rs375787139
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6BP7
The NM_004279.3(PMPCB):c.180A>G(p.Val60Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,552 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 6.8e-7 ( 0 hom. )
Consequence
PMPCB
NM_004279.3 synonymous
NM_004279.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.17
Publications
0 publications found
Genes affected
PMPCB (HGNC:9119): (peptidase, mitochondrial processing subunit beta) This gene is a member of the peptidase M16 family and encodes a protein with a zinc-binding motif. This protein is located in the mitochondrial matrix and catalyzes the cleavage of the leader peptides of precursor proteins newly imported into the mitochondria, though it only functions as part of a heterodimeric complex. [provided by RefSeq, Jul 2008]
PMPCB Gene-Disease associations (from GenCC):
- multiple mitochondrial dysfunctions syndrome 6Inheritance: AR Classification: STRONG, MODERATE Submitted by: Illumina, Labcorp Genetics (formerly Invitae), Ambry Genetics
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.75).
BP6
Variant 7-103298648-A-G is Benign according to our data. Variant chr7-103298648-A-G is described in ClinVar as Likely_benign. ClinVar VariationId is 3350848.Status of the report is no_assertion_criteria_provided, 0 stars.
BP7
Synonymous conserved (PhyloP=-2.17 with no splicing effect.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_004279.3. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| PMPCB | NM_004279.3 | MANE Select | c.180A>G | p.Val60Val | synonymous | Exon 2 of 13 | NP_004270.2 | O75439 | |
| PMPCB | NM_001438231.1 | c.180A>G | p.Val60Val | synonymous | Exon 2 of 12 | NP_001425160.1 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| PMPCB | ENST00000249269.9 | TSL:1 MANE Select | c.180A>G | p.Val60Val | synonymous | Exon 2 of 13 | ENSP00000249269.4 | O75439 | |
| PMPCB | ENST00000428154.5 | TSL:1 | c.180A>G | p.Val60Val | synonymous | Exon 2 of 12 | ENSP00000390035.1 | G3V0E4 | |
| PMPCB | ENST00000706454.1 | c.180A>G | p.Val60Val | synonymous | Exon 2 of 13 | ENSP00000516392.1 | A0A9L9PXI7 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461552Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 727114 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
1461552
Hom.:
Cov.:
30
AF XY:
AC XY:
1
AN XY:
727114
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33462
American (AMR)
AF:
AC:
0
AN:
44724
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26132
East Asian (EAS)
AF:
AC:
0
AN:
39692
South Asian (SAS)
AF:
AC:
0
AN:
86254
European-Finnish (FIN)
AF:
AC:
0
AN:
53416
Middle Eastern (MID)
AF:
AC:
0
AN:
5768
European-Non Finnish (NFE)
AF:
AC:
1
AN:
1111720
Other (OTH)
AF:
AC:
0
AN:
60384
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
33
Alfa
AF:
Hom.:
Asia WGS
AF:
AC:
1
AN:
3478
ClinVar
ClinVar submissions as Germline
View on ClinVar Significance:Likely benign
Revision:no assertion criteria provided
Pathogenic
VUS
Benign
Condition
-
-
1
PMPCB-related disorder (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
RBP_binding_hub_radar
RBP_regulation_power_radar
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
Publications
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.