chrM-8552-T-C
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4BP6_ModerateBS2
The ENST00000361899.2(MT-ATP6):c.26T>C(p.Phe9Ser) variant causes a missense change involving the alteration of a conserved nucleotide. Variant has been reported in ClinVar as Benign (★).
Frequency
Mitomap GenBank:
𝑓 0.00020 ( AC: 14 )
Consequence
MT-ATP6
ENST00000361899.2 missense
ENST00000361899.2 missense
Scores
Apogee2
Uncertain
Clinical Significance
No linked disesase in Mitomap
Conservation
PhyloP100: 7.70
Genes affected
MT-ATP6 (HGNC:7414): (mitochondrially encoded ATP synthase 6) Contributes to proton-transporting ATP synthase activity, rotational mechanism. Involved in mitochondrial ATP synthesis coupled proton transport. Part of mitochondrial proton-transporting ATP synthase complex. Implicated in Leber hereditary optic neuropathy; NARP syndrome; Parkinson's disease; multiple sclerosis; and systemic lupus erythematosus. [provided by Alliance of Genome Resources, Apr 2022]
MT-ATP8 (HGNC:7415): (mitochondrially encoded ATP synthase 8) Contributes to proton-transporting ATP synthase activity, rotational mechanism. Involved in mitochondrial ATP synthesis coupled proton transport. Part of mitochondrial proton-transporting ATP synthase complex. Implicated in multiple sclerosis and urinary bladder cancer. [provided by Alliance of Genome Resources, Apr 2022]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -7 ACMG points.
BP4
?
Apogee2 supports a benign effect, 0.40836856 < 0.5 .
BP6
?
Variant M-8552-T-C is Benign according to our data. Variant chrM-8552-T-C is described in ClinVar as [Benign]. Clinvar id is 692898.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High AC in GnomadMitoHomoplasmic at 5
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP6 | ATP6.1 use as main transcript | c.26T>C | p.Phe9Ser | missense_variant | 1/1 | ||
ATP8 | ATP8.1 use as main transcript | c.187T>C | p.Ser63Pro | missense_variant | 1/1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MT-ATP6 | ENST00000361899.2 | c.26T>C | p.Phe9Ser | missense_variant | 1/1 | P1 | |||
MT-ATP8 | ENST00000361851.1 | c.187T>C | p.Ser63Pro | missense_variant | 1/1 | P1 |
Frequencies
GnomAD4 exome Cov.: 0
GnomAD4 exome
Cov.:
0
We have no GnomAD4 genomes data on this position. Probably position not covered by the project.
Mitomap GenBank
AF:
AC:
14
Gnomad homoplasmic
AF:
AC:
5
AN:
56432
Gnomad heteroplasmic
AF:
AC:
0
AN:
56432
Mitomap
No disease associated.
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Leigh syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Wong Mito Lab, Molecular and Human Genetics, Baylor College of Medicine | Oct 17, 2019 | The NC_012920.1:m.8552T>C (YP_003024031.1:p.Phe9Ser) variant in MTATP6 gene (also (YP_003024030.1:p.Ser63Pro) variant in MTATP8 gene) is interpretated to be a Benign variant based on the modified ACMG guidelines (unpublished). This variant meets the following evidence codes: BS1, BS4 - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Apogee2
Uncertain
Hmtvar
Pathogenic
AlphaMissense
Benign
BayesDel_addAF
Uncertain
D
DEOGEN2
Benign
T
LIST_S2
Benign
T
MutationTaster
Benign
D;D
PROVEAN
Pathogenic
D
Sift4G
Pathogenic
D
GERP RS
Varity_R
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at