9-13219604-C-T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_001378778.1(MPDZ):c.1041G>A(p.Leu347Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0 ( 0 hom., cov: 32)
Failed GnomAD Quality Control
Consequence
MPDZ
NM_001378778.1 synonymous
NM_001378778.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.854
Publications
0 publications found
Genes affected
MPDZ (HGNC:7208): (multiple PDZ domain crumbs cell polarity complex component) The protein encoded by this gene has multiple PDZ domains, which are hallmarks of protein-protein interactions. The encoded protein is known to interact with the HTR2C receptor and may cause it to clump at the cell surface. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2015]
MPDZ Gene-Disease associations (from GenCC):
- hydrocephalus, nonsyndromic, autosomal recessive 2Inheritance: AR Classification: STRONG, MODERATE, LIMITED Submitted by: Genomics England PanelApp, G2P, Labcorp Genetics (formerly Invitae), Ambry Genetics, Laboratory for Molecular Medicine
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.38).
BP6
Variant 9-13219604-C-T is Benign according to our data. Variant chr9-13219604-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2865300.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.854 with no splicing effect.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| MPDZ | NM_001378778.1 | c.1041G>A | p.Leu347Leu | synonymous_variant | Exon 8 of 47 | ENST00000319217.12 | NP_001365707.1 |
Ensembl
Frequencies
GnomAD3 genomes 0.00 AC: 0AN: 151858Hom.: 0 Cov.: 32
GnomAD3 genomes
AF:
AC:
0
AN:
151858
Hom.:
Cov.:
32
Gnomad AFR
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GnomAD4 exome Cov.: 32
GnomAD4 exome
Cov.:
32
GnomAD4 genome 0.00 AC: 0AN: 151858Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74130
GnomAD4 genome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
151858
Hom.:
Cov.:
32
AF XY:
AC XY:
0
AN XY:
74130
African (AFR)
AF:
AC:
0
AN:
41410
American (AMR)
AF:
AC:
0
AN:
15180
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3462
East Asian (EAS)
AF:
AC:
0
AN:
5140
South Asian (SAS)
AF:
AC:
0
AN:
4810
European-Finnish (FIN)
AF:
AC:
0
AN:
10616
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
0
AN:
67922
Other (OTH)
AF:
AC:
0
AN:
2090
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
May 17, 2023
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
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
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