1-7962813-C-G
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM1PM2
The NM_007262.5(PARK7):āc.28C>Gā(p.Leu10Val) variant causes a missense change. The variant allele was found at a frequency of 0.00000186 in 1,611,552 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.0000067 ( 0 hom., cov: 31)
Exomes š: 0.0000014 ( 0 hom. )
Consequence
PARK7
NM_007262.5 missense
NM_007262.5 missense
Scores
10
9
Clinical Significance
Conservation
PhyloP100: 4.08
Genes affected
PARK7 (HGNC:16369): (Parkinsonism associated deglycase) The product of this gene belongs to the peptidase C56 family of proteins. It acts as a positive regulator of androgen receptor-dependent transcription. It may also function as a redox-sensitive chaperone, as a sensor for oxidative stress, and it apparently protects neurons against oxidative stress and cell death. Defects in this gene are the cause of autosomal recessive early-onset Parkinson disease 7. Two transcript variants encoding the same protein have been identified for this gene. [provided by RefSeq, Jul 2008]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 4 ACMG points.
PM1
In a mutagenesis_site Abolishes detoxification activity on methylglyocal-adducted CoA. (size 0) in uniprot entity PARK7_HUMAN
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PARK7 | NM_007262.5 | c.28C>G | p.Leu10Val | missense_variant | 2/7 | ENST00000338639.10 | NP_009193.2 | |
PARK7 | NM_001123377.2 | c.28C>G | p.Leu10Val | missense_variant | 2/7 | NP_001116849.1 | ||
PARK7 | XM_005263424.4 | c.28C>G | p.Leu10Val | missense_variant | 2/7 | XP_005263481.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PARK7 | ENST00000338639.10 | c.28C>G | p.Leu10Val | missense_variant | 2/7 | 1 | NM_007262.5 | ENSP00000340278 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000665 AC: 1AN: 150290Hom.: 0 Cov.: 31
GnomAD3 genomes
AF:
AC:
1
AN:
150290
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461262Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1AN XY: 726954
GnomAD4 exome
AF:
AC:
2
AN:
1461262
Hom.:
Cov.:
33
AF XY:
AC XY:
1
AN XY:
726954
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.00000665 AC: 1AN: 150290Hom.: 0 Cov.: 31 AF XY: 0.0000137 AC XY: 1AN XY: 73178
GnomAD4 genome
AF:
AC:
1
AN:
150290
Hom.:
Cov.:
31
AF XY:
AC XY:
1
AN XY:
73178
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Autosomal recessive early-onset Parkinson disease 7 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Nov 29, 2018 | Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C25"). This variant has not been reported in the literature in individuals with PARK7-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces leucine with valine at codon 10 of the PARK7 protein (p.Leu10Val). The leucine residue is highly conserved and there is a small physicochemical difference between leucine and valine. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T;T;T;T;T;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
.;.;.;D;.;D
M_CAP
Uncertain
D
MetaRNN
Uncertain
T;T;T;T;T;T
MetaSVM
Uncertain
T
MutationAssessor
Uncertain
M;M;M;.;M;M
MutationTaster
Benign
D;D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
.;N;N;.;N;N
REVEL
Uncertain
Sift
Benign
.;T;T;.;T;T
Sift4G
Benign
T;T;T;T;T;T
Polyphen
P;P;P;.;P;P
Vest4
0.74, 0.74, 0.70
MutPred
Gain of catalytic residue at L10 (P = 0.0438);Gain of catalytic residue at L10 (P = 0.0438);Gain of catalytic residue at L10 (P = 0.0438);Gain of catalytic residue at L10 (P = 0.0438);Gain of catalytic residue at L10 (P = 0.0438);Gain of catalytic residue at L10 (P = 0.0438);
MVP
MPC
0.21
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at