS

NC_012920.1:g.9861T>C

HGNC ID

7422

RC complex

Ensembl gene ID

ENSG00000198938

Ensembl protein ID

ENSP00000354982

Ensembl transcript ID

Uniprot ID

Uniprot name

Ncbi gene ID

Ncbi protein ID

Conservation

PhyloP 100v

-0.824

PhyloP 470way

0.666

PhastCons 100v

PhastCons 470way

0.176

Pathogenicity predictors

PolyPhen2

Benign

SIFT

Neutral

SIFT4G

Tolerated

VEST

Neutral

MitoClass 1

Neutral

SNPDryad

Neutral

MutationTaster

Polymorphism

fathmm

Tolerated

AlphaMissense

Ambiguous

CADD

Neutral

PROVEAN

Tolerated

Mutation Assessor

Neutral

EFIN SP

Neutral

EFIN HD

Neutral

MLC

Neutral

PANTHER

PhD-SNP

Pathogenicity meta-predictors

APOGEE1

Neutral

APOGEE2

Benign

CAROL

Neutral

Condel

Deleterious

COVEC WMV

Neutral

MtoolBox

Neutral

DEOGEN2

Tolerated

Meta SNP

Cancer-specific predictors

PolyPhen2 transf

High impact

SIFT transf

High impact

MutationAssessor transf

Low impact

CHASM

Neutral

Databases of Frequencies and Phenotypes

Clinvar ID

235537

Clinvar ALLELEID

237218

Clinvar CLNDISDB

Mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506;

medgen:cn517202

Clinvar CLNDN

Leigh syndrome;

not provided

Clinvar CLNSIG

Benign/likely benign

MITOMAP Allele

9861T>C

MITOMAP Disease Clinical info

MITOMAP Disease Status

Reported

MITOMAP Disease Hom/Het

+/-

MITOMAP General GenBank Freq

0.2077%

MITOMAP General GenBank Seqs

127

MITOMAP General GenBank Curated refs

21041797 11938495 20975840 22927010 16404693 16358358

MITOMAP Variant Class

polymorphism;disease

Gnomad AN

56410

Gnomad AC hom

120

Gnomad AF hom

0.0021272

Gnomad AC het

Gnomad AF het

0.000124

Gnomad filter

Pass

HelixMTdb AC hom

229

HelixMTdb AF hom

0.0011684

HelixMTdb AC het

HelixMTdb AF het

6.63e-05

HelixMTdb mean ARF

0.38276

HelixMTdb max ARF

0.91489

ToMMo JPN54K AC

ToMMo JPN54K AF

0.000737

ToMMo JPN54K AN

54302

COSMIC 90

dbSNP 156

rs878853060

Residue interaction

EVmutation

CO3: 219F -

Site A-B InterP

Site A-B IntraP

ΔΔG intra

ΔΔG intra interface

ΔΔG inter

Compensated Pathogenic Deviations

Frequency

17.06

AA ref

CPD AA alt

Aln pos

219

RefSeq protein ID

YP_008379066 , NP_008464 , YP_007316889 , YP_007316902 , YP_007316928 , YP_007316915 , YP_007316941 , YP_009024898 , YP_626426 , YP_001427428 , YP_009059465 , YP_238248 , YP_001427415 , YP_008378975 , YP_009024885 , YP_008378936 , YP_009024872 , YP_009024924 , NP_114340 , YP_002302306 , YP_009019985 , YP_002884232 , YP_009072416 , YP_026110 , YP_009072456 , YP_009072469 , NP_008607 , YP_637016 , YP_004300465 , YP_004222618 , YP_009024911 , YP_008378923 , YP_008379092 , YP_214959 , YP_659492 , YP_007625620 , YP_659453 , YP_006460523 , YP_659505 , YP_006460536 , YP_006460549 , YP_004425130 , YP_006460484 , YP_006460497 , YP_006460510 , YP_004425117 , YP_659479 , YP_006460471 , YP_007024949 , YP_007024923 , YP_009047761 , YP_007024897 , YP_009024989 , YP_214946 , YP_007024910 , YP_009025002 , NP_007841 , YP_003587311 , YP_006883024 , YP_003587388 , YP_008379105 , NP_007828 , YP_003587220 , YP_003587285 , NP_008218 , YP_002120665 , NP_008192 , NP_008205 , YP_423968 , YP_006883660 , YP_423981 , YP_003097142 , YP_009049046 , YP_004123236 , YP_004123194 , YP_004123276 , YP_002791217 , YP_004123356 , YP_008999716 , YP_004123317 , YP_004123408 , YP_004300439 , YP_004935498 , YP_003331229 , NP_149963 , YP_626400 , YP_004891158 , YP_003667 , YP_008993948 , YP_214854 , YP_008080907 , YP_220673 , YP_002929341 , YP_002929315 , YP_002929302 , YP_008379001 , NP_114353 , YP_008379118 , YP_002929328 , YP_008379079 , NP_075401 , YP_006576327 , YP_008378949 , YP_008578498 , YP_006702491 , YP_004849383 , NP_659331 , YP_009027348 , YP_009027361 , YP_009040277 , YP_004734444 , YP_009027387 , YP_009027686 , YP_009027699 , YP_009027712

