rs1554834186
Positions:
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_001195263.2(PDZD7):c.1576C>T(p.Gln526Ter) variant causes a stop gained, splice region 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 Pathogenic (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 32)
Consequence
PDZD7
NM_001195263.2 stop_gained, splice_region
NM_001195263.2 stop_gained, splice_region
Scores
1
5
Clinical Significance
Conservation
PhyloP100: 0.794
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 Pathogenic. Variant got 11 ACMG points.
PVS1
?
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant 10-101015809-G-A is Pathogenic according to our data. Variant chr10-101015809-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 545402.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-101015809-G-A is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDZD7 | NM_001195263.2 | c.1576C>T | p.Gln526Ter | stop_gained, splice_region_variant | 11/17 | ENST00000619208.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDZD7 | ENST00000619208.6 | c.1576C>T | p.Gln526Ter | stop_gained, splice_region_variant | 11/17 | 5 | NM_001195263.2 | P1 | |
PDZD7 | ENST00000644782.1 | c.1522+2290C>T | intron_variant | ||||||
PDZD7 | ENST00000474125.7 | c.*1700+2290C>T | intron_variant, NMD_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome Cov.: 33
GnomAD4 exome
Cov.:
33
GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Hearing loss, autosomal recessive 57 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jun 01, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Uncertain
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
Vest4
0.014
GERP RS
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at