chr11-3825040-G-GA

Variant names:

• chr11-3825040-G-GA
• rs771218491
• NM_014489.4:c.732dupA

Variant summary

Our verdict is Pathogenic. The variant received 12 ACMG points: 12P and 0B. PVS1 PM2 PP5_Moderate

The NM_014489.4(PGAP2):​c.732dupA​(p.Gln245ThrfsTer26) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely pathogenic (★). Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 31)
• Consequence: PGAP2 NM_014489.4 frameshift
• Clinical Significance: Likely pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 8.22
• Publications: 0 publications found

Genes affected

PGAP2 (HGNC:17893): (post-GPI attachment to proteins 2) The protein encoded by this gene plays a role in the maturation of glycosylphosphatidylinositol (GPI) anchors on GPI-anchored proteins. Mutations in this gene are associated with an autosomal recessive syndrome characterized by hyperphosphatasia and intellectual disability. [provided by RefSeq, Jul 2017]

PGAP2 Gene-Disease associations (from GenCC):

• hyperphosphatasia with intellectual disability syndrome 3

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae)
• hyperphosphatasia-intellectual disability syndrome

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Pathogenic. The variant received 12 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 11-3825040-G-GA is Pathogenic according to our data. Variant chr11-3825040-G-GA is described in ClinVar as Likely_pathogenic. ClinVar VariationId is 522122.Status of the report is criteria_provided_single_submitter, 1 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014489.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PGAP2	NM_014489.4	MANE Select	c.732dupA	p.Gln245ThrfsTer26	frameshift	Exon 6 of 7	NP_055304.1
	PGAP2	NM_001256236.2		c.732dupA	p.Gln245ThrfsTer26	frameshift	Exon 7 of 8	NP_001243165.2
	PGAP2	NM_001346397.2		c.702dupA	p.Gln235ThrfsTer26	frameshift	Exon 6 of 7	NP_001333326.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PGAP2	ENST00000278243.9	TSL:1 MANE Select	c.732dupA	p.Gln245ThrfsTer26	frameshift	Exon 6 of 7	ENSP00000278243.4
	PGAP2	ENST00000300730.10	TSL:1	c.708dupA	p.Gln237ThrfsTer26	frameshift	Exon 6 of 7	ENSP00000300730.6
	PGAP2	ENST00000396993.8	TSL:1	c.81dupA	p.Gln28ThrfsTer26	frameshift	Exon 5 of 6	ENSP00000380190.6

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD2 exomes AF: 0.00000398 AC: 1 AN: 251474 AF XY: 0.00

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00000879

Gnomad OTH exome AF: 0.00

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 31

Alfa AF: 0.000782 Hom.: 0

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

Inborn genetic diseases Pathogenic:1

Jun 21, 2023

Ambry Genetics

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.732dupA (p.Q245Tfs*26) alteration, located in exon 6 (coding exon 5) of the PGAP2 gene, consists of a duplication of A at position 732, causing a translational frameshift with a predicted alternate stop codon after 26 amino acids. This alteration occurs at the 3' terminus of the PGAP2 gene, is not expected to trigger nonsense-mediated mRNA decay, and impacts the last 23% of the protein. Premature stop codons are typically deleterious in nature, the impacted region is critical for protein function, and a significant portion of the protein is affected (Ambry internal data). Based on data from gnomAD, the c.732dupA allele has an overall frequency of <0.001% (1/251474) total alleles studied. The highest observed frequency was 0.001% (1/113764) of European (non-Finnish) alleles. Based on the available evidence, this alteration is classified as likely pathogenic.

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		8.2
Mutation Taster		=26/174	disease causing

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs771218491; hg19: chr11-3846270;