Species name

Lophocebus aterrimus, Papio hamadryas, Papio anubis, Papio cynocephalus, Papio papio, Papio kindae, Papio ursinus, Cercopithecus diana, Chlorocebus sabaeus, Chlorocebus pygerythrus, Chlorocebus cynosuros, Chlorocebus aethiops, Chlorocebus tantalus, Erythrocebus patas, Allochrocebus lhoesti, Cercopithecus albogularis, Cercopithecus mitis, Allenopithecus nigroviridis, Macaca sylvanus, Macaca thibetana, Macaca assamensis, Macaca fascicularis, Macaca arctoides, Macaca mulatta, Macaca silenus, Macaca tonkeana, Erinaceus europaeus, Phascolarctos cinereus, Microtus fortis calamorum, Heterocephalus glaber, Cercocebus torquatus, Cercocebus chrysogaster, Mandrillus sphinx, Colobus guereza, Piliocolobus badius, Procolobus verus, Nasalis larvatus, Pygathrix nigripes, Pygathrix nemaeus, Pygathrix cinerea 1 rl-2012, Pygathrix cinerea 2 rl-2012, Rhinopithecus bieti, Rhinopithecus bieti 1 rl-2012, Rhinopithecus strykeri, Rhinopithecus bieti 2 rl-2012, Rhinopithecus avunculus, Rhinopithecus roxellana, Rhinopithecus brelichi, Trachypithecus johnii, Trachypithecus shortridgei, Trachypithecus pileatus, Trachypithecus hatinhensis, Trachypithecus francoisi, Trachypithecus obscurus, Trachypithecus germaini, Trachypithecus cristatus, Pongo abelii, Symphalangus syndactylus, Nomascus gabriellae, Nomascus siki, Nomascus leucogenys, Hylobates lar, Hylobates agilis, Hylobates pileatus, Gorilla gorilla, Gorilla gorilla gorilla, Pan troglodytes, Pan paniscus, Dasyurus hallucatus, Sarcophilus harrisii, Sminthopsis crassicaudata, Tscherskia triton, Cricetulus kamensis, Rattus lutreolus, Rattus leucopus, Rattus tunneyi, Rattus praetor, Rattus fuscipes, Rattus niobe, Rattus villosissimus, Rattus sordidus, Microtus fortis fortis, Myodes regulus, Eothenomys chinensis, Microtus kikuchii, Microtus levis, Neodon irene, Thylamys elegans, Uropsilus soricipes, Crocidura russula, Crocidura shantungensis, Bradypus variegatus, Perodicticus potto, Otolemur crassicaudatus, Galago senegalensis, Galago moholi, Nycticebus coucang, Nycticebus bengalensis, Loris tardigradus, Loris lydekkerianus, Thryonomys swinderianus, Marmota himalayana, Cheirogaleus medius, Vampyrum spectrum, Uropsilus sp. 1 ft-2014, Manis pentadactyla, Lepus europaeus, Lepus timidus, Lepus townsendii, Lepus coreanus, Lepus capensis, Lepus americanus, Tarsius lariang, Tarsius dentatus, Tarsius wallacei

