rs555444131
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 1P and 5B. PM4_SupportingBP6BS2
The NM_001195263.2(PDZD7):c.1348_1350del(p.Glu450del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000747 in 1,613,768 control chromosomes in the GnomAD database, including 8 homozygotes. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.00042 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00078 ( 8 hom. )
Consequence
PDZD7
NM_001195263.2 inframe_deletion
NM_001195263.2 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 3.54
Genes affected
PDZD7 (HGNC:26257): (PDZ domain containing 7) This gene encodes a ciliary protein homologous to proteins which are mutated in Usher syndrome patients, and mutations and translocations involving this gene have been associated with two types of Usher syndrome. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2010]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM4
?
Nonframeshift variant in NON repetitive region in NM_001195263.2. Strenght limited to Supporting due to length of the change: 1aa.
BP6
?
Variant 10-101018270-TCTC-T is Benign according to our data. Variant chr10-101018270-TCTC-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 178694.We mark this variant Likely_benign, oryginal submissions are: {Benign=1, Uncertain_significance=1, Likely_benign=2}. Variant chr10-101018270-TCTC-T is described in Lovd as [Likely_benign].
BS2
?
High Homozygotes in GnomAdExome4 at 8 AR,Digenic gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDZD7 | NM_001195263.2 | c.1348_1350del | p.Glu450del | inframe_deletion | 9/17 | ENST00000619208.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDZD7 | ENST00000619208.6 | c.1348_1350del | p.Glu450del | inframe_deletion | 9/17 | 5 | NM_001195263.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000421 AC: 64AN: 152016Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000907 AC: 228AN: 251294Hom.: 3 AF XY: 0.00121 AC XY: 164AN XY: 135842
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GnomAD4 exome AF: 0.000781 AC: 1141AN: 1461634Hom.: 8 AF XY: 0.000941 AC XY: 684AN XY: 727114
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GnomAD4 genome ? AF: 0.000421 AC: 64AN: 152134Hom.: 0 Cov.: 32 AF XY: 0.000363 AC XY: 27AN XY: 74378
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:3
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
not provided Uncertain:1Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 28, 2023 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jun 12, 2014 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 20, 2020 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 14, 2013 | Glu450del in exon 9 of PDZD7: This variant is not expected to have clinical sign ificance due to a lack of conservation across species, including mammals. Of no te, the marmoset has an in-frame deletion of the glutamate (Glu) at this positio n. - |
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at