1 variant found for 8993T>G
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MT-ATP6 · c.467T>G (p.Leu156Arg)
protein-coding
Genome location
MT-ATP6 · protein-coding
protein
tRNA
rRNA
D-loop
3D structure: where is this variant?
highlighted: residue
156 of MT-ATP6 · drag to rotate, scroll to zoom.
General information
| Variant ID | MITHRIL.27129 |
|---|---|
| MitImpact ID | MI.995 |
| Chromosome | chrM |
| Position | 8993 |
| Alleles (Ref/Alt) | T/G |
| Molecule type | protein-coding |
| Gene | MT-ATP6 |
| Gene description | mitochondrially encoded ATP synthase membrane subunit 6 |
| Gene (start-end) | 8527-9207 |
| Position within gene | 467 |
| Strand | + |
| HGVS | NC_012920.1:m.8993T>G |
| Functional effect | Missense variant |
| Respiratory chain complex | V |
External identifiers
| Ensembl gene | ENSG00000198899 |
|---|---|
| Ensembl transcript | ENST00000361899 |
| Ensembl protein | ENSP00000354632 |
| UniProt | ATP6_HUMAN (P00846) |
| NCBI gene | 4508 |
| NCBI protein | YP_003024031.1 |
| OMIM | 516060 |
| HGNC | HGNC:7414 |
| dbSNP | rs199476133 |
| MITOMAP allele | 8993T>G |
Phylogenetic conservation
| PhyloP (100V) | 5.929 |
|---|---|
| PhastCons (100V) | 0.903 |
| PhyloP (470-way) | 0.742 |
| PhastCons (470-way) | 0.061 |
Amino-acid change
| Codon substitution | CTG/CGG |
|---|---|
| Reference AA | L |
| Alternate AA | R |
| AA position | 156 |
Pathogenicity predictors
| PolyPhen-2 | Probably damaging |
|---|---|
| SIFT | Deleterious |
| SIFT4G | Deleterious |
| PROVEAN | Deleterious |
| MutationAssessor | Medium |
| MutationTaster | Disease causing (auto) |
| EFIN (SwissProt) | Deleterious |
| EFIN (HumDiv) | Neutral |
| PANTHER | Deleterious |
| PhD-SNP | Deleterious |
| LIST-S2 | Neutral |
| ESM1b | Deleterious |
| VARITY-R | Deleterious |
| VARITY-ER | Deleterious |
| SNPDryad | Deleterious |
| Mitoclass1 | Deleterious |
| CADD | Deleterious |
| AlphaMissense | Likely pathogenic |
| VEST | Neutral |
| MLC | Neutral |
Meta-predictors
| APOGEE1 | Deleterious |
|---|---|
| APOGEE2 | Pathogenic |
| CAROL | Deleterious |
| Condel | Neutral |
| COVEC WMV | Deleterious |
| Meta-SNP | Deleterious |
| MToolBox | Deleterious |
| DEOGEN2 | Neutral |
Cancer-specific predictors
| PolyPhen-2 (transf.) | Low impact |
|---|---|
| SIFT (transf.) | Low impact |
| MutationAssessor (transf.) | High impact |
| CHASM | Neutral |
Clinical significance & phenotype
| MITOMAP status | Cfrm-[P] |
|---|---|
| MITOMAP clinical info | NARP-/-Leigh-Disease-/-MILS-/-ATP6/8-deficiency-/-other |
| MITOMAP disease (hom/het) | +/+ |
| MITOMAP disease GenBank freq | 0.009 |
| MITOMAP disease GenBank seqs | 6 (0) |
| ClinVar significance | Pathogenic |
| ClinVar disease |
+15 more
|
| ClinVar ID (allele ID) | 9641 (24680) |
| ClinVar disease DB | |
| ClinVar submitter IDs |
Allele frequencies
| MITOMAP known variant | False |
|---|---|
| HelixMTdb hom AF (AC) | 0 (0) |
| HelixMTdb het AF (AC) | 0 (1) |
| HelixMTdb mean (max) ARF | 0.5936 (0.5936) |
| gnomAD hom AF (AC) | 0 (0) |
| gnomAD het AF (AC) | 0 (0) |
| gnomAD AN | 56433 |
| gnomAD filter | npg |
EVmutation network
MT-ATP6 · edge thickness/opacity ∝ covariation score.
Show all 11 as text
- 221Y: 0.236277
- 218V: 0.185549
- 163N: 0.175304
- 213V: 0.153339
- 209I: 0.108743
- 205A: 0.107658
- 158V: 0.092486
- 171M: 0.084289
- 173L: 0.072801
- 195I: 0.069883
- 170L: 0.06897