Ncbi taxon ID

75566, 9557, 9555, 9556, 100937, 208091, 36229, 36224, 60711, 60710, 460675, 9534, 60712, 9538, 100224, 867370, 36225, 54135, 9546, 54602, 9551, 9541, 9540, 9544, 54601, 40843, 9365, 38626, 311220, 10181, 9530, 75569, 9561, 33548, 164648, 373033, 43780, 310352, 54133, 1194332, 1194333, 61621, 1194334, 1194336, 1194335, 66062, 61622, 224329, 66063, 1042121, 164651, 867383, 54180, 54181, 271260, 122765, 9601, 9590, 61852, 9586, 61853, 9580, 9579, 9589, 9593, 9595, 9598, 9597, 9280, 9305, 9301, 329627, 1515608, 472760, 10115, 10121, 349711, 10119, 472762, 10122, 10120, 311338, 82464, 577681, 100899, 537919, 798166, 191871, 182671, 36802, 183721, 9355, 9472, 9463, 9465, 30609, 9470, 261741, 9468, 300163, 10169, 93163, 9460, 148074, 1536768, 143292, 9983, 62621, 63225, 258242, 9981, 48086, 630277, 449501, 981131

9861 (T > A)

General info

Mitimpact ID

MI.8033

Chr

chrM

Start

9861

Ref

Alt

Gene symbol

MT-CO3

Gene position

655

Gene start

9207

Gene end

9990

Gene strand

Codon substitution

TTC/ATC

AA pos

219

AA ref

AA alt

Functional effect

missense

OMIM ID

516050

HGVS

NC_012920.1:g.9861T>A

HGNC ID

7422

RC complex

Ensembl gene ID

ENSG00000198938

Ensembl protein ID

ENSP00000354982

Ensembl transcript ID

Uniprot ID

Uniprot name

Ncbi gene ID

Ncbi protein ID

Conservation

PhyloP 100v

-0.824

PhyloP 470way

0.666

PhastCons 100v

PhastCons 470way

0.176

Pathogenicity predictors

PolyPhen2

Benign

SIFT

Neutral

SIFT4G

Damaging

VEST

Neutral

MitoClass 1

Neutral

SNPDryad

Neutral

MutationTaster

Polymorphism

fathmm

Tolerated

AlphaMissense

Ambiguous

CADD

Deleterious

PROVEAN

Tolerated

Mutation Assessor

Medium

EFIN SP

Neutral

EFIN HD

Neutral

MLC

Neutral

PANTHER

PhD-SNP

Pathogenicity meta-predictors

APOGEE1

Neutral

APOGEE2

Likely-benign

CAROL

Neutral

Condel

Deleterious

COVEC WMV

Neutral

MtoolBox

Neutral

DEOGEN2

Tolerated

Meta SNP

Cancer-specific predictors

PolyPhen2 transf

Medium impact

SIFT transf

Medium impact

MutationAssessor transf

Medium impact

CHASM

Neutral

Databases of Frequencies and Phenotypes

Clinvar ID

Clinvar ALLELEID

Clinvar CLNDISDB

Clinvar CLNDN

Clinvar CLNSIG

MITOMAP Allele

9861T>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

Gnomad AC hom

Gnomad AF hom

0.0

Gnomad AC het

Gnomad AF het

Gnomad filter

HelixMTdb AC hom

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

CO3: 219F -

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

9861 (T > G)

