Our verdict is Likely pathogenic. The variant received 7 ACMG points: 7P and 0B. PM2PM5PP3_ModeratePP5
The NM_176787.5(PIGN):c.755A>T(p.Asp252Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D252Y) has been classified as Uncertain significance.
PIGN (HGNC:8967): (phosphatidylinositol glycan anchor biosynthesis class N) This gene encodes a protein that is involved in glycosylphosphatidylinositol (GPI)-anchor biosynthesis. The GPI-anchor is a glycolipid found on many blood cells and serves to anchor proteins to the cell surface. This protein is expressed in the endoplasmic reticulum and transfers phosphoethanolamine (EtNP) to the first mannose of the GPI anchor. Two alternatively spliced variants, which encode an identical isoform, have been reported. [provided by RefSeq, Jul 2008]
Our verdict: Likely_pathogenic. The variant received 7 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PM5
Other missense variant is known to change same aminoacid residue: Variant chr18-62147021-T-C is described in CliVar as Likely_pathogenic. Clinvar id is 1012442.Status of the report is criteria_provided_single_submitter, 1 stars.
PP3
MetaRNN computational evidence supports a deleterious effect, 0.85
PP5
Variant 18-62147021-T-A is Pathogenic according to our data. Variant chr18-62147021-T-A is described in CliVar as Pathogenic. Clinvar id is 264634.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr18-62147021-T-A is described in CliVar as Pathogenic. Clinvar id is 264634.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr18-62147021-T-A is described in CliVar as Pathogenic. Clinvar id is 264634.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr18-62147021-T-A is described in CliVar as Pathogenic. Clinvar id is 264634.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr18-62147021-T-A is described in CliVar as Pathogenic. Clinvar id is 264634.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr18-62147021-T-A is described in CliVar as Pathogenic. Clinvar id is 264634.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr18-62147021-T-A is described in CliVar as Pathogenic. Clinvar id is 264634.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr18-62147021-T-A is described in CliVar as Pathogenic. Clinvar id is 264634.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr18-62147021-T-A is described in CliVar as Pathogenic. Clinvar id is 264634.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr18-62147021-T-A is described in CliVar as Pathogenic. Clinvar id is 264634.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr18-62147021-T-A is described in CliVar as Pathogenic. Clinvar id is 264634.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr18-62147021-T-A is described in CliVar as Pathogenic. Clinvar id is 264634.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr18-62147021-T-A is described in CliVar as Pathogenic. Clinvar id is 264634.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr18-62147021-T-A is described in CliVar as Pathogenic. Clinvar id is 264634.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr18-62147021-T-A is described in CliVar as Pathogenic. Clinvar id is 264634.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr18-62147021-T-A is described in CliVar as Pathogenic. Clinvar id is 264634.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr18-62147021-T-A is described in CliVar as Pathogenic. Clinvar id is 264634.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr18-62147021-T-A is described in CliVar as Pathogenic. Clinvar id is 264634.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr18-62147021-T-A is described in CliVar as Pathogenic. Clinvar id is 264634.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr18-62147021-T-A is described in CliVar as Pathogenic. Clinvar id is 264634.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr18-62147021-T-A is described in CliVar as Pathogenic. Clinvar id is 264634.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr18-62147021-T-A is described in CliVar as Pathogenic. Clinvar id is 264634.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr18-62147021-T-A is described in CliVar as Pathogenic. Clinvar id is 264634.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr18-62147021-T-A is described in CliVar as Pathogenic. Clinvar id is 264634.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr18-62147021-T-A is described in CliVar as Pathogenic. Clinvar id is 264634.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr18-62147021-T-A is described in CliVar as Pathogenic. Clinvar id is 264634.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr18-62147021-T-A is described in CliVar as Pathogenic. Clinvar id is 264634.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr18-62147021-T-A is described in CliVar as Pathogenic. Clinvar id is 264634.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr18-62147021-T-A is described in CliVar as Pathogenic. Clinvar id is 264634.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr18-62147021-T-A is described in CliVar as Pathogenic. Clinvar id is 264634.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr18-62147021-T-A is described in CliVar as Pathogenic. Clinvar id is 264634.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr18-62147021-T-A is described in CliVar as Pathogenic. Clinvar id is 264634.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr18-62147021-T-A is described in CliVar as Pathogenic. Clinvar id is 264634.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr18-62147021-T-A is described in CliVar as Pathogenic. Clinvar id is 264634.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr18-62147021-T-A is described in CliVar as Pathogenic. Clinvar id is 264634.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr18-62147021-T-A is described in CliVar as Pathogenic. Clinvar id is 264634.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr18-62147021-T-A is described in CliVar as Pathogenic. Clinvar id is 264634.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr18-62147021-T-A is described in CliVar as Pathogenic. Clinvar id is 264634.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr18-62147021-T-A is described in CliVar as Pathogenic. Clinvar id is 264634.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr18-62147021-T-A is described in CliVar as Pathogenic. Clinvar id is 264634.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr18-62147021-T-A is described in CliVar as Pathogenic. Clinvar id is 264634.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr18-62147021-T-A is described in CliVar as Pathogenic. Clinvar id is 264634.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr18-62147021-T-A is described in CliVar as Pathogenic. Clinvar id is 264634.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr18-62147021-T-A is described in CliVar as Pathogenic. Clinvar id is 264634.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr18-62147021-T-A is described in CliVar as Pathogenic. Clinvar id is 264634.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr18-62147021-T-A is described in CliVar as Pathogenic. Clinvar id is 264634.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr18-62147021-T-A is described in CliVar as Pathogenic. Clinvar id is 264634.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr18-62147021-T-A is described in CliVar as Pathogenic. Clinvar id is 264634.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr18-62147021-T-A is described in CliVar as Pathogenic. Clinvar id is 264634.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr18-62147021-T-A is described in CliVar as Pathogenic. Clinvar id is 264634.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr18-62147021-T-A is described in CliVar as Pathogenic. Clinvar id is 264634.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr18-62147021-T-A is described in CliVar as Pathogenic. Clinvar id is 264634.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr18-62147021-T-A is described in CliVar as Pathogenic. Clinvar id is 264634.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr18-62147021-T-A is described in CliVar as Pathogenic. Clinvar id is 264634.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr18-62147021-T-A is described in CliVar as Pathogenic. Clinvar id is 264634.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr18-62147021-T-A is described in CliVar as Pathogenic. Clinvar id is 264634.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr18-62147021-T-A is described in CliVar as Pathogenic. Clinvar id is 264634.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr18-62147021-T-A is described in CliVar as Pathogenic. Clinvar id is 264634.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr18-62147021-T-A is described in CliVar as Pathogenic. Clinvar id is 264634.Status of the report is no_assertion_criteria_provided, 0 stars.