rs1057517679
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP5
The NM_176869.3(PPA2):āc.280A>Gā(p.Met94Val) variant causes a missense change. The variant allele was found at a frequency of 0.0000014 in 1,425,268 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Genomes: not found (cov: 31)
Exomes š: 0.0000014 ( 0 hom. )
Consequence
PPA2
NM_176869.3 missense
NM_176869.3 missense
Scores
1
9
9
Clinical Significance
Conservation
PhyloP100: 4.84
Genes affected
PPA2 (HGNC:28883): (inorganic pyrophosphatase 2) The protein encoded by this gene is localized to the mitochondrion, is highly similar to members of the inorganic pyrophosphatase (PPase) family, and contains the signature sequence essential for the catalytic activity of PPase. PPases catalyze the hydrolysis of pyrophosphate to inorganic phosphate, which is important for the phosphate metabolism of cells. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 4-105449391-T-C is Pathogenic according to our data. Variant chr4-105449391-T-C is described in ClinVar as [Pathogenic]. Clinvar id is 372223.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PPA2 | NM_176869.3 | c.280A>G | p.Met94Val | missense_variant | 4/12 | ENST00000341695.10 | |
PPA2 | NM_006903.4 | c.280A>G | p.Met94Val | missense_variant | 4/11 | ||
PPA2 | NM_176866.2 | c.222+7290A>G | intron_variant | ||||
PPA2 | NM_176867.3 | c.157+24503A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPA2 | ENST00000341695.10 | c.280A>G | p.Met94Val | missense_variant | 4/12 | 1 | NM_176869.3 | P1 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 genomes
Cov.:
31
GnomAD4 exome AF: 0.00000140 AC: 2AN: 1425268Hom.: 0 Cov.: 27 AF XY: 0.00 AC XY: 0AN XY: 710656
GnomAD4 exome
AF:
AC:
2
AN:
1425268
Hom.:
Cov.:
27
AF XY:
AC XY:
0
AN XY:
710656
Gnomad4 AFR exome
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GnomAD4 genome Cov.: 31
GnomAD4 genome
Cov.:
31
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Sudden cardiac failure, infantile Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Nov 23, 2016 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
T;.;T;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Pathogenic
D;D;D;D
M_CAP
Benign
T
MetaRNN
Uncertain
D;D;D;D
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;M;.;.
MutationTaster
Benign
D;D;D;D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;D;D;D
REVEL
Benign
Sift
Benign
D;T;D;T
Sift4G
Benign
T;D;.;T
Polyphen
P;P;.;.
Vest4
MutPred
Loss of stability (P = 0.1129);Loss of stability (P = 0.1129);.;.;
MVP
MPC
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