General info

Mitimpact ID

MI.8032

Chr

chrM

Start

9861

Ref

Alt

Gene symbol

MT-CO3

Gene position

655

Gene start

9207

Gene end

9990

Gene strand

Codon substitution

TTC/GTC

AA pos

219

AA ref

AA alt

Functional effect

missense

OMIM ID

516050

HGVS

NC_012920.1:g.9861T>G

HGNC ID

7422

RC complex

Ensembl gene ID

ENSG00000198938

Ensembl protein ID

ENSP00000354982

Ensembl transcript ID

Uniprot ID

Uniprot name

Ncbi gene ID

Ncbi protein ID

Conservation

PhyloP 100v

-0.824

PhyloP 470way

0.666

PhastCons 100v

PhastCons 470way

0.176

Pathogenicity predictors

PolyPhen2

Benign

SIFT

Neutral

SIFT4G

Damaging

VEST

Neutral

MitoClass 1

Neutral

SNPDryad

Neutral

MutationTaster

Polymorphism

fathmm

Tolerated

AlphaMissense

Likely benign

CADD

Neutral

PROVEAN

Tolerated

Mutation Assessor

Medium

EFIN SP

Neutral

EFIN HD

Neutral

MLC

Neutral

PANTHER

PhD-SNP

Pathogenicity meta-predictors

APOGEE1

Neutral

APOGEE2

Likely-benign

CAROL

Neutral

Condel

Deleterious

COVEC WMV

Neutral

MtoolBox

Neutral

DEOGEN2

Tolerated

Meta SNP

Cancer-specific predictors

PolyPhen2 transf

Medium impact

SIFT transf

Medium impact

MutationAssessor transf

Medium impact

CHASM

Neutral

Databases of Frequencies and Phenotypes

Clinvar ID

Clinvar ALLELEID

Clinvar CLNDISDB

Clinvar CLNDN

Clinvar CLNSIG

MITOMAP Allele

9861T>G

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

Gnomad AF hom

0.0

Gnomad AC het

Gnomad AF het

0.0

Gnomad filter

Npg

HelixMTdb AC hom

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

CO3: 219F -

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

~	9861 (T/C)	9861 (T/A)	9861 (T/G)
~	9861 (TTC/CTC)	9861 (TTC/ATC)	9861 (TTC/GTC)
MitImpact id	MI.8031	MI.8033	MI.8032
Chr	chrM	chrM	chrM
Start	9861	9861	9861
Ref	T	T	T
Alt	C	A	G
Gene symbol	MT-CO3	MT-CO3	MT-CO3
Extended annotation	mitochondrially encoded cytochrome c oxidase III	mitochondrially encoded cytochrome c oxidase III	mitochondrially encoded cytochrome c oxidase III
Gene position	655	655	655
Gene start	9207	9207	9207
Gene end	9990	9990	9990
Gene strand	+	+	+
Codon substitution	TTC/CTC	TTC/ATC	TTC/GTC
AA position	219	219	219
AA ref	F	F	F
AA alt	L	I	V
Functional effect general	missense	missense	missense
Functional effect detailed	missense	missense	missense
OMIM id	516050	516050	516050
HGVS	NC_012920.1:g.9861T>C	NC_012920.1:g.9861T>A	NC_012920.1:g.9861T>G
HGNC id	7422	7422	7422
Respiratory Chain complex	IV	IV	IV
Ensembl gene id	ENSG00000198938	ENSG00000198938	ENSG00000198938
Ensembl transcript id	ENST00000362079	ENST00000362079	ENST00000362079
Ensembl protein id	ENSP00000354982	ENSP00000354982	ENSP00000354982
Uniprot id	P00414	P00414	P00414
Uniprot name	COX3_HUMAN	COX3_HUMAN	COX3_HUMAN
Ncbi gene id	4514	4514	4514
Ncbi protein id	YP_003024032.1	YP_003024032.1	YP_003024032.1
PhyloP 100V	-0.824	-0.824	-0.824
PhyloP 470Way	0.666	0.666	0.666
PhastCons 100V	0	0	0
PhastCons 470Way	0.176	0.176	0.176
PolyPhen2	benign	benign	benign
PolyPhen2 score	0.0	0.01	0.05
SIFT	neutral	neutral	neutral
SIFT score	1	0.5	0.27
SIFT4G	Tolerated	Damaging	Damaging
SIFT4G score	1.0	0.008	0.001
VEST	Neutral	Neutral	Neutral
VEST pvalue	0.21	0.14	0.11
VEST FDR	0.45	0.4	0.4
Mitoclass.1	neutral	neutral	neutral
SNPDryad	Neutral	Neutral	Neutral
SNPDryad score	0	0.24	0.35
MutationTaster	Polymorphism	Polymorphism	Polymorphism
MutationTaster score	1	1	1
MutationTaster converted rankscore	0.08975	0.08975	0.08975
