9-13107075-C-A
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_001378778.1(MPDZ):c.6103G>T(p.Asp2035Tyr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000146 in 1,434,754 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D2035N) has been classified as Uncertain significance.
Frequency
Consequence
NM_001378778.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MPDZ | NM_001378778.1 | c.6103G>T | p.Asp2035Tyr | missense_variant | 47/47 | ENST00000319217.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MPDZ | ENST00000319217.12 | c.6103G>T | p.Asp2035Tyr | missense_variant | 47/47 | 5 | NM_001378778.1 | A1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.0000322 AC: 8AN: 248234Hom.: 0 AF XY: 0.0000594 AC XY: 8AN XY: 134654
GnomAD4 exome AF: 0.0000146 AC: 21AN: 1434754Hom.: 0 Cov.: 30 AF XY: 0.0000267 AC XY: 19AN XY: 710486
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Hydrocephalus, nonsyndromic, autosomal recessive 2 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Center For Human Genetics And Laboratory Diagnostics, Dr. Klein, Dr. Rost And Colleagues | Feb 08, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at