rs786205216
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Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_002337.4(LRPAP1):c.199del(p.Gln67SerfsTer8) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000143 in 1,397,796 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 34)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Consequence
LRPAP1
NM_002337.4 frameshift
NM_002337.4 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.57
Genes affected
LRPAP1 (HGNC:6701): (LDL receptor related protein associated protein 1) This gene encodes a protein that interacts with the low density lipoprotein (LDL) receptor-related protein and facilitates its proper folding and localization by preventing the binding of ligands. Mutations in this gene have been identified in individuals with myopia 23. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2013]
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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 4-3532213-TG-T is Pathogenic according to our data. Variant chr4-3532213-TG-T is described in ClinVar as [Pathogenic]. Clinvar id is 190230.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRPAP1 | NM_002337.4 | c.199del | p.Gln67SerfsTer8 | frameshift_variant | 1/8 | ENST00000650182.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRPAP1 | ENST00000650182.1 | c.199del | p.Gln67SerfsTer8 | frameshift_variant | 1/8 | NM_002337.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 34
GnomAD3 genomes
?
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34
GnomAD3 exomes AF: 0.0000129 AC: 2AN: 154816Hom.: 0 AF XY: 0.0000245 AC XY: 2AN XY: 81684
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GnomAD4 exome AF: 0.00000143 AC: 2AN: 1397796Hom.: 0 Cov.: 32 AF XY: 0.00000290 AC XY: 2AN XY: 689442
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GnomAD4 genome ? Cov.: 34
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Myopia 23, autosomal recessive Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Dec 18, 2014 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at