Genomic variant #0000048006

Individual ID 00025128
Chromosome 2
Allele Both (homozygous)
Affects function (as reported) Affects function
Affects function (by curator) Affects function
DNA change (genomic) (Relative to hg19 / GRCh37) g.197777664_197777666delAAG
DNA change (hg38) g.196912940_196912942delAAG
Published as -
ISCN -
DB-ID PGAP1_000005
Variant remarks The mutation was not found in in 372 healthy Syrian adults using Sanger sequencing. Molecular modeling showed that this mutation disrupts the packing of the hydrophobic core and consequently of the entire β-sheet topology, thus leading to a loss of tertiary structure and enzymatic activity. Surface expression of GPI-APs on B-lymphoblastoid cell lines derived from an affected person, parents and controls showed no significant difference. Structural abnormality of GPI-anchors was tested. All GPI-APs on the affected LCLs had abnormal GPI anchors resistant to PI-PLC. This is an indication that the p.Leu197del mutation causes null or almost null activity of the PGAP1 enzyme. GPI-APs on LCLs from heterozygous parents were only partially sensitive to PI-PLC indicating haploinsufficiency. These defective sensitivities were restored by wt-PGAP1 cDNA transfection.
Reference PubMed: Murakami et al. 2014
ClinVar ID -
dbSNP ID rs587777378
Origin Germline
Segregation yes
Frequency -
Re-site -
VIP 0
Methylation -
Average frequency (large NGS studies) Variant not found in online data sets
Owner Philippe Campeau




Variant on transcripts


Gene     

AscendingTranscript     

Affects function     

Exon     

DNA change (cDNA)     

ClassClinical     

RNA change     

Protein     
PGAP1 NM_024989.3 +/+ - c.589_591delCTT - r.(?) p.(Leu197del)



Screenings


AscendingScreening ID     

Template     

Technique     

Tissue     

Remarks     

Genes screened     

Variants found     

Owner     
0000025130 DNA SEQ-NG - - PGAP1 1 Philippe Campeau