9-13107063-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBS1_Supporting
The NM_001378778.1(MPDZ):c.6115G>A(p.Ala2039Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000792 in 1,603,200 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001378778.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MPDZ | NM_001378778.1 | c.6115G>A | p.Ala2039Thr | missense_variant | Exon 47 of 47 | ENST00000319217.12 | NP_001365707.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000283 AC: 43AN: 152202Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000723 AC: 18AN: 248938Hom.: 0 AF XY: 0.0000815 AC XY: 11AN XY: 135028
GnomAD4 exome AF: 0.0000517 AC: 75AN: 1450880Hom.: 0 Cov.: 30 AF XY: 0.0000485 AC XY: 35AN XY: 720942
GnomAD4 genome AF: 0.000341 AC: 52AN: 152320Hom.: 1 Cov.: 32 AF XY: 0.000430 AC XY: 32AN XY: 74484
ClinVar
Submissions by phenotype
MPDZ-related disorder Uncertain:1
The MPDZ c.6028G>A variant is predicted to result in the amino acid substitution p.Ala2010Thr. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.12% of alleles in individuals of African descent in gnomAD. Although we suspect that this variant may be benign, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -
not provided Uncertain:1
This sequence change replaces alanine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 2010 of the MPDZ protein (p.Ala2010Thr). This variant is present in population databases (rs140627050, gnomAD 0.1%). This variant has not been reported in the literature in individuals affected with MPDZ-related conditions. ClinVar contains an entry for this variant (Variation ID: 1177484). 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: "Probably Damaging"; Align-GVGD: "Class C0"). 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. -
Hydrocephalus, nonsyndromic, autosomal recessive 2 Other:1
Variant interpreted as Uncertain significance and reported on 11-23-2020 by Invitae. GenomeConnect-Invitae Patient Insights Network assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. Registry team members make no attempt to reinterpret the clinical significance of the variant. Phenotypic details are available under supporting information. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at