MutationTaster model	complex_aae	complex_aae	complex_aae
MutationTaster AAE	F219L	F219I	F219V
fathmm	Tolerated	Tolerated	Tolerated
fathmm score	2.81	2.6	2.56
fathmm converted rankscore	0.10975	0.13204	0.13673
AlphaMissense	ambiguous	ambiguous	likely_benign
AlphaMissense score	0.3666	0.3565	0.3144
CADD	Neutral	Deleterious	Neutral
CADD score	-0.437977	2.619671	2.397935
CADD phred	0.313	20.3	18.81
PROVEAN	Tolerated	Tolerated	Tolerated
PROVEAN score	2.72	1.09	0.19
MutationAssessor	neutral	medium	medium
MutationAssessor score	-1.76	2.395	2.65
EFIN SP	Neutral	Neutral	Neutral
EFIN SP score	0.692	0.664	0.658
EFIN HD	Neutral	Neutral	Neutral
EFIN HD score	0.946	0.632	0.58
MLC	Neutral	Neutral	Neutral
MLC score	0.2251192	0.2251192	0.2251192
PANTHER score	.	.	.
PhD-SNP score	.	.	.
APOGEE1	Neutral	Neutral	Neutral
APOGEE1 score	0.48	0.34	0.41
APOGEE2	Benign	Likely-benign	Likely-benign
APOGEE2 score	0.0412672995141966	0.110675647307963	0.175267793027094
CAROL	neutral	neutral	neutral
CAROL score	0	0.48	0.71
Condel	deleterious	deleterious	deleterious
Condel score	1	0.75	0.61
COVEC WMV	neutral	neutral	neutral
COVEC WMV score	-6	-6	-6
MtoolBox	neutral	neutral	neutral
MtoolBox DS	0.1	0.15	0.15
DEOGEN2	Tolerated	Tolerated	Tolerated
DEOGEN2 score	0.010607	0.011006	0.014178
DEOGEN2 converted rankscore	0.09562	0.09875	0.12117
Meta-SNP	.	.	.
Meta-SNP score	.	.	.
PolyPhen2 transf	high impact	medium impact	medium impact
PolyPhen2 transf score	2.05	1.07	0.37
SIFT_transf	high impact	medium impact	medium impact
SIFT transf score	1.9	0.19	-0.06
MutationAssessor transf	low impact	medium impact	medium impact
MutationAssessor transf score	-2.7	0	0.25
CHASM	Neutral	Neutral	Neutral
CHASM pvalue	0.69	0.35	0.26
CHASM FDR	0.85	0.8	0.8
ClinVar id	235537.0	.	.
ClinVar Allele id	237218.0	.	.
ClinVar CLNDISDB	MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506\|MedGen:CN517202	.	.
ClinVar CLNDN	Leigh_syndrome\|not_provided	.	.
ClinVar CLNSIG	Benign/Likely_benign	.	.
MITOMAP Disease Clinical info	AD	.	.
MITOMAP Disease Status	Reported	.	.
MITOMAP Disease Hom/Het	+/-	./.	./.
MITOMAP General GenBank Freq	0.2077%	.	.
MITOMAP General GenBank Seqs	127	.	.
MITOMAP General Curated refs	21041797;11938495;20975840;22927010;16404693;16358358	.	.
MITOMAP Variant Class	polymorphism;disease	.	.
gnomAD 3.1 AN	56410.0	.	56433.0
gnomAD 3.1 AC Homo	120.0	.	0.0
gnomAD 3.1 AF Hom	0.00212728	.	0.0
gnomAD 3.1 AC Het	7.0	.	0.0
gnomAD 3.1 AF Het	0.000124091	.	0.0
gnomAD 3.1 filter	PASS	.	npg
HelixMTdb AC Hom	229.0	.	.
HelixMTdb AF Hom	0.0011684687	.	.
HelixMTdb AC Het	13.0	.	.
HelixMTdb AF Het	6.6332286e-05	.	.
HelixMTdb mean ARF	0.38276	.	.
HelixMTdb max ARF	0.91489	.	.
ToMMo 54KJPN AC	40	.	.
ToMMo 54KJPN AF	0.000737	.	.
ToMMo 54KJPN AN	54302	.	.
COSMIC 90	.	.	.
dbSNP 156 id	rs878853060	.	.

choose

choose version

9861 (T > C)

General info

Conservation

Pathogenicity predictors

Pathogenicity meta-predictors

Cancer-specific predictors

Databases of Frequencies and Phenotypes

Residue interaction

Compensated Pathogenic Deviations

9861 (T > A)

General info

Conservation

Pathogenicity predictors

Pathogenicity meta-predictors

Cancer-specific predictors

Databases of Frequencies and Phenotypes

Residue interaction

Compensated Pathogenic Deviations

9861 (T > G)

General info

Conservation

Pathogenicity predictors

Pathogenicity meta-predictors

Cancer-specific predictors

Databases of Frequencies and Phenotypes

Residue interaction

Compensated Pathogenic Deviations