10-101008575-CTG-C
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PVS1_ModeratePM2
The NM_001195263.2(PDZD7):c.2992_2993delCA(p.Gln998AspfsTer5) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000013 in 1,535,552 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001195263.2 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PDZD7 | NM_001195263.2 | c.2992_2993delCA | p.Gln998AspfsTer5 | frameshift_variant | Exon 17 of 17 | ENST00000619208.6 | NP_001182192.1 | |
PDZD7 | XM_011540177.4 | c.2992_2993delCA | p.Gln998AspfsTer5 | frameshift_variant | Exon 18 of 18 | XP_011538479.1 | ||
PDZD7 | XM_047425767.1 | c.2992_2993delCA | p.Gln998AspfsTer5 | frameshift_variant | Exon 17 of 17 | XP_047281723.1 | ||
PDZD7 | XM_011540178.4 | c.2989_2990delCA | p.Gln997AspfsTer5 | frameshift_variant | Exon 17 of 17 | XP_011538480.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PDZD7 | ENST00000619208.6 | c.2992_2993delCA | p.Gln998AspfsTer5 | frameshift_variant | Exon 17 of 17 | 5 | NM_001195263.2 | ENSP00000480489.1 | ||
PDZD7 | ENST00000474125.7 | n.*2939_*2940delCA | non_coding_transcript_exon_variant | Exon 13 of 13 | 2 | ENSP00000474447.1 | ||||
PDZD7 | ENST00000474125.7 | n.*2939_*2940delCA | 3_prime_UTR_variant | Exon 13 of 13 | 2 | ENSP00000474447.1 |
Frequencies
GnomAD3 genomes AF: 0.00000659 AC: 1AN: 151652Hom.: 0 Cov.: 31
GnomAD4 exome AF: 7.23e-7 AC: 1AN: 1383900Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 682860
GnomAD4 genome AF: 0.00000659 AC: 1AN: 151652Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74048
ClinVar
Submissions by phenotype
not provided Uncertain:1
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. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. This variant has not been reported in the literature in individuals affected with PDZD7-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Gln998Aspfs*5) in the PDZD7 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 36 amino acid(s) of the PDZD7 protein. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at