rs111287837
Positions:
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PVS1PM2
The NM_001195263.2(PDZD7):c.2368A>T(p.Lys790Ter) variant causes a stop gained change. The variant allele was found at a frequency of 0.000000725 in 1,379,904 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 7.2e-7 ( 0 hom. )
Consequence
PDZD7
NM_001195263.2 stop_gained
NM_001195263.2 stop_gained
Scores
1
5
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.91
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 10 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;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDZD7 | NM_001195263.2 | c.2368A>T | p.Lys790Ter | stop_gained | 15/17 | ENST00000619208.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDZD7 | ENST00000619208.6 | c.2368A>T | p.Lys790Ter | stop_gained | 15/17 | 5 | NM_001195263.2 | P1 | |
PDZD7 | ENST00000474125.7 | c.*2315A>T | 3_prime_UTR_variant, NMD_transcript_variant | 11/13 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome AF: 7.25e-7 AC: 1AN: 1379904Hom.: 0 Cov.: 91 AF XY: 0.00000147 AC XY: 1AN XY: 680016
GnomAD4 exome
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1
AN:
1379904
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Cov.:
91
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AC XY:
1
AN XY:
680016
Gnomad4 AFR exome
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GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
Vest4
0.20
GERP RS
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at